title: Exon arrays of Roadmap cell types; Fetal  primary tissue, day 108; DS17387-exon

description:
sample_term_id: UBERON_0001225
assay_term_id: OBI_0001463
nucleic_acid_term_id: SO_0000356
Exon profiling of NREMC cell types, these coincide with chromatin accessibility sequencing assays.
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.7193
sample alias: fKidney_renal_cortex.H-23790d108
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.7074

value: day 108


title: ChIP-Seq analysis of H3K4me3; chondr. dif cls; Lib:MC:20100729:02--ChIP:MC:20100726:02:chondrogenic dif cells:H3K4Me3

status: Public on Mar 31 2011

type: SRA

city: Cambridge

first: BROAD

last: INSTITUTE

state: MA

country: USA

institute: Broad Institute

description:
sample_term_id: CL_0000138
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib:MC:20100729:02--ChIP:MC:20100726:02:chondrogenic dif cells:H3K4Me3
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.5775
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.5935
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

library_source: genomic

data_processing:
**********************************************************************

ANALYSIS FILE NAME: GSM670034_BI.Chondrocytes_from_Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells.H3K4me3.59.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:MC:20100729:02--ChIP:MC:20100726:02:chondrogenic dif cells:H3K4Me3.hg19.level.1.release.3
ANALYSIS TITLE: Mapping of Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me3 ChIP-Seq on Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells, Donor 59 were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.6570
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 3

QUALITY SCORES:
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 63
FINDPEAKS_SCORE: 0.6058
FINDPEAKS_PERCENTILE: 80
HOTSPOT_SCORE: 0.6121
HOTSPOT_PERCENTILE: 84
IROC_SCORE: 0.9944
IROC_PERCENTILE: 28
POISSON_SCORE: 0.6309
POISSON_PERCENTILE: 80

**********************************************************************

ANALYSIS FILE NAME: GSM670034_BI.Chondrocytes_from_Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells.H3K4me3.59.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:MC:20100729:02--ChIP:MC:20100726:02:chondrogenic dif cells:H3K4Me3.hg19.level.2.release.3
ANALYSIS TITLE: Raw Signal Density Graphs of Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me3 ChIP-Seq read mappings from Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells, Donor 59 were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.6780
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 3
BROWSER_TRACK_NAME: CfBMDMSC H3K4me3 59
BROWSER_TRACK_DESCRIPTION: BI Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells Histone H3K4me3 Donor 59 Library Lib:MC:20100729:02--ChIP:MC:20100726:02:chondrogenic dif cells:H3K4Me3 EA Release 3

QUALITY SCORES:
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 63
FINDPEAKS_SCORE: 0.6058
FINDPEAKS_PERCENTILE: 80
HOTSPOT_SCORE: 0.6121
HOTSPOT_PERCENTILE: 84
IROC_SCORE: 0.9944
IROC_PERCENTILE: 28
POISSON_SCORE: 0.6309
POISSON_PERCENTILE: 80

**********************************************************************

molecule: genomic DNA

organism: Homo sapiens

source_name: chondrocytes derived via in vitro culture from mesenchymal stem cells; Lib:MC:20100729:02--ChIP:MC:20100726:02:chondrogenic dif cells:H3K4Me3

extract_protocol: Library construction protocol: Single read - Illumina

tag: sample alias

tag: sample common name

value: healthy

tag: molecule

value: genomic DNA

tag: disease

tag: markers

value: Medium:NA; Differentiation Method:alginate hydrogel scaffold (SR Herlofsen et al, Tissue Eng Part A. 2011)

value: chondrogenic dif cells

value: Unknown

value: Primary Cell Culture

value: Rikshospitalet University Hospital

value: Protein A-Sepharose 4B

value: 10 million cells

value: SDS lysis

value: 70 ul bed volume

value: Millipore

value: Histone H3K4me3

value: Bioruptor


title: Exon arrays of Roadmap cell types; Fetal  primary tissue, day 108; DS17317-exon

status: Public on Apr 14 2011

type: RNA

city: Seattle

first: Northwest

last: REMC

state: WA

institute: University of Washington

description:
sample_term_id: UBERON_0002108
assay_term_id: OBI_0001463
nucleic_acid_term_id: SO_0000356
Exon profiling of NREMC cell types, these coincide with chromatin accessibility sequencing assays.
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.7201
sample alias: fIntestine_Small.H-23769d108
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.7055

hyb_protocol: Hybridizations were carried out according the manufacturer (Affymetrix) protocol

scan_protocol: Affymetrix Gene Chip Scanner 3000

data_processing: Intensity files from the scanned exon arrays were analyzed at the exon level (Affymetrix ExACT 1.2.1 software). Sample data were quantile normalized with PM-GCBG background correction and PLIER (Probe Logarithmic Intensity Error) summarized

label: biotin

molecule: total RNA

label_protocol: A Whole Transcript Sense Target Labeling Assay (Affymetrix) was used to reduce the rRNA, perform in vitro transcription (IVT) and create labeled sense strand DNA for hybridization to the arrays.

growth_protocol: Followed vendor recommendations for growth protocol/media

extract_protocol: At cell harvest, a subset of cells was stored at -20 C in RNALater. Total RNA from 5 X 10^6 cells were purified using Ribopure (Ambion) according to vendor recommended protocols. Total RNA quality was assessed on RNA 6000 Nano Chips (Agilent) using a Bioanalyzer (Agilent).

value: University of Washington, Congenital Defects Lab. Ian Glass

value: Primary Tissue

value: Fetal Intestine, Small

value: UW

value: fetal

value: Male


title: Exon arrays of Roadmap cell types; flow sorted CD14+ Cells, year 34; DS17391-exon

description:
sample_term_id: CL_0001054
assay_term_id: OBI_0001463
nucleic_acid_term_id: SO_0000356
Exon profiling of NREMC cell types, these coincide with chromatin accessibility sequencing assays.
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.7223
sample alias: CD14.RO_01727
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.6959

value: FHCRC HEIMFELD

value: Primary Cell

value: CD14 Primary Cells

value: year 34

value: Female

value: Caucasian


title: ChIP-Seq analysis of H3K9me3 in BM-MSC cells; Lib:MC:20100713:13--ChIP:MC:20100706:13:BM-MSC:H3K9Me3

description:
sample_term_id: EFO_0000586
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib:MC:20100713:13--ChIP:MC:20100706:13:BM-MSC:H3K9Me3
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.5769
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.5950
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

data_processing:
**********************************************************************

ANALYSIS FILE NAME: GSM670028_BI.Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells.H3K9me3.60.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:MC:20100713:13--ChIP:MC:20100706:13:BM-MSC:H3K9Me3.hg19.level.1.release.3
ANALYSIS TITLE: Mapping of Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K9me3 ChIP-Seq on Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells, Donor 60 were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.6446
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 3

QUALITY SCORES:
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 60
FINDPEAKS_SCORE: 0.0221
FINDPEAKS_PERCENTILE: 27
HOTSPOT_SCORE: 0.0559
HOTSPOT_PERCENTILE: 12
IROC_SCORE: 0.878
IROC_PERCENTILE: 65
POISSON_SCORE: 0.2031
POISSON_PERCENTILE: 27

**********************************************************************

ANALYSIS FILE NAME: GSM670028_BI.Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells.H3K9me3.60.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:MC:20100713:13--ChIP:MC:20100706:13:BM-MSC:H3K9Me3.hg19.level.2.release.3
ANALYSIS TITLE: Raw Signal Density Graphs of Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K9me3 ChIP-Seq read mappings from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells, Donor 60 were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.6656
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 3
BROWSER_TRACK_NAME: BMDMSC H3K9me3 60
BROWSER_TRACK_DESCRIPTION: BI Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells Histone H3K9me3 Donor 60 Library Lib:MC:20100713:13--ChIP:MC:20100706:13:BM-MSC:H3K9Me3 EA Release 3

QUALITY SCORES:
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 60
FINDPEAKS_SCORE: 0.0221
FINDPEAKS_PERCENTILE: 27
HOTSPOT_SCORE: 0.0559
HOTSPOT_PERCENTILE: 12
IROC_SCORE: 0.878
IROC_PERCENTILE: 65
POISSON_SCORE: 0.2031
POISSON_PERCENTILE: 27

**********************************************************************

source_name: bone marrow was aspirated from the iliac crest, isolated by density gradient and adhesion to plastic, and expanded in monolayer culture, containing 10% FBS; Lib:MC:20100713:13--ChIP:MC:20100706:13:BM-MSC:H3K9Me3

value: healthy

value: genomic DNA

value: BM-MSC

value: Unknown

value: Primary Cell Culture

value: Rikshospitalet University Hospital

value: Protein A-Sepharose 4B

value: 10 million cells

value: SDS lysis

value: Abcam

value: Histone H3K9me3


title: Exon arrays of Roadmap cell types; flow sorted CD19+ Cells, year 34; DS17281-exon

description:
sample_term_id: CL_0000236
assay_term_id: OBI_0001463
nucleic_acid_term_id: SO_0000356
Exon profiling of NREMC cell types, these coincide with chromatin accessibility sequencing assays.
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.7221
sample alias: CD19.RO_01727
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.6969

value: FHCRC HEIMFELD

value: CD19 Primary Cells


title: Exon arrays of Roadmap cell types; flow sorted CD8+ Cells, year 34; DS17332-exon

description:
sample_term_id: CL_0000625
assay_term_id: OBI_0001463
nucleic_acid_term_id: SO_0000356
Exon profiling of NREMC cell types, these coincide with chromatin accessibility sequencing assays.
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.7213
sample alias: CD8.RO_01727
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.7031

value: Primary Cell

value: CD8 Primary Cells


title: Exon arrays of Roadmap cell types; Fetal  primary tissue, day 108; DS17313-exon

description:
sample_term_id: UBERON_0000059
assay_term_id: OBI_0001463
nucleic_acid_term_id: SO_0000356
Exon profiling of NREMC cell types, these coincide with chromatin accessibility sequencing assays.
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.7207
sample alias: fIntestine_Large.H-23769d108
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.7041

value: University of Washington, Congenital Defects Lab. Ian Glass

value: Primary Tissue

value: Fetal Intestine, Large

value: UW

value: fetal

value: day 108

value: Male


title: Exon arrays of Roadmap cell types; Fetal  primary tissue, day 113; DS17451-exon

description:
sample_term_id: UBERON_0001224
assay_term_id: OBI_0001463
nucleic_acid_term_id: SO_0000356
Exon profiling of NREMC cell types, these coincide with chromatin accessibility sequencing assays.
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.7187
sample alias: fKidney_renal_pelvis.H-23833d113
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.7119

value: Fetal Renal Pelvis

value: day 113


title: ChIP-Seq analysis of H3K27me3 in AdiposeNuclei cells; Lib:XZ:20100731:18--ChIP:XZ:20100726:18:AdiposeNuclei:H3K27Me3

description:
sample_term_id: UBERON_0014455
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib:XZ:20100731:18--ChIP:XZ:20100726:18:AdiposeNuclei:H3K27Me3
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.5776
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.5944
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

data_processing:
**********************************************************************

ANALYSIS FILE NAME: GSM670035_BI.Adipose_Nuclei.H3K27me3.94.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100731:18--ChIP:XZ:20100726:18:AdiposeNuclei:H3K27Me3.hg19.level.1.release.3
ANALYSIS TITLE: Mapping of Adipose Nuclei Histone H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K27me3 ChIP-Seq on Adipose Nuclei, Donor 94 were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.6535
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 3

QUALITY SCORES:
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 52
FINDPEAKS_SCORE: 0.0611
FINDPEAKS_PERCENTILE: 40
HOTSPOT_SCORE: 0.1599
HOTSPOT_PERCENTILE: 55
IROC_SCORE: 0.8496
IROC_PERCENTILE: 35
POISSON_SCORE: 0.3715
POISSON_PERCENTILE: 65

**********************************************************************

ANALYSIS FILE NAME: GSM670035_BI.Adipose_Nuclei.H3K27me3.94.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100731:18--ChIP:XZ:20100726:18:AdiposeNuclei:H3K27Me3.hg19.level.2.release.3
ANALYSIS TITLE: Raw Signal Density Graphs of Adipose Nuclei Histone H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K27me3 ChIP-Seq read mappings from Adipose Nuclei, Donor 94 were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.6745
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 3
BROWSER_TRACK_NAME: AN H3K27me3 94
BROWSER_TRACK_DESCRIPTION: BI Adipose Nuclei Histone H3K27me3 Donor 94 Library Lib:XZ:20100731:18--ChIP:XZ:20100726:18:AdiposeNuclei:H3K27Me3 EA Release 3

QUALITY SCORES:
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 52
FINDPEAKS_SCORE: 0.0611
FINDPEAKS_PERCENTILE: 40
HOTSPOT_SCORE: 0.1599
HOTSPOT_PERCENTILE: 55
IROC_SCORE: 0.8496
IROC_PERCENTILE: 35
POISSON_SCORE: 0.3715
POISSON_PERCENTILE: 65

**********************************************************************

source_name: Nuclei derived from crude preps of adipose tissue; Lib:XZ:20100731:18--ChIP:XZ:20100726:18:AdiposeNuclei:H3K27Me3

value: Adipose Nuclei

value: surgery

value: genomic DNA

value: Female

value: abdomen

value: Harvard University

value: Protein A-Sepharose 4B

value: 10 million cells

value: 70 ul bed volume

value: Millipore

value: Histone H3K27me3

value: Bioruptor


title: ChIP-Seq analysis of H3K4me1 in adult kidney cells; Lib:XZ:20100827:06--ChIP:XZ:20100824:06:adult kidney:H3K4Me1

description:
sample_term_id: UBERON_0002113
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib:XZ:20100827:06--ChIP:XZ:20100824:06:adult kidney:H3K4Me1
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.5766
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.3349
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

data_processing:
**********************************************************************

ANALYSIS FILE NAME: GSM670025_BI.Adult_Kidney.H3K4me1.27.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100827:06--ChIP:XZ:20100824:06:adult kidney:H3K4Me1.hg19.level.1.release.3
ANALYSIS TITLE: Mapping of Adult Kidney Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me1 ChIP-Seq on Adult Kidney, Donor 27 were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.6592
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 3

QUALITY SCORES:
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 50
FINDPEAKS_SCORE: 0.0991
FINDPEAKS_PERCENTILE: 14
HOTSPOT_SCORE: 0.203
HOTSPOT_PERCENTILE: 18
IROC_SCORE: 0.9154
IROC_PERCENTILE: 14
POISSON_SCORE: 0.3591
POISSON_PERCENTILE: 11

**********************************************************************

ANALYSIS FILE NAME: GSM670025_BI.Adult_Kidney.H3K4me1.27.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100827:06--ChIP:XZ:20100824:06:adult kidney:H3K4Me1.hg19.level.2.release.3
ANALYSIS TITLE: Raw Signal Density Graphs of Adult Kidney Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me1 ChIP-Seq read mappings from Adult Kidney, Donor 27 were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.6802
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 3
BROWSER_TRACK_NAME: AK H3K4me1 27
BROWSER_TRACK_DESCRIPTION: BI Adult Kidney Histone H3K4me1 Donor 27 Library Lib:XZ:20100827:06--ChIP:XZ:20100824:06:adult kidney:H3K4Me1 EA Release 3

QUALITY SCORES:
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 50
FINDPEAKS_SCORE: 0.0991
FINDPEAKS_PERCENTILE: 14
HOTSPOT_SCORE: 0.203
HOTSPOT_PERCENTILE: 18
IROC_SCORE: 0.9154
IROC_PERCENTILE: 14
POISSON_SCORE: 0.3591
POISSON_PERCENTILE: 11

**********************************************************************

source_name: Primary kidney tissue; Lib:XZ:20100827:06--ChIP:XZ:20100824:06:adult kidney:H3K4Me1

value: Adult Kidney

value: "normal, renal cell CA (clear cell type)"

value: white

value: Primary Tissue

value: kidney

value: MGH Pathology

value: SDS lysis

value: Abcam

value: Histone H3K4me1


title: Exon arrays of Roadmap cell types; flow sorted CD3+ Cells,year 21; DS17198-exon

description:
sample_term_id: CL_0000084
assay_term_id: OBI_0001463
nucleic_acid_term_id: SO_0000356
Exon profiling of NREMC cell types, these coincide with chromatin accessibility sequencing assays.
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.7219
sample alias: CD3.RO_01721
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.5322

value: FHCRC HEIMFELD

value: Primary Cell

value: CD3 Primary Cells

value: year 21

value: Male

value: Caucasian


title: ChIP-Seq analysis of H3K9ac in AdiposeNuclei cells; Lib:XZ:20100731:26--ChIP:XZ:20100726:26:AdiposeNuclei:H3K9Ac

description:
sample_term_id: UBERON_0014455
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib:XZ:20100731:26--ChIP:XZ:20100726:26:AdiposeNuclei:H3K9Ac
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.5768
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.5945
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

data_processing:
**********************************************************************

ANALYSIS FILE NAME: GSM670027_BI.Adipose_Nuclei.H3K9ac.95.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100731:26--ChIP:XZ:20100726:26:AdiposeNuclei:H3K9Ac.hg19.level.1.release.3
ANALYSIS TITLE: Mapping of Adipose Nuclei Histone H3K9ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K9ac ChIP-Seq on Adipose Nuclei, Donor 95 were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.6466
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 3

QUALITY SCORES:
NUMBER_OF_H3K9ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 40
FINDPEAKS_SCORE: 0.1165
FINDPEAKS_PERCENTILE: 20
HOTSPOT_SCORE: 0.1957
HOTSPOT_PERCENTILE: 32
IROC_SCORE: 0.9968
IROC_PERCENTILE: 80
POISSON_SCORE: 0.2533
POISSON_PERCENTILE: 24

**********************************************************************

ANALYSIS FILE NAME: GSM670027_BI.Adipose_Nuclei.H3K9ac.95.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100731:26--ChIP:XZ:20100726:26:AdiposeNuclei:H3K9Ac.hg19.level.2.release.3
ANALYSIS TITLE: Raw Signal Density Graphs of Adipose Nuclei Histone H3K9ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K9ac ChIP-Seq read mappings from Adipose Nuclei, Donor 95 were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.6676
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 3
BROWSER_TRACK_NAME: AN H3K9ac 95
BROWSER_TRACK_DESCRIPTION: BI Adipose Nuclei Histone H3K9ac Donor 95 Library Lib:XZ:20100731:26--ChIP:XZ:20100726:26:AdiposeNuclei:H3K9Ac EA Release 3

QUALITY SCORES:
NUMBER_OF_H3K9ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 40
FINDPEAKS_SCORE: 0.1165
FINDPEAKS_PERCENTILE: 20
HOTSPOT_SCORE: 0.1957
HOTSPOT_PERCENTILE: 32
IROC_SCORE: 0.9968
IROC_PERCENTILE: 80
POISSON_SCORE: 0.2533
POISSON_PERCENTILE: 24

**********************************************************************

source_name: Nuclei derived from crude preps of adipose tissue; Lib:XZ:20100731:26--ChIP:XZ:20100726:26:AdiposeNuclei:H3K9Ac

value: Adipose Nuclei

value: surgery

value: genomic DNA

value: Female

value: abdomen

value: Harvard University

value: Protein A-Sepharose 4B

value: 10 million cells

value: 70 ul bed volume

value: Histone H3K9ac


title: Exon arrays of Roadmap cell types; flow sorted CD4+ Cells,year 21; DS17212-exon

description:
sample_term_id: CL_0000492
assay_term_id: OBI_0001463
nucleic_acid_term_id: SO_0000356
Exon profiling of NREMC cell types, these coincide with chromatin accessibility sequencing assays.
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.7217
sample alias: CD4.RO_01721
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.5345

value: CD4 Primary Cells


title: Exon arrays of Roadmap cell types; Fetal  primary tissue, day 107; DS17158-exon

description:
sample_term_id: UBERON_0000059
assay_term_id: OBI_0001463
nucleic_acid_term_id: SO_0000356
Exon profiling of NREMC cell types, these coincide with chromatin accessibility sequencing assays.
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.7209
sample alias: fIntestine_Large.H-23758d107
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.7038

value: University of Washington, Congenital Defects Lab. Ian Glass

value: Primary Tissue

value: Fetal Intestine, Large

value: UW

value: fetal

value: day 107


title: ChIP-Seq analysis of H3K9me3 in BM-MSC cells; Lib:MC:20100706:13--ChIP:MC:20100628:13:BM-MSC:H3K9Me3

description:
sample_term_id: EFO_0000586
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib:MC:20100706:13--ChIP:MC:20100628:13:BM-MSC:H3K9Me3
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.5759
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.5953
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

data_processing:
**********************************************************************

ANALYSIS FILE NAME: GSM670018_BI.Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells.H3K9me3.58.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:MC:20100706:13--ChIP:MC:20100628:13:BM-MSC:H3K9Me3.hg19.level.1.release.3
ANALYSIS TITLE: Mapping of Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K9me3 ChIP-Seq on Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells, Donor 58 were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.6519
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 3

QUALITY SCORES:
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 60
FINDPEAKS_SCORE: 0.0384
FINDPEAKS_PERCENTILE: 35
HOTSPOT_SCORE: 0.0916
HOTSPOT_PERCENTILE: 35
IROC_SCORE: 0.7202
IROC_PERCENTILE: 15
POISSON_SCORE: 0.2831
POISSON_PERCENTILE: 42

**********************************************************************

ANALYSIS FILE NAME: GSM670018_BI.Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells.H3K9me3.58.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:MC:20100706:13--ChIP:MC:20100628:13:BM-MSC:H3K9Me3.hg19.level.2.release.3
ANALYSIS TITLE: Raw Signal Density Graphs of Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K9me3 ChIP-Seq read mappings from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells, Donor 58 were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.6729
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 3
BROWSER_TRACK_NAME: BMDMSC H3K9me3 58
BROWSER_TRACK_DESCRIPTION: BI Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells Histone H3K9me3 Donor 58 Library Lib:MC:20100706:13--ChIP:MC:20100628:13:BM-MSC:H3K9Me3 EA Release 3

QUALITY SCORES:
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 60
FINDPEAKS_SCORE: 0.0384
FINDPEAKS_PERCENTILE: 35
HOTSPOT_SCORE: 0.0916
HOTSPOT_PERCENTILE: 35
IROC_SCORE: 0.7202
IROC_PERCENTILE: 15
POISSON_SCORE: 0.2831
POISSON_PERCENTILE: 42

**********************************************************************

source_name: bone marrow was aspirated from the iliac crest, isolated by density gradient and adhesion to plastic, and expanded in monolayer culture, containing 10% FBS; Lib:MC:20100706:13--ChIP:MC:20100628:13:BM-MSC:H3K9Me3

value: healthy

value: BM-MSC

value: Unknown

value: Primary Cell Culture

value: Rikshospitalet University Hospital

value: SDS lysis

value: Abcam

value: Histone H3K9me3

value: Bioruptor


title: Exon arrays of Roadmap cell types; flow sorted CD8+ Cells,year 21; DS17203-exon

description:
sample_term_id: CL_0000625
assay_term_id: OBI_0001463
nucleic_acid_term_id: SO_0000356
Exon profiling of NREMC cell types, these coincide with chromatin accessibility sequencing assays.
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.7215
sample alias: CD8.RO_01721
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.5352

value: FHCRC HEIMFELD

value: Primary Cell

value: CD8 Primary Cells

value: year 21

value: Male

value: Caucasian


title: Exon arrays of Roadmap cell types; Fetal Brain primary tissue, day 122; DS12631-exon

description:
sample_term_id: UBERON_0000955
assay_term_id: OBI_0001463
nucleic_acid_term_id: SO_0000356
Exon profiling of NREMC cell types, these coincide with chromatin accessibility sequencing assays.
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.7012
sample alias: fBrain.H-22510d122
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.2448

value: University of Washington, Congenital Defects Lab. Ian Glass

value: Primary Tissue

value: fetal brain

value: UW

value: fetal

value: 122 days


title: Exon arrays of Roadmap cell types; Fetal  primary tissue, day 113; DS17464-exon

description:
sample_term_id: UBERON_0002168
assay_term_id: OBI_0001463
nucleic_acid_term_id: SO_0000356
Exon profiling of NREMC cell types, these coincide with chromatin accessibility sequencing assays.
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.7279
sample alias: fLung_Left.H-23833d113
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.7275

value: Fetal Lung, Left

value: day 113


title: ChIP-Seq analysis of H3K4me3 in BM-MSC cells; Lib:MC:20100713:09--ChIP:MC:20100706:09:BM-MSC:H3K4Me3

description:
sample_term_id: EFO_0000586
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib:MC:20100713:09--ChIP:MC:20100706:09:BM-MSC:H3K4Me3
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.5760
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.5950
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

data_processing:
**********************************************************************

ANALYSIS FILE NAME: GSM670019_BI.Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells.H3K4me3.60.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:MC:20100713:09--ChIP:MC:20100706:09:BM-MSC:H3K4Me3.hg19.level.1.release.3
ANALYSIS TITLE: Mapping of Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me3 ChIP-Seq on Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells, Donor 60 were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.6513
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 3

QUALITY SCORES:
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 63
FINDPEAKS_SCORE: 0.3889
FINDPEAKS_PERCENTILE: 48
HOTSPOT_SCORE: 0.4154
HOTSPOT_PERCENTILE: 52
IROC_SCORE: 0.9949
IROC_PERCENTILE: 32
POISSON_SCORE: 0.4568
POISSON_PERCENTILE: 60

**********************************************************************

ANALYSIS FILE NAME: GSM670019_BI.Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells.H3K4me3.60.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:MC:20100713:09--ChIP:MC:20100706:09:BM-MSC:H3K4Me3.hg19.level.2.release.3
ANALYSIS TITLE: Raw Signal Density Graphs of Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me3 ChIP-Seq read mappings from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells, Donor 60 were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.6723
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 3
BROWSER_TRACK_NAME: BMDMSC H3K4me3 60
BROWSER_TRACK_DESCRIPTION: BI Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells Histone H3K4me3 Donor 60 Library Lib:MC:20100713:09--ChIP:MC:20100706:09:BM-MSC:H3K4Me3 EA Release 3

QUALITY SCORES:
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 63
FINDPEAKS_SCORE: 0.3889
FINDPEAKS_PERCENTILE: 48
HOTSPOT_SCORE: 0.4154
HOTSPOT_PERCENTILE: 52
IROC_SCORE: 0.9949
IROC_PERCENTILE: 32
POISSON_SCORE: 0.4568
POISSON_PERCENTILE: 60

**********************************************************************

source_name: bone marrow was aspirated from the iliac crest, isolated by density gradient and adhesion to plastic, and expanded in monolayer culture, containing 10% FBS; Lib:MC:20100713:09--ChIP:MC:20100706:09:BM-MSC:H3K4Me3

value: healthy

value: genomic DNA

value: BM-MSC

value: Unknown

value: Primary Cell Culture

value: Rikshospitalet University Hospital

value: Protein A-Sepharose 4B

value: 10 million cells

value: SDS lysis

value: 70 ul bed volume

value: Millipore

value: Histone H3K4me3


title: ChIP-Seq analysis of H3K36me3; chondr. dif cls; Lib:MC:20100726:03--ChIP:MC:20100713:03:chondrogenic dif cells:H3K36Me3

description:
sample_term_id: CL_0000138
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib:MC:20100726:03--ChIP:MC:20100713:03:chondrogenic dif cells:H3K36Me3
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.5753
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.5949
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

data_processing:
**********************************************************************

ANALYSIS FILE NAME: GSM670012_BI.Chondrocytes_from_Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells.H3K36me3.57.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:MC:20100726:03--ChIP:MC:20100713:03:chondrogenic dif cells:H3K36Me3.hg19.level.1.release.3
ANALYSIS TITLE: Mapping of Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K36me3 ChIP-Seq on Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells, Donor 57 were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.6600
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 3

QUALITY SCORES:
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 59
FINDPEAKS_SCORE: 0.3933
FINDPEAKS_PERCENTILE: 81
HOTSPOT_SCORE: 0.3624
HOTSPOT_PERCENTILE: 88
IROC_SCORE: 0.9929
IROC_PERCENTILE: 77
POISSON_SCORE: 0.5575
POISSON_PERCENTILE: 81

**********************************************************************

ANALYSIS FILE NAME: GSM670012_BI.Chondrocytes_from_Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells.H3K36me3.57.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:MC:20100726:03--ChIP:MC:20100713:03:chondrogenic dif cells:H3K36Me3.hg19.level.2.release.3
ANALYSIS TITLE: Raw Signal Density Graphs of Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K36me3 ChIP-Seq read mappings from Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells, Donor 57 were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.6810
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 3
BROWSER_TRACK_NAME: CfBMDMSC H3K36me3 57
BROWSER_TRACK_DESCRIPTION: BI Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells Histone H3K36me3 Donor 57 Library Lib:MC:20100726:03--ChIP:MC:20100713:03:chondrogenic dif cells:H3K36Me3 EA Release 3

QUALITY SCORES:
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 59
FINDPEAKS_SCORE: 0.3933
FINDPEAKS_PERCENTILE: 81
HOTSPOT_SCORE: 0.3624
HOTSPOT_PERCENTILE: 88
IROC_SCORE: 0.9929
IROC_PERCENTILE: 77
POISSON_SCORE: 0.5575
POISSON_PERCENTILE: 81

**********************************************************************

source_name: chondrocytes derived via in vitro culture from mesenchymal stem cells; Lib:MC:20100726:03--ChIP:MC:20100713:03:chondrogenic dif cells:H3K36Me3

value: Medium:NA; Differentiation Method:alginate hydrogel scaffold (SR Herlofsen et al, Tissue Eng Part A. 2011)

value: chondrogenic dif cells

value: Abcam

value: Histone H3K36me3

value: Bioruptor


title: Exon arrays of Roadmap cell types; Fetal Kidney, Left primary tissue, day 110; DS16579-exon

description:
sample_term_id: UBERON_0004538
assay_term_id: OBI_0001463
nucleic_acid_term_id: SO_0000356
Exon profiling of NREMC cell types, these coincide with chromatin accessibility sequencing assays.
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.7199
sample alias: fKidney_Left.H-23604d110
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.5381

value: University of Washington, Congenital Defects Lab. Ian Glass

value: Primary Tissue

value: Fetal Kidney, Left

value: UW

value: fetal

value: day 110

value: Female


title: ChIP-Seq analysis of H3K27me3 in BM-MSC cells; Lib:MC:20100706:11--ChIP:MC:20100628:11:BM-MSC:H3K27Me3

description:
sample_term_id: EFO_0000586
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib:MC:20100706:11--ChIP:MC:20100628:11:BM-MSC:H3K27Me3
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.5750
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.5953
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

data_processing:
**********************************************************************

ANALYSIS FILE NAME: GSM670009_BI.Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells.H3K27me3.58.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:MC:20100706:11--ChIP:MC:20100628:11:BM-MSC:H3K27Me3.hg19.level.1.release.3
ANALYSIS TITLE: Mapping of Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells Histone H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K27me3 ChIP-Seq on Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells, Donor 58 were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.6587
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 3

QUALITY SCORES:
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 52
FINDPEAKS_SCORE: 0.1132
FINDPEAKS_PERCENTILE: 60
HOTSPOT_SCORE: 0.1976
HOTSPOT_PERCENTILE: 60
IROC_SCORE: 0.9079
IROC_PERCENTILE: 55
POISSON_SCORE: 0.4547
POISSON_PERCENTILE: 80

**********************************************************************

ANALYSIS FILE NAME: GSM670009_BI.Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells.H3K27me3.58.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:MC:20100706:11--ChIP:MC:20100628:11:BM-MSC:H3K27Me3.hg19.level.2.release.3
ANALYSIS TITLE: Raw Signal Density Graphs of Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells Histone H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K27me3 ChIP-Seq read mappings from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells, Donor 58 were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.6797
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 3
BROWSER_TRACK_NAME: BMDMSC H3K27me3 58
BROWSER_TRACK_DESCRIPTION: BI Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells Histone H3K27me3 Donor 58 Library Lib:MC:20100706:11--ChIP:MC:20100628:11:BM-MSC:H3K27Me3 EA Release 3

QUALITY SCORES:
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 52
FINDPEAKS_SCORE: 0.1132
FINDPEAKS_PERCENTILE: 60
HOTSPOT_SCORE: 0.1976
HOTSPOT_PERCENTILE: 60
IROC_SCORE: 0.9079
IROC_PERCENTILE: 55
POISSON_SCORE: 0.4547
POISSON_PERCENTILE: 80

**********************************************************************

source_name: bone marrow was aspirated from the iliac crest, isolated by density gradient and adhesion to plastic, and expanded in monolayer culture, containing 10% FBS; Lib:MC:20100706:11--ChIP:MC:20100628:11:BM-MSC:H3K27Me3

value: healthy

value: genomic DNA

value: BM-MSC

value: Unknown

value: Primary Cell Culture

value: Rikshospitalet University Hospital

value: Protein A-Sepharose 4B

value: 10 million cells

value: Histone H3K27me3


title: Exon arrays of Roadmap cell types; Fetal Kidney, Left primary tissue, day 115; DS16805-exon

description:
sample_term_id: UBERON_0004538
assay_term_id: OBI_0001463
nucleic_acid_term_id: SO_0000356
Exon profiling of NREMC cell types, these coincide with chromatin accessibility sequencing assays.
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.7197
sample alias: fKidney_Left.H-23640d115
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.5385

value: day 115

value: Male


title: ChIP-Seq analysis of H3K27me3 in BM-MSC cells; Lib:MC:20100713:04--ChIP:MC:20100706:04:BM-MSC:H3K27Me3

description:
sample_term_id: EFO_0000586
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib:MC:20100713:04--ChIP:MC:20100706:04:BM-MSC:H3K27Me3
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.5748
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.5948
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

data_processing:
**********************************************************************

ANALYSIS FILE NAME: GSM670007_BI.Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells.H3K27me3.59.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:MC:20100713:04--ChIP:MC:20100706:04:BM-MSC:H3K27Me3.hg19.level.1.release.3
ANALYSIS TITLE: Mapping of Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells Histone H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K27me3 ChIP-Seq on Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells, Donor 59 were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.6591
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 3

QUALITY SCORES:
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 52
FINDPEAKS_SCORE: 0.0632
FINDPEAKS_PERCENTILE: 50
HOTSPOT_SCORE: 0.1422
HOTSPOT_PERCENTILE: 40
IROC_SCORE: 0.8697
IROC_PERCENTILE: 45
POISSON_SCORE: 0.3512
POISSON_PERCENTILE: 50

**********************************************************************

ANALYSIS FILE NAME: GSM670007_BI.Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells.H3K27me3.59.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:MC:20100713:04--ChIP:MC:20100706:04:BM-MSC:H3K27Me3.hg19.level.2.release.3
ANALYSIS TITLE: Raw Signal Density Graphs of Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells Histone H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K27me3 ChIP-Seq read mappings from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells, Donor 59 were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.6801
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 3
BROWSER_TRACK_NAME: BMDMSC H3K27me3 59
BROWSER_TRACK_DESCRIPTION: BI Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells Histone H3K27me3 Donor 59 Library Lib:MC:20100713:04--ChIP:MC:20100706:04:BM-MSC:H3K27Me3 EA Release 3

QUALITY SCORES:
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 52
FINDPEAKS_SCORE: 0.0632
FINDPEAKS_PERCENTILE: 50
HOTSPOT_SCORE: 0.1422
HOTSPOT_PERCENTILE: 40
IROC_SCORE: 0.8697
IROC_PERCENTILE: 45
POISSON_SCORE: 0.3512
POISSON_PERCENTILE: 50

**********************************************************************

source_name: bone marrow was aspirated from the iliac crest, isolated by density gradient and adhesion to plastic, and expanded in monolayer culture, containing 10% FBS; Lib:MC:20100713:04--ChIP:MC:20100706:04:BM-MSC:H3K27Me3

value: SDS lysis

value: 70 ul bed volume

value: Millipore

value: Bioruptor


title: ChIP-Seq analysis of H3K4me3; chondr. dif cls; Lib:MC:20100726:02--ChIP:MC:20100713:02:chondrogenic dif cells:H3K4Me3

description:
sample_term_id: CL_0000138
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib:MC:20100726:02--ChIP:MC:20100713:02:chondrogenic dif cells:H3K4Me3
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.5745
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.5949
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

data_processing:
**********************************************************************

ANALYSIS FILE NAME: GSM670004_BI.Chondrocytes_from_Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells.H3K4me3.57.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:MC:20100726:02--ChIP:MC:20100713:02:chondrogenic dif cells:H3K4Me3.hg19.level.1.release.3
ANALYSIS TITLE: Mapping of Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me3 ChIP-Seq on Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells, Donor 57 were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.6564
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 3

QUALITY SCORES:
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 63
FINDPEAKS_SCORE: 0.5671
FINDPEAKS_PERCENTILE: 72
HOTSPOT_SCORE: 0.5794
HOTSPOT_PERCENTILE: 72
IROC_SCORE: 0.9927
IROC_PERCENTILE: 20
POISSON_SCORE: 0.6093
POISSON_PERCENTILE: 72

**********************************************************************

ANALYSIS FILE NAME: GSM670004_BI.Chondrocytes_from_Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells.H3K4me3.57.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:MC:20100726:02--ChIP:MC:20100713:02:chondrogenic dif cells:H3K4Me3.hg19.level.2.release.3
ANALYSIS TITLE: Raw Signal Density Graphs of Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me3 ChIP-Seq read mappings from Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells, Donor 57 were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.6774
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 3
BROWSER_TRACK_NAME: CfBMDMSC H3K4me3 57
BROWSER_TRACK_DESCRIPTION: BI Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells Histone H3K4me3 Donor 57 Library Lib:MC:20100726:02--ChIP:MC:20100713:02:chondrogenic dif cells:H3K4Me3 EA Release 3

QUALITY SCORES:
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 63
FINDPEAKS_SCORE: 0.5671
FINDPEAKS_PERCENTILE: 72
HOTSPOT_SCORE: 0.5794
HOTSPOT_PERCENTILE: 72
IROC_SCORE: 0.9927
IROC_PERCENTILE: 20
POISSON_SCORE: 0.6093
POISSON_PERCENTILE: 72

**********************************************************************

source_name: chondrocytes derived via in vitro culture from mesenchymal stem cells; Lib:MC:20100726:02--ChIP:MC:20100713:02:chondrogenic dif cells:H3K4Me3

value: Medium:NA; Differentiation Method:alginate hydrogel scaffold (SR Herlofsen et al, Tissue Eng Part A. 2011)

value: chondrogenic dif cells

value: Histone H3K4me3


title: ChIP-Seq analysis of WCE; chondr. dif cls; Lib:MC:20100726:14--ChIP:MC:20100713:14:chondrogenic dif cells:WCE

description:
sample_term_id: CL_0000138
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib:MC:20100726:14--ChIP:MC:20100713:14:chondrogenic dif cells:WCE
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.5770
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.5951
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

data_processing:
**********************************************************************

ANALYSIS FILE NAME: GSM670029_BI.Chondrocytes_from_Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells.Input.58.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:MC:20100726:14--ChIP:MC:20100713:14:chondrogenic dif cells:WCE.hg19.level.1.release.3
ANALYSIS TITLE: Mapping of Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina reads produced by ChIP-Seq Input on Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells, Donor 58 were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.6469
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 3

QUALITY SCORES:
NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 61
FINDPEAKS_SCORE: 0.0069
FINDPEAKS_PERCENTILE: 60
HOTSPOT_SCORE: 0.0151
HOTSPOT_PERCENTILE: 60
IROC_SCORE: 0.0
IROC_PERCENTILE: 38
POISSON_SCORE: 0.059
POISSON_PERCENTILE: 57

**********************************************************************

ANALYSIS FILE NAME: GSM670029_BI.Chondrocytes_from_Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells.Input.58.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:MC:20100726:14--ChIP:MC:20100713:14:chondrogenic dif cells:WCE.hg19.level.2.release.3
ANALYSIS TITLE: Raw Signal Density Graphs of Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina ChIP-Seq Input read mappings from Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells, Donor 58 were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.6679
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 3
BROWSER_TRACK_NAME: CfBMDMSC Input 58
BROWSER_TRACK_DESCRIPTION: BI Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells ChIP-Seq Input Donor 58 Library Lib:MC:20100726:14--ChIP:MC:20100713:14:chondrogenic dif cells:WCE EA Release 3

QUALITY SCORES:
NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 61
FINDPEAKS_SCORE: 0.0069
FINDPEAKS_PERCENTILE: 60
HOTSPOT_SCORE: 0.0151
HOTSPOT_PERCENTILE: 60
IROC_SCORE: 0.0
IROC_PERCENTILE: 38
POISSON_SCORE: 0.059
POISSON_PERCENTILE: 57

**********************************************************************

source_name: chondrocytes derived via in vitro culture from mesenchymal stem cells; Lib:MC:20100726:14--ChIP:MC:20100713:14:chondrogenic dif cells:WCE

value: healthy

value: genomic DNA

value: standard

value: ChIP-Seq Input

value: Input


title: Exon arrays of Roadmap cell types; flow sorted CD14+ Cells,year 21; DS17215-exon

description:
sample_term_id: CL_0001054
assay_term_id: OBI_0001463
nucleic_acid_term_id: SO_0000356
Exon profiling of NREMC cell types, these coincide with chromatin accessibility sequencing assays.
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.7225
sample alias: CD14.RO_01721
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.5355

value: FHCRC HEIMFELD

value: Primary Cell

value: CD14 Primary Cells

value: year 21

value: Caucasian


title: ChIP-Seq analysis of H3K27me3 in AdiposeNuclei cells; Lib:XZ:20100731:25--ChIP:XZ:20100726:25:AdiposeNuclei:H3K27Me3

description:
sample_term_id: UBERON_0014455
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib:XZ:20100731:25--ChIP:XZ:20100726:25:AdiposeNuclei:H3K27Me3
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.5758
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.5945
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

data_processing:
**********************************************************************

ANALYSIS FILE NAME: GSM670017_BI.Adipose_Nuclei.H3K27me3.95.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100731:25--ChIP:XZ:20100726:25:AdiposeNuclei:H3K27Me3.hg19.level.1.release.3
ANALYSIS TITLE: Mapping of Adipose Nuclei Histone H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K27me3 ChIP-Seq on Adipose Nuclei, Donor 95 were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.6537
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 3

QUALITY SCORES:
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 52
FINDPEAKS_SCORE: 0.0622
FINDPEAKS_PERCENTILE: 45
HOTSPOT_SCORE: 0.1503
HOTSPOT_PERCENTILE: 50
IROC_SCORE: 0.8528
IROC_PERCENTILE: 40
POISSON_SCORE: 0.383
POISSON_PERCENTILE: 70

**********************************************************************

ANALYSIS FILE NAME: GSM670017_BI.Adipose_Nuclei.H3K27me3.95.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100731:25--ChIP:XZ:20100726:25:AdiposeNuclei:H3K27Me3.hg19.level.2.release.3
ANALYSIS TITLE: Raw Signal Density Graphs of Adipose Nuclei Histone H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K27me3 ChIP-Seq read mappings from Adipose Nuclei, Donor 95 were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.6747
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 3
BROWSER_TRACK_NAME: AN H3K27me3 95
BROWSER_TRACK_DESCRIPTION: BI Adipose Nuclei Histone H3K27me3 Donor 95 Library Lib:XZ:20100731:25--ChIP:XZ:20100726:25:AdiposeNuclei:H3K27Me3 EA Release 3

QUALITY SCORES:
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 52
FINDPEAKS_SCORE: 0.0622
FINDPEAKS_PERCENTILE: 45
HOTSPOT_SCORE: 0.1503
HOTSPOT_PERCENTILE: 50
IROC_SCORE: 0.8528
IROC_PERCENTILE: 40
POISSON_SCORE: 0.383
POISSON_PERCENTILE: 70

**********************************************************************

source_name: Nuclei derived from crude preps of adipose tissue; Lib:XZ:20100731:25--ChIP:XZ:20100726:25:AdiposeNuclei:H3K27Me3

value: Adipose Nuclei

value: surgery

value: Female

value: Primary Tissue

value: abdomen

value: Harvard University

value: Protein A-Sepharose 4B

value: 10 million cells

value: SDS lysis

value: Histone H3K27me3


title: ChIP-Seq analysis of H3K4me3 in AdiposeNuclei cells; Lib:XZ:20100731:09--ChIP:XZ:20100726:09:AdiposeNuclei:H3K4Me3

description:
sample_term_id: UBERON_0014455
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib:XZ:20100731:09--ChIP:XZ:20100726:09:AdiposeNuclei:H3K4Me3
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.5739
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.5947
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

data_processing:
**********************************************************************

ANALYSIS FILE NAME: GSM669998_BI.Adipose_Nuclei.H3K4me3.93.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100731:09--ChIP:XZ:20100726:09:AdiposeNuclei:H3K4Me3.hg19.level.1.release.3
ANALYSIS TITLE: Mapping of Adipose Nuclei Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me3 ChIP-Seq on Adipose Nuclei, Donor 93 were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.6500
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 3

QUALITY SCORES:
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 63
FINDPEAKS_SCORE: 0.2537
FINDPEAKS_PERCENTILE: 32
HOTSPOT_SCORE: 0.2851
HOTSPOT_PERCENTILE: 36
IROC_SCORE: 0.9996
IROC_PERCENTILE: 64
POISSON_SCORE: 0.3499
POISSON_PERCENTILE: 36

**********************************************************************

ANALYSIS FILE NAME: GSM669998_BI.Adipose_Nuclei.H3K4me3.93.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100731:09--ChIP:XZ:20100726:09:AdiposeNuclei:H3K4Me3.hg19.level.2.release.3
ANALYSIS TITLE: Raw Signal Density Graphs of Adipose Nuclei Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me3 ChIP-Seq read mappings from Adipose Nuclei, Donor 93 were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.6710
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 3
BROWSER_TRACK_NAME: AN H3K4me3 93
BROWSER_TRACK_DESCRIPTION: BI Adipose Nuclei Histone H3K4me3 Donor 93 Library Lib:XZ:20100731:09--ChIP:XZ:20100726:09:AdiposeNuclei:H3K4Me3 EA Release 3

QUALITY SCORES:
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 63
FINDPEAKS_SCORE: 0.2537
FINDPEAKS_PERCENTILE: 32
HOTSPOT_SCORE: 0.2851
HOTSPOT_PERCENTILE: 36
IROC_SCORE: 0.9996
IROC_PERCENTILE: 64
POISSON_SCORE: 0.3499
POISSON_PERCENTILE: 36

**********************************************************************

source_name: Nuclei derived from crude preps of adipose tissue; Lib:XZ:20100731:09--ChIP:XZ:20100726:09:AdiposeNuclei:H3K4Me3

value: genomic DNA

value: 70 ul bed volume

value: Millipore

value: Histone H3K4me3

value: Bioruptor


title: ChIP-Seq analysis of WCE in BM-MSC cells; Lib:MC:20100713:14--ChIP:MC:20100706:14:BM-MSC:WCE

description:
sample_term_id: EFO_0000586
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib:MC:20100713:14--ChIP:MC:20100706:14:BM-MSC:WCE
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.5747
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.5950
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

data_processing:
**********************************************************************

ANALYSIS FILE NAME: GSM670006_BI.Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells.Input.60.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:MC:20100713:14--ChIP:MC:20100706:14:BM-MSC:WCE.hg19.level.1.release.3
ANALYSIS TITLE: Mapping of Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina reads produced by ChIP-Seq Input on Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells, Donor 60 were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.6506
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 3

QUALITY SCORES:
NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 61
FINDPEAKS_SCORE: 0.0059
FINDPEAKS_PERCENTILE: 23
HOTSPOT_SCORE: 0.0098
HOTSPOT_PERCENTILE: 43
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.0535
POISSON_PERCENTILE: 50

**********************************************************************

ANALYSIS FILE NAME: GSM670006_BI.Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells.Input.60.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:MC:20100713:14--ChIP:MC:20100706:14:BM-MSC:WCE.hg19.level.2.release.3
ANALYSIS TITLE: Raw Signal Density Graphs of Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina ChIP-Seq Input read mappings from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells, Donor 60 were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.6716
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 3
BROWSER_TRACK_NAME: BMDMSC Input 60
BROWSER_TRACK_DESCRIPTION: BI Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells ChIP-Seq Input Donor 60 Library Lib:MC:20100713:14--ChIP:MC:20100706:14:BM-MSC:WCE EA Release 3

QUALITY SCORES:
NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 61
FINDPEAKS_SCORE: 0.0059
FINDPEAKS_PERCENTILE: 23
HOTSPOT_SCORE: 0.0098
HOTSPOT_PERCENTILE: 43
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.0535
POISSON_PERCENTILE: 50

**********************************************************************

source_name: bone marrow was aspirated from the iliac crest, isolated by density gradient and adhesion to plastic, and expanded in monolayer culture, containing 10% FBS; Lib:MC:20100713:14--ChIP:MC:20100706:14:BM-MSC:WCE

value: healthy

value: BM-MSC

value: Unknown

value: Primary Cell Culture

value: Rikshospitalet University Hospital

value: standard

value: ChIP-Seq Input

value: Input


title: Exon arrays of Roadmap cell types; flow sorted CD34+ cells from cord blood; DS14200-exon

status: Public on Jul 06 2011

description:
sample_term_id: CL_0000837
assay_term_id: OBI_0001463
nucleic_acid_term_id: SO_0000356
Exon profiling of NREMC cell types, these coincide with chromatin accessibility sequencing assays.
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.7549
sample alias: RO 01549
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.2401

value: FHCRC HEIMFELD

value: Primary Cell

value: CD34 Primary Cells

value: 33 years

value: Female

value: Caucasian


title: ChIP-Seq analysis of H3K4me1; chondr. dif cls; Lib:MC:20100729:01--ChIP:MC:20100726:01:chondrogenic dif cells:H3K4Me1

description:
sample_term_id: CL_0000138
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib:MC:20100729:01--ChIP:MC:20100726:01:chondrogenic dif cells:H3K4Me1
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.5741
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.5935
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

data_processing:
**********************************************************************

ANALYSIS FILE NAME: GSM670000_BI.Chondrocytes_from_Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells.H3K4me1.59.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:MC:20100729:01--ChIP:MC:20100726:01:chondrogenic dif cells:H3K4Me1.hg19.level.1.release.3
ANALYSIS TITLE: Mapping of Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me1 ChIP-Seq on Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells, Donor 59 were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.6516
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 3

QUALITY SCORES:
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 50
FINDPEAKS_SCORE: 0.6159
FINDPEAKS_PERCENTILE: 96
HOTSPOT_SCORE: 0.6161
HOTSPOT_PERCENTILE: 96
IROC_SCORE: 0.9983
IROC_PERCENTILE: 93
POISSON_SCORE: 0.7046
POISSON_PERCENTILE: 96

**********************************************************************

ANALYSIS FILE NAME: GSM670000_BI.Chondrocytes_from_Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells.H3K4me1.59.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:MC:20100729:01--ChIP:MC:20100726:01:chondrogenic dif cells:H3K4Me1.hg19.level.2.release.3
ANALYSIS TITLE: Raw Signal Density Graphs of Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me1 ChIP-Seq read mappings from Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells, Donor 59 were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.6726
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 3
BROWSER_TRACK_NAME: CfBMDMSC H3K4me1 59
BROWSER_TRACK_DESCRIPTION: BI Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells Histone H3K4me1 Donor 59 Library Lib:MC:20100729:01--ChIP:MC:20100726:01:chondrogenic dif cells:H3K4Me1 EA Release 3

QUALITY SCORES:
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 50
FINDPEAKS_SCORE: 0.6159
FINDPEAKS_PERCENTILE: 96
HOTSPOT_SCORE: 0.6161
HOTSPOT_PERCENTILE: 96
IROC_SCORE: 0.9983
IROC_PERCENTILE: 93
POISSON_SCORE: 0.7046
POISSON_PERCENTILE: 96

**********************************************************************

source_name: chondrocytes derived via in vitro culture from mesenchymal stem cells; Lib:MC:20100729:01--ChIP:MC:20100726:01:chondrogenic dif cells:H3K4Me1

value: genomic DNA

value: Medium:NA; Differentiation Method:alginate hydrogel scaffold (SR Herlofsen et al, Tissue Eng Part A. 2011)

value: chondrogenic dif cells

value: Protein A-Sepharose 4B

value: 10 million cells

value: SDS lysis

value: 70 ul bed volume

value: Abcam

value: Histone H3K4me1


title: ChIP-Seq analysis of H3K9ac in BM-MSC cells; Lib:MC:20100713:05--ChIP:MC:20100706:05:BM-MSC:H3K9Ac

description:
sample_term_id: EFO_0000586
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib:MC:20100713:05--ChIP:MC:20100706:05:BM-MSC:H3K9Ac
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.5740
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.5948
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

data_processing:
**********************************************************************

ANALYSIS FILE NAME: GSM669999_BI.Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells.H3K9ac.59.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:MC:20100713:05--ChIP:MC:20100706:05:BM-MSC:H3K9Ac.hg19.level.1.release.3
ANALYSIS TITLE: Mapping of Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells Histone H3K9ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K9ac ChIP-Seq on Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells, Donor 59 were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.6540
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 3

QUALITY SCORES:
NUMBER_OF_H3K9ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 40
FINDPEAKS_SCORE: 0.0744
FINDPEAKS_PERCENTILE: 8
HOTSPOT_SCORE: 0.1158
HOTSPOT_PERCENTILE: 4
IROC_SCORE: 0.9903
IROC_PERCENTILE: 36
POISSON_SCORE: 0.1712
POISSON_PERCENTILE: 4

**********************************************************************

ANALYSIS FILE NAME: GSM669999_BI.Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells.H3K9ac.59.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:MC:20100713:05--ChIP:MC:20100706:05:BM-MSC:H3K9Ac.hg19.level.2.release.3
ANALYSIS TITLE: Raw Signal Density Graphs of Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells Histone H3K9ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K9ac ChIP-Seq read mappings from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells, Donor 59 were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.6750
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 3
BROWSER_TRACK_NAME: BMDMSC H3K9ac 59
BROWSER_TRACK_DESCRIPTION: BI Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells Histone H3K9ac Donor 59 Library Lib:MC:20100713:05--ChIP:MC:20100706:05:BM-MSC:H3K9Ac EA Release 3

QUALITY SCORES:
NUMBER_OF_H3K9ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 40
FINDPEAKS_SCORE: 0.0744
FINDPEAKS_PERCENTILE: 8
HOTSPOT_SCORE: 0.1158
HOTSPOT_PERCENTILE: 4
IROC_SCORE: 0.9903
IROC_PERCENTILE: 36
POISSON_SCORE: 0.1712
POISSON_PERCENTILE: 4

**********************************************************************

source_name: bone marrow was aspirated from the iliac crest, isolated by density gradient and adhesion to plastic, and expanded in monolayer culture, containing 10% FBS; Lib:MC:20100713:05--ChIP:MC:20100706:05:BM-MSC:H3K9Ac

value: healthy

value: BM-MSC

value: Unknown

value: Primary Cell Culture

value: Rikshospitalet University Hospital

value: Histone H3K9ac

value: Bioruptor


title: ChIP-Seq analysis of H3K9me3 in BM-MSC cells; Lib:MC:20100713:06--ChIP:MC:20100706:06:BM-MSC:H3K9Me3

description:
sample_term_id: EFO_0000586
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib:MC:20100713:06--ChIP:MC:20100706:06:BM-MSC:H3K9Me3
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.5730
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.5948
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

data_processing:
**********************************************************************

ANALYSIS FILE NAME: GSM669989_BI.Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells.H3K9me3.59.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:MC:20100713:06--ChIP:MC:20100706:06:BM-MSC:H3K9Me3.hg19.level.1.release.3
ANALYSIS TITLE: Mapping of Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K9me3 ChIP-Seq on Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells, Donor 59 were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.6521
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 3

QUALITY SCORES:
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 60
FINDPEAKS_SCORE: 0.0183
FINDPEAKS_PERCENTILE: 8
HOTSPOT_SCORE: 0.0432
HOTSPOT_PERCENTILE: 4
IROC_SCORE: 0.9439
IROC_PERCENTILE: 92
POISSON_SCORE: 0.124
POISSON_PERCENTILE: 4

**********************************************************************

ANALYSIS FILE NAME: GSM669989_BI.Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells.H3K9me3.59.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:MC:20100713:06--ChIP:MC:20100706:06:BM-MSC:H3K9Me3.hg19.level.2.release.3
ANALYSIS TITLE: Raw Signal Density Graphs of Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K9me3 ChIP-Seq read mappings from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells, Donor 59 were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.6731
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 3
BROWSER_TRACK_NAME: BMDMSC H3K9me3 59
BROWSER_TRACK_DESCRIPTION: BI Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells Histone H3K9me3 Donor 59 Library Lib:MC:20100713:06--ChIP:MC:20100706:06:BM-MSC:H3K9Me3 EA Release 3

QUALITY SCORES:
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 60
FINDPEAKS_SCORE: 0.0183
FINDPEAKS_PERCENTILE: 8
HOTSPOT_SCORE: 0.0432
HOTSPOT_PERCENTILE: 4
IROC_SCORE: 0.9439
IROC_PERCENTILE: 92
POISSON_SCORE: 0.124
POISSON_PERCENTILE: 4

**********************************************************************

source_name: bone marrow was aspirated from the iliac crest, isolated by density gradient and adhesion to plastic, and expanded in monolayer culture, containing 10% FBS; Lib:MC:20100713:06--ChIP:MC:20100706:06:BM-MSC:H3K9Me3

value: Histone H3K9me3