title: ChIP-Seq analysis of H3K4me3; chondr. dif cls; Lib:MC:20100729:09--ChIP:MC:20100726:09: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:20100729:09--ChIP:MC:20100726:09:chondrogenic dif cells:H3K4Me3
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.5731
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.5932
****************
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: GSM669990_BI.Chondrocytes_from_Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells.H3K4me3.60.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:MC:20100729:09--ChIP:MC:20100726:09: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 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.6509
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: 0.694
FINDPEAKS_PERCENTILE: 96
HOTSPOT_SCORE: 0.6988
HOTSPOT_PERCENTILE: 96
IROC_SCORE: 0.9935
IROC_PERCENTILE: 24
POISSON_SCORE: 0.7011
POISSON_PERCENTILE: 96

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

ANALYSIS FILE NAME: GSM669990_BI.Chondrocytes_from_Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells.H3K4me3.60.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:MC:20100729:09--ChIP:MC:20100726:09: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 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.6719
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 60
BROWSER_TRACK_DESCRIPTION: BI Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells Histone H3K4me3 Donor 60 Library Lib:MC:20100729:09--ChIP:MC:20100726:09:chondrogenic dif cells:H3K4Me3 EA Release 3

QUALITY SCORES:
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 63
FINDPEAKS_SCORE: 0.694
FINDPEAKS_PERCENTILE: 96
HOTSPOT_SCORE: 0.6988
HOTSPOT_PERCENTILE: 96
IROC_SCORE: 0.9935
IROC_PERCENTILE: 24
POISSON_SCORE: 0.7011
POISSON_PERCENTILE: 96

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

source_name: chondrocytes derived via in vitro culture from mesenchymal stem cells; Lib:MC:20100729:09--ChIP:MC:20100726:09:chondrogenic dif cells:H3K4Me3

value: genomic DNA

value: Millipore

value: Histone H3K4me3


title: ChIP-Seq analysis of H3K4me1; chondr. dif cls; Lib:MC:20100726:01--ChIP:MC:20100713:01:chondrogenic dif cells:H3K4Me1

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:20100726:01--ChIP:MC:20100713:01:chondrogenic dif cells:H3K4Me1
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.5765
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
****************

library_source: genomic

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

ANALYSIS FILE NAME: GSM670024_BI.Chondrocytes_from_Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells.H3K4me1.57.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:MC:20100726:01--ChIP:MC:20100713:01: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 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.6514
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: 0.6314
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.6298
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.9986
IROC_PERCENTILE: 100
POISSON_SCORE: 0.7148
POISSON_PERCENTILE: 100

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

ANALYSIS FILE NAME: GSM670024_BI.Chondrocytes_from_Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells.H3K4me1.57.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:MC:20100726:01--ChIP:MC:20100713:01: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 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.6724
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 57
BROWSER_TRACK_DESCRIPTION: BI Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells Histone H3K4me1 Donor 57 Library Lib:MC:20100726:01--ChIP:MC:20100713:01:chondrogenic dif cells:H3K4Me1 EA Release 3

QUALITY SCORES:
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 50
FINDPEAKS_SCORE: 0.6314
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.6298
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.9986
IROC_PERCENTILE: 100
POISSON_SCORE: 0.7148
POISSON_PERCENTILE: 100

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

molecule: genomic DNA

organism: Homo sapiens

source_name: chondrocytes derived via in vitro culture from mesenchymal stem cells; Lib:MC:20100726:01--ChIP:MC:20100713:01:chondrogenic dif cells:H3K4Me1

extract_protocol: Library construction protocol: Single read - Illumina

tag: sample alias

tag: sample common name

value: healthy

tag: molecule

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: Abcam

value: Histone H3K4me1

value: Bioruptor


title: Exon arrays of Roadmap cell types; Fetal  primary tissue, day 115; DS16712-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.7205
sample alias: fIntestine_Small.H-23640d115
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.7051

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: day 115

value: Male


title: Exon arrays of Roadmap cell types; flow sorted CD34+ cells from cord blood; DS11202-exon

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.7376
sample alias: RO 01508
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.1645

value: FHCRC HEIMFELD

value: Primary Cell

value: CD34 Primary Cells

value: Hispanic


title: ChIP-Seq analysis of H3K4me1 in BM-MSC cells; Lib:MC:20100713:08--ChIP:MC:20100706:08:BM-MSC:H3K4Me1

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:20100713:08--ChIP:MC:20100706:08:BM-MSC:H3K4Me1
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.5721
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: GSM669980_BI.Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells.H3K4me1.60.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:MC:20100713:08--ChIP:MC:20100706:08:BM-MSC:H3K4Me1.hg19.level.1.release.3
ANALYSIS TITLE: Mapping of Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me1 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.6450
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: 0.2346
FINDPEAKS_PERCENTILE: 32
HOTSPOT_SCORE: 0.3071
HOTSPOT_PERCENTILE: 32
IROC_SCORE: 0.9741
IROC_PERCENTILE: 50
POISSON_SCORE: 0.4041
POISSON_PERCENTILE: 32

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

ANALYSIS FILE NAME: GSM669980_BI.Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells.H3K4me1.60.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:MC:20100713:08--ChIP:MC:20100706:08:BM-MSC:H3K4Me1.hg19.level.2.release.3
ANALYSIS TITLE: Raw Signal Density Graphs of Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me1 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.6660
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 H3K4me1 60
BROWSER_TRACK_DESCRIPTION: BI Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells Histone H3K4me1 Donor 60 Library Lib:MC:20100713:08--ChIP:MC:20100706:08:BM-MSC:H3K4Me1 EA Release 3

QUALITY SCORES:
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 50
FINDPEAKS_SCORE: 0.2346
FINDPEAKS_PERCENTILE: 32
HOTSPOT_SCORE: 0.3071
HOTSPOT_PERCENTILE: 32
IROC_SCORE: 0.9741
IROC_PERCENTILE: 50
POISSON_SCORE: 0.4041
POISSON_PERCENTILE: 32

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

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:20100713:08--ChIP:MC:20100706:08:BM-MSC:H3K4Me1

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


title: Exon arrays of Roadmap cell types; Fetal Intestine, Small primary tissue, day 105; DS16822-exon

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.7203
sample alias: fIntestine_Small.H-23663d105
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.5417

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

value: Primary Tissue

value: Fetal Intestine, Small

value: day 105

value: Female


title: ChIP-Seq analysis of H3K4me1 in AdiposeNuclei cells; Lib:XZ:20100731:15--ChIP:XZ:20100726:15:AdiposeNuclei:H3K4Me1

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:20100731:15--ChIP:XZ:20100726:15:AdiposeNuclei:H3K4Me1
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.5716
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: GSM669975_BI.Adipose_Nuclei.H3K4me1.94.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100731:15--ChIP:XZ:20100726:15:AdiposeNuclei:H3K4Me1.hg19.level.1.release.3
ANALYSIS TITLE: Mapping of Adipose Nuclei Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me1 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.6599
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: 0.5394
FINDPEAKS_PERCENTILE: 82
HOTSPOT_SCORE: 0.5409
HOTSPOT_PERCENTILE: 82
IROC_SCORE: 0.997
IROC_PERCENTILE: 86
POISSON_SCORE: 0.6535
POISSON_PERCENTILE: 82

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

ANALYSIS FILE NAME: GSM669975_BI.Adipose_Nuclei.H3K4me1.94.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100731:15--ChIP:XZ:20100726:15:AdiposeNuclei:H3K4Me1.hg19.level.2.release.3
ANALYSIS TITLE: Raw Signal Density Graphs of Adipose Nuclei Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me1 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.6809
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 H3K4me1 94
BROWSER_TRACK_DESCRIPTION: BI Adipose Nuclei Histone H3K4me1 Donor 94 Library Lib:XZ:20100731:15--ChIP:XZ:20100726:15:AdiposeNuclei:H3K4Me1 EA Release 3

QUALITY SCORES:
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 50
FINDPEAKS_SCORE: 0.5394
FINDPEAKS_PERCENTILE: 82
HOTSPOT_SCORE: 0.5409
HOTSPOT_PERCENTILE: 82
IROC_SCORE: 0.997
IROC_PERCENTILE: 86
POISSON_SCORE: 0.6535
POISSON_PERCENTILE: 82

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

source_name: Nuclei derived from crude preps of adipose tissue; Lib:XZ:20100731:15--ChIP:XZ:20100726:15:AdiposeNuclei:H3K4Me1

value: Adipose Nuclei

value: surgery

value: abdomen

value: Harvard University

value: SDS lysis

value: 70 ul bed volume

value: Abcam

value: Histone H3K4me1

value: Bioruptor


title: Exon arrays of Roadmap cell types; Fetal Heart primary tissue, day 110; DS16621-exon

description:
sample_term_id: UBERON_0000948
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.7211
sample alias: fHeart.H-23617d110
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.5286

value: Fetal Heart

value: UW

value: fetal

value: day 110

value: Male


title: ChIP-Seq analysis of H3K9me3 in AdiposeNuclei cells; Lib:XZ:20100731:20--ChIP:XZ:20100726:20:AdiposeNuclei:H3K9Me3

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:20100731:20--ChIP:XZ:20100726:20:AdiposeNuclei:H3K9Me3
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.5717
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: GSM669976_BI.Adipose_Nuclei.H3K9me3.94.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100731:20--ChIP:XZ:20100726:20:AdiposeNuclei:H3K9Me3.hg19.level.1.release.3
ANALYSIS TITLE: Mapping of Adipose Nuclei Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K9me3 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.6485
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: 0.1377
FINDPEAKS_PERCENTILE: 77
HOTSPOT_SCORE: 0.1991
HOTSPOT_PERCENTILE: 77
IROC_SCORE: 0.8998
IROC_PERCENTILE: 77
POISSON_SCORE: 0.3728
POISSON_PERCENTILE: 77

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

ANALYSIS FILE NAME: GSM669976_BI.Adipose_Nuclei.H3K9me3.94.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100731:20--ChIP:XZ:20100726:20:AdiposeNuclei:H3K9Me3.hg19.level.2.release.3
ANALYSIS TITLE: Raw Signal Density Graphs of Adipose Nuclei Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K9me3 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.6695
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 H3K9me3 94
BROWSER_TRACK_DESCRIPTION: BI Adipose Nuclei Histone H3K9me3 Donor 94 Library Lib:XZ:20100731:20--ChIP:XZ:20100726:20:AdiposeNuclei:H3K9Me3 EA Release 3

QUALITY SCORES:
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 60
FINDPEAKS_SCORE: 0.1377
FINDPEAKS_PERCENTILE: 77
HOTSPOT_SCORE: 0.1991
HOTSPOT_PERCENTILE: 77
IROC_SCORE: 0.8998
IROC_PERCENTILE: 77
POISSON_SCORE: 0.3728
POISSON_PERCENTILE: 77

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

source_name: Nuclei derived from crude preps of adipose tissue; Lib:XZ:20100731:20--ChIP:XZ:20100726:20:AdiposeNuclei:H3K9Me3

value: genomic DNA

value: Primary Tissue

value: Protein A-Sepharose 4B

value: 10 million cells

value: Histone H3K9me3


title: ChIP-Seq analysis of H3K4me3 in AdiposeNuclei cells; Lib:XZ:20100731:23--ChIP:XZ:20100726:23: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:20100731:23--ChIP:XZ:20100726:23:AdiposeNuclei:H3K4Me3
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.5729
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: GSM669988_BI.Adipose_Nuclei.H3K4me3.95.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100731:23--ChIP:XZ:20100726:23: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 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.6505
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: 0.503
FINDPEAKS_PERCENTILE: 68
HOTSPOT_SCORE: 0.5141
HOTSPOT_PERCENTILE: 68
IROC_SCORE: 0.9959
IROC_PERCENTILE: 36
POISSON_SCORE: 0.5483
POISSON_PERCENTILE: 68

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

ANALYSIS FILE NAME: GSM669988_BI.Adipose_Nuclei.H3K4me3.95.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100731:23--ChIP:XZ:20100726:23: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 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.6715
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 95
BROWSER_TRACK_DESCRIPTION: BI Adipose Nuclei Histone H3K4me3 Donor 95 Library Lib:XZ:20100731:23--ChIP:XZ:20100726:23:AdiposeNuclei:H3K4Me3 EA Release 3

QUALITY SCORES:
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 63
FINDPEAKS_SCORE: 0.503
FINDPEAKS_PERCENTILE: 68
HOTSPOT_SCORE: 0.5141
HOTSPOT_PERCENTILE: 68
IROC_SCORE: 0.9959
IROC_PERCENTILE: 36
POISSON_SCORE: 0.5483
POISSON_PERCENTILE: 68

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

source_name: Nuclei derived from crude preps of adipose tissue; Lib:XZ:20100731:23--ChIP:XZ:20100726:23:AdiposeNuclei:H3K4Me3

value: Adipose Nuclei

value: surgery

value: Female

value: abdomen

value: Millipore

value: Histone H3K4me3


title: Exon arrays of Roadmap cell types; Fetal  primary tissue, day 108; DS17307-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.7195
sample alias: fKidney_renal_cortex.H-23769d108
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.7070

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

value: Fetal Renal Cortex

value: day 108


title: ChIP-Seq analysis of H3K9me3 in AdiposeNuclei cells; Lib:XZ:20100731:13--ChIP:XZ:20100726:13:AdiposeNuclei:H3K9Me3

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:20100731:13--ChIP:XZ:20100726:13:AdiposeNuclei:H3K9Me3
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.5722
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: GSM669981_BI.Adipose_Nuclei.H3K9me3.93.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100731:13--ChIP:XZ:20100726:13:AdiposeNuclei:H3K9Me3.hg19.level.1.release.3
ANALYSIS TITLE: Mapping of Adipose Nuclei Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K9me3 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.6479
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: 0.0997
FINDPEAKS_PERCENTILE: 69
HOTSPOT_SCORE: 0.1605
HOTSPOT_PERCENTILE: 65
IROC_SCORE: 0.8735
IROC_PERCENTILE: 62
POISSON_SCORE: 0.3322
POISSON_PERCENTILE: 58

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

ANALYSIS FILE NAME: GSM669981_BI.Adipose_Nuclei.H3K9me3.93.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100731:13--ChIP:XZ:20100726:13:AdiposeNuclei:H3K9Me3.hg19.level.2.release.3
ANALYSIS TITLE: Raw Signal Density Graphs of Adipose Nuclei Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K9me3 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.6689
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 H3K9me3 93
BROWSER_TRACK_DESCRIPTION: BI Adipose Nuclei Histone H3K9me3 Donor 93 Library Lib:XZ:20100731:13--ChIP:XZ:20100726:13:AdiposeNuclei:H3K9Me3 EA Release 3

QUALITY SCORES:
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 60
FINDPEAKS_SCORE: 0.0997
FINDPEAKS_PERCENTILE: 69
HOTSPOT_SCORE: 0.1605
HOTSPOT_PERCENTILE: 65
IROC_SCORE: 0.8735
IROC_PERCENTILE: 62
POISSON_SCORE: 0.3322
POISSON_PERCENTILE: 58

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

source_name: Nuclei derived from crude preps of adipose tissue; Lib:XZ:20100731:13--ChIP:XZ:20100726:13:AdiposeNuclei:H3K9Me3

value: Harvard University

value: SDS lysis

value: 70 ul bed volume

value: Abcam

value: Bioruptor


title: ChIP-Seq analysis of H3K27me3; chondr. dif cls; Lib:MC:20100726:04--ChIP:MC:20100713:04:chondrogenic dif cells:H3K27Me3

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:20100726:04--ChIP:MC:20100713:04:chondrogenic dif cells:H3K27Me3
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.5700
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: GSM669959_BI.Chondrocytes_from_Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells.H3K27me3.57.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:MC:20100726:04--ChIP:MC:20100713:04:chondrogenic dif cells:H3K27Me3.hg19.level.1.release.3
ANALYSIS TITLE: Mapping of Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells Histone H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K27me3 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.6546
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: 0.1222
FINDPEAKS_PERCENTILE: 70
HOTSPOT_SCORE: 0.1991
HOTSPOT_PERCENTILE: 65
IROC_SCORE: 0.9156
IROC_PERCENTILE: 65
POISSON_SCORE: 0.4823
POISSON_PERCENTILE: 85

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

ANALYSIS FILE NAME: GSM669959_BI.Chondrocytes_from_Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells.H3K27me3.57.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:MC:20100726:04--ChIP:MC:20100713:04:chondrogenic dif cells:H3K27Me3.hg19.level.2.release.3
ANALYSIS TITLE: Raw Signal Density Graphs of Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells Histone H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K27me3 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.6756
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 H3K27me3 57
BROWSER_TRACK_DESCRIPTION: BI Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells Histone H3K27me3 Donor 57 Library Lib:MC:20100726:04--ChIP:MC:20100713:04:chondrogenic dif cells:H3K27Me3 EA Release 3

QUALITY SCORES:
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 52
FINDPEAKS_SCORE: 0.1222
FINDPEAKS_PERCENTILE: 70
HOTSPOT_SCORE: 0.1991
HOTSPOT_PERCENTILE: 65
IROC_SCORE: 0.9156
IROC_PERCENTILE: 65
POISSON_SCORE: 0.4823
POISSON_PERCENTILE: 85

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

source_name: chondrocytes derived via in vitro culture from mesenchymal stem cells; Lib:MC:20100726:04--ChIP:MC:20100713:04:chondrogenic dif cells:H3K27Me3

value: healthy

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: Unknown

value: Primary Cell Culture

value: Rikshospitalet University Hospital

value: Protein A-Sepharose 4B

value: Histone H3K27me3


title: ChIP-Seq analysis of WCE in BM-MSC cells; Lib:MC:20100706:14--ChIP:MC:20100628:14: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:20100706:14--ChIP:MC:20100628:14:BM-MSC:WCE
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.5699
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: GSM669958_BI.Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells.Input.58.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:MC:20100706:14--ChIP:MC:20100628:14: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 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.6566
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: 0.0166
HOTSPOT_PERCENTILE: 63
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.064
POISSON_PERCENTILE: 67

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

ANALYSIS FILE NAME: GSM669958_BI.Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells.Input.58.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:MC:20100706:14--ChIP:MC:20100628:14: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 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.6776
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 58
BROWSER_TRACK_DESCRIPTION: BI Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells ChIP-Seq Input Donor 58 Library Lib:MC:20100706:14--ChIP:MC:20100628:14: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: 0.0166
HOTSPOT_PERCENTILE: 63
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.064
POISSON_PERCENTILE: 67

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

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:20100706:14--ChIP:MC:20100628:14:BM-MSC:WCE

value: BM-MSC

value: standard

value: ChIP-Seq Input

value: Input


title: ChIP-Seq analysis of H3K9me3 in AdiposeNuclei cells; Lib:XZ:20100731:06--ChIP:XZ:20100726:06:AdiposeNuclei:H3K9Me3

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:20100731:06--ChIP:XZ:20100726:06:AdiposeNuclei:H3K9Me3
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.5709
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.5946
****************
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: GSM669968_BI.Adipose_Nuclei.H3K9me3.92.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100731:06--ChIP:XZ:20100726:06:AdiposeNuclei:H3K9Me3.hg19.level.1.release.3
ANALYSIS TITLE: Mapping of Adipose Nuclei Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K9me3 ChIP-Seq on Adipose Nuclei, Donor 92 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.6478
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: 0.1001
FINDPEAKS_PERCENTILE: 73
HOTSPOT_SCORE: 0.1619
HOTSPOT_PERCENTILE: 69
IROC_SCORE: 0.8983
IROC_PERCENTILE: 73
POISSON_SCORE: 0.3042
POISSON_PERCENTILE: 46

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

ANALYSIS FILE NAME: GSM669968_BI.Adipose_Nuclei.H3K9me3.92.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100731:06--ChIP:XZ:20100726:06:AdiposeNuclei:H3K9Me3.hg19.level.2.release.3
ANALYSIS TITLE: Raw Signal Density Graphs of Adipose Nuclei Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K9me3 ChIP-Seq read mappings from Adipose Nuclei, Donor 92 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.6688
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 H3K9me3 92
BROWSER_TRACK_DESCRIPTION: BI Adipose Nuclei Histone H3K9me3 Donor 92 Library Lib:XZ:20100731:06--ChIP:XZ:20100726:06:AdiposeNuclei:H3K9Me3 EA Release 3

QUALITY SCORES:
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 60
FINDPEAKS_SCORE: 0.1001
FINDPEAKS_PERCENTILE: 73
HOTSPOT_SCORE: 0.1619
HOTSPOT_PERCENTILE: 69
IROC_SCORE: 0.8983
IROC_PERCENTILE: 73
POISSON_SCORE: 0.3042
POISSON_PERCENTILE: 46

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

source_name: Nuclei derived from crude preps of adipose tissue; Lib:XZ:20100731:06--ChIP:XZ:20100726:06:AdiposeNuclei:H3K9Me3

value: Adipose Nuclei

value: surgery

value: Female

value: Primary Tissue

value: abdomen

value: Harvard University

value: 10 million cells

value: SDS lysis

value: Histone H3K9me3


title: ChIP-Seq analysis of H3K27me3 in BM-MSC cells; Lib:MC:20100713:11--ChIP:MC:20100706:11: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:20100713:11--ChIP:MC:20100706:11:BM-MSC:H3K27Me3
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.5698
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: GSM669957_BI.Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells.H3K27me3.60.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:MC:20100713:11--ChIP:MC:20100706:11: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 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.6525
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: 0.0488
FINDPEAKS_PERCENTILE: 35
HOTSPOT_SCORE: 0.1304
HOTSPOT_PERCENTILE: 35
IROC_SCORE: 0.8416
IROC_PERCENTILE: 30
POISSON_SCORE: 0.3433
POISSON_PERCENTILE: 45

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

ANALYSIS FILE NAME: GSM669957_BI.Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells.H3K27me3.60.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:MC:20100713:11--ChIP:MC:20100706:11: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 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.6735
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 60
BROWSER_TRACK_DESCRIPTION: BI Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells Histone H3K27me3 Donor 60 Library Lib:MC:20100713:11--ChIP:MC:20100706:11:BM-MSC:H3K27Me3 EA Release 3

QUALITY SCORES:
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 52
FINDPEAKS_SCORE: 0.0488
FINDPEAKS_PERCENTILE: 35
HOTSPOT_SCORE: 0.1304
HOTSPOT_PERCENTILE: 35
IROC_SCORE: 0.8416
IROC_PERCENTILE: 30
POISSON_SCORE: 0.3433
POISSON_PERCENTILE: 45

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

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:20100713:11--ChIP:MC:20100706:11:BM-MSC:H3K27Me3

value: healthy

value: genomic DNA

value: Unknown

value: Primary Cell Culture

value: 70 ul bed volume

value: Millipore

value: Bioruptor


title: ChIP-Seq analysis of H3K36me3 in AdiposeNuclei cells; Lib:XZ:20100731:03--ChIP:XZ:20100726:03:AdiposeNuclei:H3K36Me3

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:20100731:03--ChIP:XZ:20100726:03:AdiposeNuclei:H3K36Me3
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.5693
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.5946
****************
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: GSM669952_BI.Adipose_Nuclei.H3K36me3.92.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100731:03--ChIP:XZ:20100726:03:AdiposeNuclei:H3K36Me3.hg19.level.1.release.3
ANALYSIS TITLE: Mapping of Adipose Nuclei Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K36me3 ChIP-Seq on Adipose Nuclei, Donor 92 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.6585
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: 0.3214
FINDPEAKS_PERCENTILE: 58
HOTSPOT_SCORE: 0.3256
HOTSPOT_PERCENTILE: 65
IROC_SCORE: 0.9906
IROC_PERCENTILE: 65
POISSON_SCORE: 0.4877
POISSON_PERCENTILE: 50

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

ANALYSIS FILE NAME: GSM669952_BI.Adipose_Nuclei.H3K36me3.92.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100731:03--ChIP:XZ:20100726:03:AdiposeNuclei:H3K36Me3.hg19.level.2.release.3
ANALYSIS TITLE: Raw Signal Density Graphs of Adipose Nuclei Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K36me3 ChIP-Seq read mappings from Adipose Nuclei, Donor 92 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.6795
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 H3K36me3 92
BROWSER_TRACK_DESCRIPTION: BI Adipose Nuclei Histone H3K36me3 Donor 92 Library Lib:XZ:20100731:03--ChIP:XZ:20100726:03:AdiposeNuclei:H3K36Me3 EA Release 3

QUALITY SCORES:
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 59
FINDPEAKS_SCORE: 0.3214
FINDPEAKS_PERCENTILE: 58
HOTSPOT_SCORE: 0.3256
HOTSPOT_PERCENTILE: 65
IROC_SCORE: 0.9906
IROC_PERCENTILE: 65
POISSON_SCORE: 0.4877
POISSON_PERCENTILE: 50

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

source_name: Nuclei derived from crude preps of adipose tissue; Lib:XZ:20100731:03--ChIP:XZ:20100726:03:AdiposeNuclei:H3K36Me3

value: Protein A-Sepharose 4B

value: Abcam

value: Histone H3K36me3


title: ChIP-Seq analysis of H3K9ac in rectal mucosa cells; Lib:XZ:20100503:12--ChIP:XZ:20100420:12:rectal mucosa:H3K9Ac

description:
sample_term_id: UBERON_0003346
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib:XZ:20100503:12--ChIP:XZ:20100420:12:rectal mucosa:H3K9Ac
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.5690
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.3351
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************
BED and WIG files were replaced on April 29, 2014

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

ANALYSIS FILE NAME: GSM669949_BI.Rectal_Mucosa.H3K9ac.31.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100503:12--ChIP:XZ:20100420:12:rectal mucosa:H3K9Ac.hg19.level.1.release.3
ANALYSIS TITLE: Mapping of Rectal Mucosa Histone H3K9ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K9ac ChIP-Seq on Rectal Mucosa, Donor 31 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.6464
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: 0.2896
FINDPEAKS_PERCENTILE: 76
HOTSPOT_SCORE: 0.3374
HOTSPOT_PERCENTILE: 76
IROC_SCORE: 0.9975
IROC_PERCENTILE: 88
POISSON_SCORE: 0.3741
POISSON_PERCENTILE: 72

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

ANALYSIS FILE NAME: GSM669949_BI.Rectal_Mucosa.H3K9ac.31.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100503:12--ChIP:XZ:20100420:12:rectal mucosa:H3K9Ac.hg19.level.2.release.3
ANALYSIS TITLE: Raw Signal Density Graphs of Rectal Mucosa Histone H3K9ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K9ac ChIP-Seq read mappings from Rectal Mucosa, Donor 31 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.6674
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: RM H3K9ac 31
BROWSER_TRACK_DESCRIPTION: BI Rectal Mucosa Histone H3K9ac Donor 31 Library Lib:XZ:20100503:12--ChIP:XZ:20100420:12:rectal mucosa:H3K9Ac EA Release 3

QUALITY SCORES:
NUMBER_OF_H3K9ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 40
FINDPEAKS_SCORE: 0.2896
FINDPEAKS_PERCENTILE: 76
HOTSPOT_SCORE: 0.3374
HOTSPOT_PERCENTILE: 76
IROC_SCORE: 0.9975
IROC_PERCENTILE: 88
POISSON_SCORE: 0.3741
POISSON_PERCENTILE: 72

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

source_name: Primary rectal mucosal tissue; Lib:XZ:20100503:12--ChIP:XZ:20100420:12:rectal mucosa:H3K9Ac

value: Rectal Mucosa

value: surgery

value: "normal mucosa, diverticular disease"

value: mucosa

value: white

value: Female

value: rectum

value: MGH Pathology

value: Histone H3K9ac


title: ChIP-Seq analysis of H3K36me3 in AdiposeNuclei cells; Lib:XZ:20100731:24--ChIP:XZ:20100726:24:AdiposeNuclei:H3K36Me3

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:20100731:24--ChIP:XZ:20100726:24:AdiposeNuclei:H3K36Me3
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.5738
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: GSM669997_BI.Adipose_Nuclei.H3K36me3.95.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100731:24--ChIP:XZ:20100726:24:AdiposeNuclei:H3K36Me3.hg19.level.1.release.3
ANALYSIS TITLE: Mapping of Adipose Nuclei Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K36me3 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.6596
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: 0.5477
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.4951
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.9983
IROC_PERCENTILE: 100
POISSON_SCORE: 0.6715
POISSON_PERCENTILE: 96

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

ANALYSIS FILE NAME: GSM669997_BI.Adipose_Nuclei.H3K36me3.95.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100731:24--ChIP:XZ:20100726:24:AdiposeNuclei:H3K36Me3.hg19.level.2.release.3
ANALYSIS TITLE: Raw Signal Density Graphs of Adipose Nuclei Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K36me3 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.6806
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 H3K36me3 95
BROWSER_TRACK_DESCRIPTION: BI Adipose Nuclei Histone H3K36me3 Donor 95 Library Lib:XZ:20100731:24--ChIP:XZ:20100726:24:AdiposeNuclei:H3K36Me3 EA Release 3

QUALITY SCORES:
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 59
FINDPEAKS_SCORE: 0.5477
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.4951
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.9983
IROC_PERCENTILE: 100
POISSON_SCORE: 0.6715
POISSON_PERCENTILE: 96

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

source_name: Nuclei derived from crude preps of adipose tissue; Lib:XZ:20100731:24--ChIP:XZ:20100726:24:AdiposeNuclei:H3K36Me3

value: Adipose Nuclei

value: genomic DNA

value: Primary Tissue

value: abdomen

value: Harvard University

value: 10 million cells

value: SDS lysis


title: ChIP-Seq analysis of H3K36me3 in BM-MSC cells; Lib:MC:20100713:10--ChIP:MC:20100706:10:BM-MSC:H3K36Me3

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:20100713:10--ChIP:MC:20100706:10:BM-MSC:H3K36Me3
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.5692
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: GSM669951_BI.Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells.H3K36me3.60.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:MC:20100713:10--ChIP:MC:20100706:10:BM-MSC:H3K36Me3.hg19.level.1.release.3
ANALYSIS TITLE: Mapping of Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K36me3 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.6563
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: 0.146
FINDPEAKS_PERCENTILE: 38
HOTSPOT_SCORE: 0.194
HOTSPOT_PERCENTILE: 35
IROC_SCORE: 0.9463
IROC_PERCENTILE: 38
POISSON_SCORE: 0.4134
POISSON_PERCENTILE: 38

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

ANALYSIS FILE NAME: GSM669951_BI.Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells.H3K36me3.60.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:MC:20100713:10--ChIP:MC:20100706:10:BM-MSC:H3K36Me3.hg19.level.2.release.3
ANALYSIS TITLE: Raw Signal Density Graphs of Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K36me3 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.6773
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 H3K36me3 60
BROWSER_TRACK_DESCRIPTION: BI Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells Histone H3K36me3 Donor 60 Library Lib:MC:20100713:10--ChIP:MC:20100706:10:BM-MSC:H3K36Me3 EA Release 3

QUALITY SCORES:
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 59
FINDPEAKS_SCORE: 0.146
FINDPEAKS_PERCENTILE: 38
HOTSPOT_SCORE: 0.194
HOTSPOT_PERCENTILE: 35
IROC_SCORE: 0.9463
IROC_PERCENTILE: 38
POISSON_SCORE: 0.4134
POISSON_PERCENTILE: 38

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

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:20100713:10--ChIP:MC:20100706:10:BM-MSC:H3K36Me3

value: healthy

value: BM-MSC

value: Unknown

value: Primary Cell Culture

value: Rikshospitalet University Hospital

value: Protein A-Sepharose 4B

value: 70 ul bed volume

value: Abcam

value: Histone H3K36me3

value: Bioruptor


title: ChIP-Seq analysis of WCE in Skeletal muscle cells; Lib:XZ:20100628:21--ChIP:XZ:20100621:21:Skeletal muscle:WCE

description:
sample_term_id: UBERON_0001134
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib:XZ:20100628:21--ChIP:XZ:20100621:21:Skeletal muscle:WCE
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.5689
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.3355
****************
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: GSM669948_BI.Skeletal_Muscle.Input.63.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100628:21--ChIP:XZ:20100621:21:Skeletal muscle:WCE.hg19.level.1.release.3
ANALYSIS TITLE: Mapping of Skeletal Muscle ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina reads produced by ChIP-Seq Input on Skeletal Muscle, Donor 63 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.6578
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: 0.0082
FINDPEAKS_PERCENTILE: 87
HOTSPOT_SCORE: 0.027
HOTSPOT_PERCENTILE: 77
IROC_SCORE: 0.9805
IROC_PERCENTILE: 55
POISSON_SCORE: 0.093
POISSON_PERCENTILE: 83

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

ANALYSIS FILE NAME: GSM669948_BI.Skeletal_Muscle.Input.63.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100628:21--ChIP:XZ:20100621:21:Skeletal muscle:WCE.hg19.level.2.release.3
ANALYSIS TITLE: Raw Signal Density Graphs of Skeletal Muscle ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina ChIP-Seq Input read mappings from Skeletal Muscle, Donor 63 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.6788
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: SM Input 63
BROWSER_TRACK_DESCRIPTION: BI Skeletal Muscle ChIP-Seq Input Donor 63 Library Lib:XZ:20100628:21--ChIP:XZ:20100621:21:Skeletal muscle:WCE EA Release 3

QUALITY SCORES:
NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 61
FINDPEAKS_SCORE: 0.0082
FINDPEAKS_PERCENTILE: 87
HOTSPOT_SCORE: 0.027
HOTSPOT_PERCENTILE: 77
IROC_SCORE: 0.9805
IROC_PERCENTILE: 55
POISSON_SCORE: 0.093
POISSON_PERCENTILE: 83

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

source_name: Primary skeletal muscle tissue; Lib:XZ:20100628:21--ChIP:XZ:20100621:21:Skeletal muscle:WCE

value: Skeletal Muscle

value: surgery

value: "NL muscle,... Osteomylitis - BKA"

value: Skeletal muscle

value: white

value: Male

value: unknown

value: MGH Pathology

value: 54 years

value: standard

value: ChIP-Seq Input

value: Input


title: ChIP-Seq analysis of WCE in AdiposeNuclei cells; Lib:XZ:20100731:21--ChIP:XZ:20100726:21:AdiposeNuclei:WCE

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:20100731:21--ChIP:XZ:20100726:21:AdiposeNuclei:WCE
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.5681
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: GSM669940_BI.Adipose_Nuclei.Input.94.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100731:21--ChIP:XZ:20100726:21:AdiposeNuclei:WCE.hg19.level.1.release.3
ANALYSIS TITLE: Mapping of Adipose Nuclei ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina reads produced by ChIP-Seq Input 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.6501
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: 0.0071
FINDPEAKS_PERCENTILE: 73
HOTSPOT_SCORE: 0.0096
HOTSPOT_PERCENTILE: 40
IROC_SCORE: 0.0
IROC_PERCENTILE: 38
POISSON_SCORE: 0.0413
POISSON_PERCENTILE: 37

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

ANALYSIS FILE NAME: GSM669940_BI.Adipose_Nuclei.Input.94.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100731:21--ChIP:XZ:20100726:21:AdiposeNuclei:WCE.hg19.level.2.release.3
ANALYSIS TITLE: Raw Signal Density Graphs of Adipose Nuclei ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina ChIP-Seq Input 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.6711
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 Input 94
BROWSER_TRACK_DESCRIPTION: BI Adipose Nuclei ChIP-Seq Input Donor 94 Library Lib:XZ:20100731:21--ChIP:XZ:20100726:21:AdiposeNuclei:WCE EA Release 3

QUALITY SCORES:
NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 61
FINDPEAKS_SCORE: 0.0071
FINDPEAKS_PERCENTILE: 73
HOTSPOT_SCORE: 0.0096
HOTSPOT_PERCENTILE: 40
IROC_SCORE: 0.0
IROC_PERCENTILE: 38
POISSON_SCORE: 0.0413
POISSON_PERCENTILE: 37

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

source_name: Nuclei derived from crude preps of adipose tissue; Lib:XZ:20100731:21--ChIP:XZ:20100726:21:AdiposeNuclei:WCE

value: Adipose Nuclei

value: genomic DNA

value: Female

value: Primary Tissue

value: abdomen

value: Harvard University

value: SDS lysis


title: ChIP-Seq analysis of H3K9ac in BM-MSC cells; Lib:MC:20100706:12--ChIP:MC:20100628:12: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:20100706:12--ChIP:MC:20100628:12:BM-MSC:H3K9Ac
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.5678
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: GSM669937_BI.Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells.H3K9ac.58.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:MC:20100706:12--ChIP:MC:20100628:12: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 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.6534
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: 0.3634
FINDPEAKS_PERCENTILE: 88
HOTSPOT_SCORE: 0.3973
HOTSPOT_PERCENTILE: 80
IROC_SCORE: 0.9986
IROC_PERCENTILE: 100
POISSON_SCORE: 0.421
POISSON_PERCENTILE: 80

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

ANALYSIS FILE NAME: GSM669937_BI.Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells.H3K9ac.58.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:MC:20100706:12--ChIP:MC:20100628:12: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 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.6744
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 58
BROWSER_TRACK_DESCRIPTION: BI Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells Histone H3K9ac Donor 58 Library Lib:MC:20100706:12--ChIP:MC:20100628:12:BM-MSC:H3K9Ac EA Release 3

QUALITY SCORES:
NUMBER_OF_H3K9ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 40
FINDPEAKS_SCORE: 0.3634
FINDPEAKS_PERCENTILE: 88
HOTSPOT_SCORE: 0.3973
HOTSPOT_PERCENTILE: 80
IROC_SCORE: 0.9986
IROC_PERCENTILE: 100
POISSON_SCORE: 0.421
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:20100706:12--ChIP:MC:20100628:12:BM-MSC:H3K9Ac

value: healthy

value: BM-MSC

value: Unknown

value: Primary Cell Culture

value: Rikshospitalet University Hospital

value: Protein A-Sepharose 4B

value: 10 million cells

value: 70 ul bed volume

value: Abcam

value: Histone H3K9ac

value: Bioruptor


title: ChIP-Seq analysis of H3K9ac in AdiposeNuclei cells; Lib:XZ:20100731:19--ChIP:XZ:20100726:19: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:20100731:19--ChIP:XZ:20100726:19:AdiposeNuclei:H3K9Ac
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.5679
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: GSM669938_BI.Adipose_Nuclei.H3K9ac.94.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100731:19--ChIP:XZ:20100726:19: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 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.6462
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: 0.1697
FINDPEAKS_PERCENTILE: 52
HOTSPOT_SCORE: 0.2325
HOTSPOT_PERCENTILE: 68
IROC_SCORE: 0.9926
IROC_PERCENTILE: 52
POISSON_SCORE: 0.3183
POISSON_PERCENTILE: 64

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

ANALYSIS FILE NAME: GSM669938_BI.Adipose_Nuclei.H3K9ac.94.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100731:19--ChIP:XZ:20100726:19: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 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.6672
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 94
BROWSER_TRACK_DESCRIPTION: BI Adipose Nuclei Histone H3K9ac Donor 94 Library Lib:XZ:20100731:19--ChIP:XZ:20100726:19:AdiposeNuclei:H3K9Ac EA Release 3

QUALITY SCORES:
NUMBER_OF_H3K9ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 40
FINDPEAKS_SCORE: 0.1697
FINDPEAKS_PERCENTILE: 52
HOTSPOT_SCORE: 0.2325
HOTSPOT_PERCENTILE: 68
IROC_SCORE: 0.9926
IROC_PERCENTILE: 52
POISSON_SCORE: 0.3183
POISSON_PERCENTILE: 64

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

source_name: Nuclei derived from crude preps of adipose tissue; Lib:XZ:20100731:19--ChIP:XZ:20100726:19:AdiposeNuclei:H3K9Ac

value: Adipose Nuclei

value: surgery

value: genomic DNA


title: ChIP-Seq analysis of WCE in BM-MSC cells; Lib:MC:20100713:07--ChIP:MC:20100706:07: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:20100713:07--ChIP:MC:20100706:07:BM-MSC:WCE
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.5728
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: GSM669987_BI.Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells.Input.59.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:MC:20100713:07--ChIP:MC:20100706:07: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 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.6568
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: 0.0061
FINDPEAKS_PERCENTILE: 30
HOTSPOT_SCORE: 0.0142
HOTSPOT_PERCENTILE: 50
IROC_SCORE: 0.0
IROC_PERCENTILE: 38
POISSON_SCORE: 0.0614
POISSON_PERCENTILE: 63

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

ANALYSIS FILE NAME: GSM669987_BI.Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells.Input.59.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:MC:20100713:07--ChIP:MC:20100706:07: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 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.6778
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 59
BROWSER_TRACK_DESCRIPTION: BI Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells ChIP-Seq Input Donor 59 Library Lib:MC:20100713:07--ChIP:MC:20100706:07:BM-MSC:WCE EA Release 3

QUALITY SCORES:
NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 61
FINDPEAKS_SCORE: 0.0061
FINDPEAKS_PERCENTILE: 30
HOTSPOT_SCORE: 0.0142
HOTSPOT_PERCENTILE: 50
IROC_SCORE: 0.0
IROC_PERCENTILE: 38
POISSON_SCORE: 0.0614
POISSON_PERCENTILE: 63

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

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:20100713:07--ChIP:MC:20100706:07:BM-MSC:WCE

value: standard

value: ChIP-Seq Input

value: Input


title: Exon arrays of Roadmap cell types; Fetal Thymus primary tissue, day 147; DS16490-exon

description:
sample_term_id: UBERON_0002370
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.7183
sample alias: fThymus.H-23589d147
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.5361

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

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

value: Primary Tissue

value: Fetal Thymus

value: UW

value: fetal

value: day 147

value: Female