title: ChIP-Seq analysis of H3K36me3 in AdiposeNuclei cells; Lib:XZ:20100731:10--ChIP:XZ:20100726:10: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:20100731:10--ChIP:XZ:20100726:10:AdiposeNuclei:H3K36Me3
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.5755
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: GSM670014_BI.Adipose_Nuclei.H3K36me3.93.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100731:10--ChIP:XZ:20100726:10: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 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.6589
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: 0.2211
FINDPEAKS_PERCENTILE: 46
HOTSPOT_SCORE: 0.2924
HOTSPOT_PERCENTILE: 54
IROC_SCORE: 0.9693
IROC_PERCENTILE: 46
POISSON_SCORE: 0.3817
POISSON_PERCENTILE: 31

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

ANALYSIS FILE NAME: GSM670014_BI.Adipose_Nuclei.H3K36me3.93.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100731:10--ChIP:XZ:20100726:10: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 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.6799
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 93
BROWSER_TRACK_DESCRIPTION: BI Adipose Nuclei Histone H3K36me3 Donor 93 Library Lib:XZ:20100731:10--ChIP:XZ:20100726:10:AdiposeNuclei:H3K36Me3 EA Release 3

QUALITY SCORES:
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 59
FINDPEAKS_SCORE: 0.2211
FINDPEAKS_PERCENTILE: 46
HOTSPOT_SCORE: 0.2924
HOTSPOT_PERCENTILE: 54
IROC_SCORE: 0.9693
IROC_PERCENTILE: 46
POISSON_SCORE: 0.3817
POISSON_PERCENTILE: 31

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

source_name: Nuclei derived from crude preps of adipose tissue; Lib:XZ:20100731:10--ChIP:XZ:20100726:10:AdiposeNuclei:H3K36Me3

value: Protein A-Sepharose 4B

value: 10 million cells

value: Histone H3K36me3


title: ChIP-Seq analysis of H3K36me3 in BM-MSC cells; Lib:MC:20100713:03--ChIP:MC:20100706:03:BM-MSC:H3K36Me3

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: 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:20100713:03--ChIP:MC:20100706:03:BM-MSC:H3K36Me3
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.5737
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
****************

library_source: genomic

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

ANALYSIS FILE NAME: GSM669996_BI.Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells.H3K36me3.59.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:MC:20100713:03--ChIP:MC:20100706:03: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 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.6488
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: 0.2227
FINDPEAKS_PERCENTILE: 50
HOTSPOT_SCORE: 0.2426
HOTSPOT_PERCENTILE: 42
IROC_SCORE: 0.9735
IROC_PERCENTILE: 50
POISSON_SCORE: 0.4506
POISSON_PERCENTILE: 46

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

ANALYSIS FILE NAME: GSM669996_BI.Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells.H3K36me3.59.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:MC:20100713:03--ChIP:MC:20100706:03: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 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.6698
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 59
BROWSER_TRACK_DESCRIPTION: BI Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells Histone H3K36me3 Donor 59 Library Lib:MC:20100713:03--ChIP:MC:20100706:03:BM-MSC:H3K36Me3 EA Release 3

QUALITY SCORES:
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 59
FINDPEAKS_SCORE: 0.2227
FINDPEAKS_PERCENTILE: 50
HOTSPOT_SCORE: 0.2426
HOTSPOT_PERCENTILE: 42
IROC_SCORE: 0.9735
IROC_PERCENTILE: 50
POISSON_SCORE: 0.4506
POISSON_PERCENTILE: 46

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

molecule: genomic DNA

organism: Homo sapiens

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:20100713:03--ChIP:MC:20100706:03:BM-MSC:H3K36Me3

extract_protocol: Library construction protocol: Single read - Illumina

tag: sample alias

tag: sample common name

value: healthy

tag: molecule

value: genomic DNA

tag: disease

tag: markers

value: BM-MSC

value: Unknown

value: Primary Cell Culture

value: Rikshospitalet University Hospital

value: SDS lysis

value: 70 ul bed volume

value: Abcam

value: Bioruptor


title: paternal Low protein diet 8

status: Public on Jan 14 2011

city: Jerusalem

first: naomi

last: habib

address: Givat-Ram

department: Computer Scince

country: Israel

institute: Hebrew University

description: small RNA in the liver with paternal Low protein diet

library_source: transcriptomic

data_processing: Deep sequencing reads where mapped to the mouse genome (July 2007 assembly of the mouse genome - mm9, NCBI Build 37, {Waterston, 2002 #1087}), where at least the first 18 bases of the read matches to the genome and the remainder matches to the 3¢ adaptor sequence. In this mapping we allow up to 2 mismatched positions. Reads that had six or more matching locations in the genome were discarded. We retained reads with five or less matches to allow situations of micro-RNA families with highly similar sequence.

molecule: total RNA

organism: Mus musculus

source_name: liver cells

growth_protocol: At three weeks of age offspring were sacrificed by isoflurane and cervical dislocation, and median lobe of liver was rapidly dissected out and flash-frozen in liquid N2

extract_protocol: Total RNA was isolated from ground liver tissue using mirVana (Ambion). The RNA was quantified by absorbance at 260 nm. 18–35 nt small RNA was purified from 100 µg of total RNA using a 15% denaturing urea-polyacrylamide gel (National Diagnostics). 100 pmol of 3′ preadenylated adapter (5′-rAppTCG TAT GCC GTC TTC TGC TTG T/ddC/-3′) was ligated to the purified small RNAs using T4 RNA ligase (Ambion, Austin, TX, USA) at 37° for 2 h in 20 µl in 50 mM Tris-HCl, pH 7.5, 10 mM MgCl2, 10 mM DTT, 60 μg/mL BSA, 10% (v/v) DMSO, and 40 U RNasin (Promega, Madison, WI, USA). 3′ ligated product was purified from a 15% denaturing urea-polyacrylamide gel (National Diagnostics), and then ligated to 100 pmol of 5′ RNA adapter (5′-GUU CAG AGU UCU ACA GUC CGA CGA UC-3´) using T4 RNA ligase (Ambion) at room temperature for 6 h in 20 µl in 50 mM Tris-HCl, pH 7.8, 10 mM MgCl2, 10 mM DTT, 1 mM ATP, and 10% DMSO. The ligated product was purified from a 10% denaturing urea-polyacrylamide gel (National Diagnostics). Half the ligated product was used to synthesize cDNA using Superscript III (Invitrogen) and the reverse transcription primer (5′-CAA GCA GAA GAC GGC ATA CGA-3′), and half was used as a minus RT control. The small RNA library was amplified using forward (5′-AAT GAT ACG GCG ACC ACC GAC AGG TTC AGA GTT CTA CAG TCC GA-3′) and reverse (5′-CAA GCA GAA GAC GGC ATA CGA-3′) primers, and then purified from a NuSieve GTG agarose gel (Lonza, Basel, Switzerland).

treatment_protocol: Females were weaned to control diet. Males were raised on diet (control or low-protein) until 9-12 weeks of age, at which point they were placed with females for one or two days.

tag: strain

tag: age

value: 3 weeks


title: paternal control diet 7

description: small RNA in the liver with paternal control diet


title: ChIP-Seq analysis of H3K4me3 in BM-MSC cells; Lib:MC:20100713:02--ChIP:MC:20100706:02:BM-MSC:H3K4Me3

description:
sample_term_id: EFO_0000586
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib:MC:20100713:02--ChIP:MC:20100706:02:BM-MSC:H3K4Me3
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.5732
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: GSM669991_BI.Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells.H3K4me3.59.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:MC:20100713:02--ChIP:MC:20100706:02:BM-MSC:H3K4Me3.hg19.level.1.release.3
ANALYSIS TITLE: Mapping of Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me3 ChIP-Seq on Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells, Donor 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.6575
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: 0.4171
FINDPEAKS_PERCENTILE: 56
HOTSPOT_SCORE: 0.4278
HOTSPOT_PERCENTILE: 56
IROC_SCORE: 0.9998
IROC_PERCENTILE: 88
POISSON_SCORE: 0.4435
POISSON_PERCENTILE: 52

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

ANALYSIS FILE NAME: GSM669991_BI.Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells.H3K4me3.59.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:MC:20100713:02--ChIP:MC:20100706:02:BM-MSC:H3K4Me3.hg19.level.2.release.3
ANALYSIS TITLE: Raw Signal Density Graphs of Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me3 ChIP-Seq read mappings from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells, Donor 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.6785
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 3
BROWSER_TRACK_NAME: BMDMSC H3K4me3 59
BROWSER_TRACK_DESCRIPTION: BI Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells Histone H3K4me3 Donor 59 Library Lib:MC:20100713:02--ChIP:MC:20100706:02:BM-MSC:H3K4Me3 EA Release 3

QUALITY SCORES:
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 63
FINDPEAKS_SCORE: 0.4171
FINDPEAKS_PERCENTILE: 56
HOTSPOT_SCORE: 0.4278
HOTSPOT_PERCENTILE: 56
IROC_SCORE: 0.9998
IROC_PERCENTILE: 88
POISSON_SCORE: 0.4435
POISSON_PERCENTILE: 52

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

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:20100713:02--ChIP:MC:20100706:02:BM-MSC:H3K4Me3

value: Millipore

value: Histone H3K4me3


title: paternal Low protein diet 5

description: small RNA in the liver with  paternal Low protein diet


title: paternal Low protein diet 4


title: paternal control diet 6

description: small RNA in the liver with  paternal control diet


title: ChIP-Seq analysis of H3K36me3 in AdiposeNuclei cells; Lib:XZ:20100731:17--ChIP:XZ:20100726:17: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:20100731:17--ChIP:XZ:20100726:17:AdiposeNuclei:H3K36Me3
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.5720
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: GSM669979_BI.Adipose_Nuclei.H3K36me3.94.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100731:17--ChIP:XZ:20100726:17: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 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.6590
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: 0.3345
FINDPEAKS_PERCENTILE: 62
HOTSPOT_SCORE: 0.3287
HOTSPOT_PERCENTILE: 69
IROC_SCORE: 0.9904
IROC_PERCENTILE: 62
POISSON_SCORE: 0.503
POISSON_PERCENTILE: 58

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

ANALYSIS FILE NAME: GSM669979_BI.Adipose_Nuclei.H3K36me3.94.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100731:17--ChIP:XZ:20100726:17: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 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.6800
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 94
BROWSER_TRACK_DESCRIPTION: BI Adipose Nuclei Histone H3K36me3 Donor 94 Library Lib:XZ:20100731:17--ChIP:XZ:20100726:17:AdiposeNuclei:H3K36Me3 EA Release 3

QUALITY SCORES:
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 59
FINDPEAKS_SCORE: 0.3345
FINDPEAKS_PERCENTILE: 62
HOTSPOT_SCORE: 0.3287
HOTSPOT_PERCENTILE: 69
IROC_SCORE: 0.9904
IROC_PERCENTILE: 62
POISSON_SCORE: 0.503
POISSON_PERCENTILE: 58

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

source_name: Nuclei derived from crude preps of adipose tissue; Lib:XZ:20100731:17--ChIP:XZ:20100726:17:AdiposeNuclei:H3K36Me3

value: Adipose Nuclei

value: surgery

value: Female

value: Primary Tissue

value: abdomen

value: Harvard University


title: paternal control diet 3


title: paternal control diet 2


title: ThioMac-H3ac-Kdo2-1h-ChIP-Seq

status: Public on Jan 01 2011

city: La Jolla

first: Christopher

last: Benner

state: California

address: 9500 Gilman Dr. MC 0640

department: Medicine

institute: University of California, San Diego (UCSD)

description: Chromatin IP against H3ac in ThioMac treated with Kdo2 for 1h

data_processing:
Alignment: Reads were truncated to 25 bp (ChIP-Seq) or 32 bp (RNA, GRO-Seq) and aligned to the mouse mm8 genome (NCBI Build 36) using eland. Only reads that mapped to a single, unique position were used for downstream analysis.
Data analysis was performed using HOMER, a software suite for ChIP-Seq analysis and created in part to support this study (http://biowhat.ucsd.edu/homer/). Each ChIP-Seq experiment was normalized to a total of 10^7 uniquely mapped tags by adjusting the number of tags at each position in the genome to the correct fractional amount given the total tags mapped. UCSC Genome Browser bedGraph files were created by calculating ChIP-Fragment pileups given a fragment size of ~150 bp.
bedGraph files were replaced Sept 01, 2010 and have been re-formatted for use with the updated UCSC Genome Browser.

growth_protocol: Peritoneal macrophages were harvested by peritoneal lavage with 10 ml ice-cold PBS 3 days after peritoneal injection of 3 ml thioglycollate broth. Peritoneal cells were washed once with PBS, and seeded in 10% fetal calf serum (FCS)/DMEM containing 100 U/ml penicillin/streptomycin in tissue culture-treated petri dishes overnight. Non-adherent cells were washed off with room temperature PBS.

extract_protocol: For ChIP-Seq, lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody. Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation, ChIP DNA was PCR-amplified with Illumina primers for 12-16 cycles and library fragments of 200-300 bp (ChIP) (insert plus adaptor and PCR primer sequences) were isolated from a 2% agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer or Genome Analyzer II following the manufacturer's protocols.

tag: cell type

value: macrophage

tag: chip antibody

value: H3ac (Millipore 06-599 LOT 25233)

tag: treatment

value: Kdo2 Lipid A for 1 hour

tag: transgenes

tag: genetic background


title: BMDM-H3K4me3-ChIP-Seq

description: Chromatin IP against H3K4me3 in BMDM

source_name: bone marrow-derived macrophages

growth_protocol: Bone marrow was harvested and washed once with PBS, seeded/cultured in DMEM containing 20 % FCS, 30 % L-cell conditioned media (as source of macrophage colony stimulating factor, M-CSF), and 100 U/ml penicillin/streptomycin in non-tissue culture-treated petri dishes. After 6-8 days of culture, non-adherent cells were washed off with room temperature PBS and macrophages were obtained as a homogeneous population of adherent cells which were scraped and subsequently seeded onto tissue culture-treated petri dishes overnight in RPMI 1640 containing 10% FCS, 100 U/ml penicillin/streptomycin, and 10ng/ml M-CSF.


title: paternal Low protein diet 1

description: small RNA in the liver with paternal low protein diet


title: ThioMac-PolII-Kdo2-1h-ChIP-Seq

description: Chromatin IP against RNA Polymerase II in ThioMac treated with Kdo2 for 1h

value: RNA Polymerase II (Santa Cruz sc-899 X LOT D0204)


title: ThioMac-H3K4me3-Kdo2-1h-ChIP-Seq

description: Chromatin IP against H3K4me3 in ThioMac treated with Kdo2 for 1h


title: ThioMac-PolII-ChIP-Seq

description: Chromatin IP against RNA Polymerase II


title: delta-uvrY rep 3

type: RNA

city: Marburg an der Lahn

first: Jürgen

last: Lassak

state: Hessen

address: Karl-von-Frisch Strasse

department: Ecophysiology

country: Germany

institute: Max-Planck-Institute for Terrestrial Microbiology

hyb_protocol: Samples were loaded onto the arrays and hybridization was done over night (16 hours) at 45°C, using argon pressure to move the samples within the arrays.

scan_protocol: After the hybridization the chip is washed with the “febit GT-standard (external incubation)” hybridization profile and a standard detection using the appropriate filter set in  the Geniom® One Instrument.

data_processing: To assess the reproducibility of the biological replicates, the Pearson Correlation Coefficients were calculated.

label: biotin

organism: Shewanella oneidensis MR-1

source_name: total bacterial cells

label_protocol: febit uses the MICROBExpressTM kit from Ambion to remove 16S and 23S rRNA from RNA samples. For each array 3 μg of total RNA were purified according to the manufacturer’s instructions. Following, the MessageAmpTMII-Bacteria kit from Ambion was applied for labelling the mRNA. The kit provides a transcription of RNA in cDNA, following a transcription in cRNA while enrichment of all nucleic acid molecules is included. After labelling samples were dried in a speed-vac and fragmented with a fragmentation buffer. Finally, febit’s proprietary standard Longmer Hybridization Buffer (15 μl per array) was added.

growth_protocol: cells were grown aerobically in LB to stationary phase (OD600nm=4.0)

extract_protocol: Total RNA was extracted from S. oneidensis MR-1 cells using the hot phenol method. Residual chromosomal DNA was removed using Turbo DNA-freeTM (Applied Biosystems) following the manufacturer’s instructions.

treatment_protocol: no treatment

tag: growth stage

value: logarithmic aerobic growing cells

tag: genotype

value: uvrY null


title: delta-uvrY rep 2


title: Exon arrays of Roadmap cell types; Fetal Heart primary tissue, day 96; DS15839-exon

status: Public on Feb 02 2011

city: Seattle

first: Northwest

last: REMC

state: WA

institute: University of Washington

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.5434
sample alias: fHeart.H-23468d96
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.5290
EDACC Genboree Run Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FRUN%2FEDACC.5435

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_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: Fetal Heart

value: UW

value: fetal

value: day 96

value: Male


title: delta-uvrY rep 1


title: wild-type rep 3

value: wild type


title: Exon arrays of Roadmap cell types; Fetal Kidney, Right primary tissue, day 117; DS15651-exon

description:
sample_term_id: UBERON_0004539
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.5462
sample alias: fKidney_Right.H-23435d117
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.5365
EDACC Genboree Run Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FRUN%2FEDACC.5463

value: Fetal Kidney, Right

value: day 117

value: Female


title: wild-type rep 1


title: wild-type rep 2


title: Exon arrays of Roadmap cell types; Fetal Adrenal Gland primary tissue, day 85; DS15123-exon

description:
sample_term_id: UBERON_0002369
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.5478
sample alias: fAdrenal.H-23327d85
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.5318
EDACC Genboree Run Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FRUN%2FEDACC.5479

value: Primary Tissue

value: Fetal Adrenal Gland

value: day 85


title: Exon arrays of Roadmap cell types; Fetal Heart primary tissue, day 103; DS16018-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.5470
sample alias: fHeart.H-23500d103
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.5270
EDACC Genboree Run Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FRUN%2FEDACC.5471

value: day 103


title: Exon arrays of Roadmap cell types; Fetal Lung, Left primary tissue, day 117; DS15637-exon

description:
sample_term_id: UBERON_0002168
assay_term_id: OBI_0001463
nucleic_acid_term_id: SO_0000356
Exon profiling of NREMC cell types, these coincide with chromatin accessibility sequencing assays.
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.5458
sample alias: fLung_Left.H-23435d117
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.5397
EDACC Genboree Run Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FRUN%2FEDACC.5459

value: Fetal Lung, Left


title: Exon arrays of Roadmap cell types; flow sorted CD34+ Primary Cells, Mobilized, year 23; DS14040-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.5430
sample alias: CD34.RO_01525
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.5315
EDACC Genboree Run Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FRUN%2FEDACC.5431

value: FHCRC HEIMFELD

value: Primary Cell

value: Mobilized CD34 Primary Cells

value: year 23

value: Caucasian


title: Meibomian Glands Female Normal  Replicate 3

status: Public on Dec 31 2010

city: Boston

first: David

middle: A

last: Sullivan

address: 20 Staniford Street

institute: Schepens Eye Research Institute

description: The eyelids used in this study were obtained from tissues removed during surgeries. Immediately after removal the eyelids were placed in RNAlater (Ambion, Austin, TX) and stored at 4º C overnight.  The tissues were then store at -80º C until needed. Prior to the surgeries, the meibomian gland disease state of the patient was evaluated by an opthamologist using the meibum quality criteria described by Bron et al., 1991

hyb_protocol: Labeled cRNA was used to probe HumanHT-12 v3 Expression BeadChips.  Hybridization, washing, and scanning of the Illumina arrays were carried out according to the manufacturer’s instructions.  Briefly, cRNA/hybridization buffer mixtures were incubated at 65°C for 5 minutes, followed by brief centrifugation to collect.  The mixtures were added to BeadChips and then BeadChips inserted into hybridization chambers, and hybridization was carried out at 58°C for 16-18 hours at rocking speed set to 5.  BeadChips were washed and stained in the following steps:  1) 55°C for 10 minutes static in HighTemp Wash Buffer in a Hybex waterbath, 2) ambient temperature shaking for 5 minutes in E1BC wash buffer, 3) ambient temperature shaking for 10 minutes in ethanol, 4) ambient temperature shaking for 2 minutes in E1BC buffer, 5) ambient temperature for 10 minutes rocking in Block E1 buffer, 6) ambient temperature for 10 minutes rocking in Block E1 buffer containing 1ug/ml Cy3-streptavidin, and 7) ambient temperature shaking for 5 minutes in E1BC buffer.  BeadArrays were dried in a centrifuge for 4 minutes.

scan_protocol: BeadArrays were scanned with a BeadArray scanner.  Illumina BeadScan software was used to produce .idat, .xml, and .tif files for each array on a slide and .sdf files for each barcode on a slide of 12 arrays.  Raw data were extracted using Illumina BeadStudio software v 3.

data_processing:
Following quality assessment, data from the replicate beads on each array were summarized into raw intensity values with and without background subtraction in an Excel report containing the project description (sample key), gene identifiers and corresponding probe IDs, table of detection p-values, tables of normalized data with and without background subtraction, array quality control metrics, and array quality control metric cut-offs and definitions.
Cubic spline normalizaed data produced by BeadStudio software were selected for use in this study.  In Excel,  the cubic spline data were further processed by setting  negative values to zero and then adding 16 to all intensities.
The raw data provided has no background subtraction.

source_name: Sections of eye lids removed during surgeries

label_protocol: Samples for mRNA profiling studies were processed by Asuragen, Inc., according to the company’s standard operating procedures.  The purity and quantity of total RNA samples were determined by absorbance readings at 260 and 280 nm using a NanoDrop ND-1000 UV spectrophotometer.  The integrity of total RNA was qualified by Agilent Bioanalyzer 2100 capillary electrophoresis.  Total RNA (100 ng per sample) was used for preparation of biotin-labeled targets (cRNA) using a MessageAmp™ II-based protocol (Ambion Inc., Austin, TX) and one round of amplification.  The cRNA yields were quantified by UV spectrophotometry and the distribution of transcript sizes was assessed using the Agilent Bioanalyzer 2100 capillary electrophoresis system.

extract_protocol: Total RNA was isolated from the lid tissues using a RNAqueous Kit (Ambion). After thawing, the tarsal plates, containing the meibomian glands, were trimmed of excessive skin and connective tissues.  The tarsal plates were weighed to ensure that the tissue did not exceed the 75 mg capacity of the RNAqueous spin columns and then cut into small pieces using a fresh razor blade.  The tissues were then place in a microfuge tube containing RNAqueous Lysis Buffer and homogenized using Pellet Pestle Cordless Motor (Kimble Chase, Vineland, NJ).  Total RNA was then bound to the spin columns following the procedure Ambion provide with the RNAqueous Kit. To elute the RNA each column was washed twice with 85°C nuclease free water, an initial elution of 30µl followed by 20 µl. The RNA concentration and 260/280 nm ratio of each sample was determined using a NanoDrop 1000 Spectrophotometer (Thermo Scientific, Waltham MA) and the integrity of the RNA assayed on a Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA) with RNA Nano 6000 Series II Chips (Agilent Technologies).

tag: gender

tag: meibomian gland secretion grade

tag: meibomian gland disease state

tag: tissue

value: tarsal plate of the eyelid


title: Meibomian Glands Female Normal  Replicate 5


title: Exon arrays of Roadmap cell types; Fetal Brain primary tissue, day 96; DS14815-exon

description:
sample_term_id: UBERON_0000955
assay_term_id: OBI_0001463
nucleic_acid_term_id: SO_0000356
Exon profiling of NREMC cell types, these coincide with chromatin accessibility sequencing assays.
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.5474
sample alias: fBrain.H-23284d96
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.3113
EDACC Genboree Run Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FRUN%2FEDACC.5475

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

value: fetal brain

value: UW

value: fetal

value: day 96


title: Meibomian Glands Male Normal Replicate 6

value: Male


title: Exon arrays of Roadmap cell types; iPS DF 6.9 Cell Line, Induced pluripotent stem cells; DS15164-exon

description:
sample_term_id: NTR_0001172
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.5448
sample alias: iPS_6_9
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.5336
EDACC Genboree Run Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FRUN%2FEDACC.5449

source_name: iPS DF 6.9 Cell Line, Induced pluripotent stem cel, derived from fibroblast. the first set of numbers before the period refer to different clones, the number after the period indicates the sub-clone.; DS15164-exon

value: James Thomson, Morgridge Institute for Research, University of Wisconsin-Madison

value: Cell Line

tag: line

value: iPS DF 6.9 Cell Line

tag: lineage

value: Derived from newborn foreskin fibroblast:Cat# CRL-2097TM, ATCC

value: Induced pluripotent stem cell

tag: passage

tag: medium

tag: sex

value: Unknown

tag: batch


title: Exon arrays of Roadmap cell types; Fetal Kidney primary tissue, day 105; DS16139-exon

description:
sample_term_id: UBERON_0002113
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.5450
sample alias: fKidney.H-23524d105
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.5303
EDACC Genboree Run Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FRUN%2FEDACC.5451

tag: disease

value: Primary Tissue

value: Fetal Kidney

value: day 105


title: Exon arrays of Roadmap cell types; Fetal Heart primary tissue, day 117; DS15643-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.5472
sample alias: fHeart.H-23435d117
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.5266
EDACC Genboree Run Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FRUN%2FEDACC.5473

value: Fetal Heart

value: day 117

value: Female


title: Exon arrays of Roadmap cell types; Fetal Kidney, Right primary tissue, day 147; DS16440-exon

description:
sample_term_id: UBERON_0004539
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.5438
sample alias: fKidney_Right.H-23589d147
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.5401
EDACC Genboree Run Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FRUN%2FEDACC.5439

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

value: Fetal Kidney, Right

value: day 147


title: Meibomian Glands Male Normal Replicate 2

tag: age

value: tarsal plate of the eyelid


title: Exon arrays of Roadmap cell types; iPS DF 19.7 Cell Line, Induced pluripotent stem cells; DS15148-exon

description:
sample_term_id: NTR_0001174
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.5452
sample alias: iPS_19_7
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.5339
EDACC Genboree Run Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FRUN%2FEDACC.5453

source_name: iPS DF 19.7 Cell Line, Induced pluripotent stem cel, derived from fibroblast. the first set of numbers before the period refer to different clones, the number after the period indicates the sub-clone.; DS15148-exon

value: iPS DF 19.7 Cell Line


title: Exon arrays of Roadmap cell types; Fetal Lung primary tissue, day 112; DS15461-exon

description:
sample_term_id: UBERON_0002048
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.5440
sample alias: fLung.H-23399d112
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.5307
EDACC Genboree Run Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FRUN%2FEDACC.5441

value: Fetal Lung

value: UW

value: fetal

value: day 112


title: Exon arrays of Roadmap cell types; Fetal Kidney, Left primary tissue, day 147; DS16445-exon

description:
sample_term_id: UBERON_0004538
assay_term_id: OBI_0001463
nucleic_acid_term_id: SO_0000356
Exon profiling of NREMC cell types, these coincide with chromatin accessibility sequencing assays.
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.5464
sample alias: fKidney_Left.H-23589d147
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.5393
EDACC Genboree Run Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FRUN%2FEDACC.5465

value: Fetal Kidney, Left


title: Exon arrays of Roadmap cell types; Fetal Lung primary tissue, day 82; DS15573-exon

description:
sample_term_id: UBERON_0002048
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.5442
sample alias: fLung.H-23419d82
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.5311
EDACC Genboree Run Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FRUN%2FEDACC.5443

value: day 82

value: Male


title: Exon arrays of Roadmap cell types; Fetal Heart primary tissue, day 110; DS16582-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.5466
sample alias: fHeart.H-23604d110
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.5278
EDACC Genboree Run Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FRUN%2FEDACC.5467

value: Primary Tissue

value: day 110


title: Meibomian Glands Male Normal  Replicate4


title: Meibomian Glands Female Normal Replicate 1


title: Exon arrays of Roadmap cell types; Fetal Heart primary tissue, day 105; DS16146-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.5436
sample alias: fHeart.H-23524d105
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.5274
EDACC Genboree Run Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FRUN%2FEDACC.5437

value: Fetal Heart

value: day 105


title: Exon arrays of Roadmap cell types; Fetal Brain primary tissue, day 85; DS14717-exon

description:
sample_term_id: UBERON_0000955
assay_term_id: OBI_0001463
nucleic_acid_term_id: SO_0000356
Exon profiling of NREMC cell types, these coincide with chromatin accessibility sequencing assays.
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.5476
sample alias: fBrain.H-23266d85
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.3146
EDACC Genboree Run Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FRUN%2FEDACC.5477

value: fetal brain

value: day 85

value: Female


title: Exon arrays of Roadmap cell types; Fetal Lung, Right primary tissue, day 117; DS15632-exon

description:
sample_term_id: UBERON_0002167
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.5444
sample alias: fLung_Right.H-23435d117
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.5405
EDACC Genboree Run Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FRUN%2FEDACC.5445

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

value: Fetal Lung, Right

value: day 117


title: Exon arrays of Roadmap cell types; Fetal Heart primary tissue, day 147; DS16500-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.5468
sample alias: fHeart.H-23589d147
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.5282
EDACC Genboree Run Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FRUN%2FEDACC.5469

value: day 147


title: ChIP-Seq analysis of WCE in human hSKM cells; Lib:MC:20100222:16--ChIP:MC:20100216:16:hSKM:WCE

status: Public on Nov 12 2010

description:
sample_term_id: CL_0000594
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib:MC:20100222:16--ChIP:MC:20100216:16:hSKM:WCE
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.3180
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.3211
****************
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: GSM621756_BI.Muscle_Satellite_Cultured_Cells.Input.hSKM-3.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:MC:20100222:16--ChIP:MC:20100216:16:hSKM:WCE.hg19.level.1
ANALYSIS TITLE: Mapping of Muscle Satellite Cultured Cells ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina reads produced by ChIP-Seq Input on Muscle Satellite Cultured Cells, Donor hSKM-3 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.4708
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 2

QUALITY SCORES:
NUMBER_OF_Input_EXPERIMENTS_SCORED: 67
FINDPEAKS_SCORE: 0.0059
FINDPEAKS_PERCENTILE: 19
HOTSPOT_SCORE: 0.0379
HOTSPOT_PERCENTILE: 44
IROC_SCORE: 0.9548
IROC_PERCENTILE: 74
POISSON_SCORE: 0.21
POISSON_PERCENTILE: 36

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

ANALYSIS FILE NAME: GSM621756_BI.Muscle_Satellite_Cultured_Cells.Input.hSKM-3.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:MC:20100222:16--ChIP:MC:20100216:16:hSKM:WCE.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Muscle Satellite Cultured Cells ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina ChIP-Seq Input read mappings from Muscle Satellite Cultured Cells, Donor hSKM-3 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.4982
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 2
BROWSER_TRACK_NAME: MS Input 3
BROWSER_TRACK_DESCRIPTION: BI Muscle Satellite Cultured Cells ChIP-Seq Input Donor hSKM-3 EA Release 2

QUALITY SCORES:
NUMBER_OF_Input_EXPERIMENTS_SCORED: 67
FINDPEAKS_SCORE: 0.0059
FINDPEAKS_PERCENTILE: 19
HOTSPOT_SCORE: 0.0379
HOTSPOT_PERCENTILE: 44
IROC_SCORE: 0.9548
IROC_PERCENTILE: 74
POISSON_SCORE: 0.21
POISSON_PERCENTILE: 36

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

source_name: "Expanded from muscle spindle cells (Muoio et al; Diabetes 51, 901 (2002))"; Lib:MC:20100222:16--ChIP:MC:20100216:16:hSKM:WCE

value: mesoderm

value: DMEM

tag: molecule

value: genomic DNA

value: unknown

value: hSKM

value: in vivo

value: Cell Line

value: differentiated

tag: Sex

value: Unknown

value: Duke University

value: standard

value: SDS lysis

value: ChIP-Seq Input

value: Input

value: Bioruptor


title: ChIP-Seq analysis of H3K4me2 in human hSKM cells; Lib:MC:20100222:09--ChIP:MC:20100216:09:hSKM:H3K4Me2

description:
sample_term_id: CL_0000594
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib:MC:20100222:09--ChIP:MC:20100216:09:hSKM:H3K4Me2
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.3182
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.3211
****************
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: GSM621758_BI.Muscle_Satellite_Cultured_Cells.H3K4me2.hSKM-3.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:MC:20100222:09--ChIP:MC:20100216:09:hSKM:H3K4Me2.hg19.level.1
ANALYSIS TITLE: Mapping of Muscle Satellite Cultured Cells Histone H3K4me2 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me2 ChIP-Seq on Muscle Satellite Cultured Cells, Donor hSKM-3 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.4792
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 2

QUALITY SCORES:
NUMBER_OF_H3K4me2_EXPERIMENTS_SCORED: 8
FINDPEAKS_SCORE: 0.6298
FINDPEAKS_PERCENTILE: 63
HOTSPOT_SCORE: 0.5852
HOTSPOT_PERCENTILE: 63
IROC_SCORE: 0.999
IROC_PERCENTILE: 38
POISSON_SCORE: 0.6815
POISSON_PERCENTILE: 63

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

ANALYSIS FILE NAME: GSM621758_BI.Muscle_Satellite_Cultured_Cells.H3K4me2.hSKM-3.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:MC:20100222:09--ChIP:MC:20100216:09:hSKM:H3K4Me2.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Muscle Satellite Cultured Cells Histone H3K4me2 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me2 ChIP-Seq read mappings from Muscle Satellite Cultured Cells, Donor hSKM-3 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.5066
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 2
BROWSER_TRACK_NAME: MS H3K4me2 3
BROWSER_TRACK_DESCRIPTION: BI Muscle Satellite Cultured Cells Histone H3K4me2 Donor hSKM-3 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K4me2_EXPERIMENTS_SCORED: 8
FINDPEAKS_SCORE: 0.6298
FINDPEAKS_PERCENTILE: 63
HOTSPOT_SCORE: 0.5852
HOTSPOT_PERCENTILE: 63
IROC_SCORE: 0.999
IROC_PERCENTILE: 38
POISSON_SCORE: 0.6815
POISSON_PERCENTILE: 63

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

source_name: "Expanded from muscle spindle cells (Muoio et al; Diabetes 51, 901 (2002))"; Lib:MC:20100222:09--ChIP:MC:20100216:09:hSKM:H3K4Me2

value: Protein A-Sepharose 4B

value: 10 million cells

value: 70 ul bed volume

value: Abcam

value: Histone H3K4me2


title: ChIP-Seq analysis of H3K4me1 in human hSKM cells; Lib:MC:20100222:08--ChIP:MC:20100216:08:hSKM:H3K4Me1

description:
sample_term_id: CL_0000594
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib:MC:20100222:08--ChIP:MC:20100216:08:hSKM:H3K4Me1
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.3183
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.3211
****************
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: GSM621759_BI.Muscle_Satellite_Cultured_Cells.H3K4me1.hSKM-3.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:MC:20100222:08--ChIP:MC:20100216:08:hSKM:H3K4Me1.hg19.level.1
ANALYSIS TITLE: Mapping of Muscle Satellite Cultured Cells Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me1 ChIP-Seq on Muscle Satellite Cultured Cells, Donor hSKM-3 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.4637
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 2

QUALITY SCORES:
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED: 43
FINDPEAKS_SCORE: 0.5517
FINDPEAKS_PERCENTILE: 86
HOTSPOT_SCORE: 0.5267
HOTSPOT_PERCENTILE: 84
IROC_SCORE: 0.9984
IROC_PERCENTILE: 86
POISSON_SCORE: 0.6793
POISSON_PERCENTILE: 84

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

ANALYSIS FILE NAME: GSM621759_BI.Muscle_Satellite_Cultured_Cells.H3K4me1.hSKM-3.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:MC:20100222:08--ChIP:MC:20100216:08:hSKM:H3K4Me1.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Muscle Satellite Cultured Cells Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me1 ChIP-Seq read mappings from Muscle Satellite Cultured Cells, Donor hSKM-3 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.4911
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 2
BROWSER_TRACK_NAME: MS H3K4me1 3
BROWSER_TRACK_DESCRIPTION: BI Muscle Satellite Cultured Cells Histone H3K4me1 Donor hSKM-3 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED: 43
FINDPEAKS_SCORE: 0.5517
FINDPEAKS_PERCENTILE: 86
HOTSPOT_SCORE: 0.5267
HOTSPOT_PERCENTILE: 84
IROC_SCORE: 0.9984
IROC_PERCENTILE: 86
POISSON_SCORE: 0.6793
POISSON_PERCENTILE: 84

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

source_name: "Expanded from muscle spindle cells (Muoio et al; Diabetes 51, 901 (2002))"; Lib:MC:20100222:08--ChIP:MC:20100216:08:hSKM:H3K4Me1

value: mesoderm

value: DMEM

value: genomic DNA

value: unknown

value: Histone H3K4me1


title: ChIP-Seq analysis of H3K9ac in human hSKM cells; Lib:MC:20100222:13--ChIP:MC:20100216:13:hSKM:H3K9Ac

description:
sample_term_id: CL_0000594
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib:MC:20100222:13--ChIP:MC:20100216:13:hSKM:H3K9Ac
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.3181
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.3211
****************
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: GSM621757_BI.Muscle_Satellite_Cultured_Cells.H3K9ac.hSKM-3.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:MC:20100222:13--ChIP:MC:20100216:13:hSKM:H3K9Ac.hg19.level.1
ANALYSIS TITLE: Mapping of Muscle Satellite Cultured Cells Histone H3K9ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K9ac ChIP-Seq on Muscle Satellite Cultured Cells, Donor hSKM-3 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.4791
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 2

QUALITY SCORES:
NUMBER_OF_H3K9ac_EXPERIMENTS_SCORED: 35
FINDPEAKS_SCORE: 0.5362
FINDPEAKS_PERCENTILE: 89
HOTSPOT_SCORE: 0.5156
HOTSPOT_PERCENTILE: 89
IROC_SCORE: 0.9984
IROC_PERCENTILE: 91
POISSON_SCORE: 0.6049
POISSON_PERCENTILE: 80

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

ANALYSIS FILE NAME: GSM621757_BI.Muscle_Satellite_Cultured_Cells.H3K9ac.hSKM-3.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:MC:20100222:13--ChIP:MC:20100216:13:hSKM:H3K9Ac.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Muscle Satellite Cultured Cells Histone H3K9ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K9ac ChIP-Seq read mappings from Muscle Satellite Cultured Cells, Donor hSKM-3 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.5065
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 2
BROWSER_TRACK_NAME: MS H3K9ac 3
BROWSER_TRACK_DESCRIPTION: BI Muscle Satellite Cultured Cells Histone H3K9ac Donor hSKM-3 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K9ac_EXPERIMENTS_SCORED: 35
FINDPEAKS_SCORE: 0.5362
FINDPEAKS_PERCENTILE: 89
HOTSPOT_SCORE: 0.5156
HOTSPOT_PERCENTILE: 89
IROC_SCORE: 0.9984
IROC_PERCENTILE: 91
POISSON_SCORE: 0.6049
POISSON_PERCENTILE: 80

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

source_name: "Expanded from muscle spindle cells (Muoio et al; Diabetes 51, 901 (2002))"; Lib:MC:20100222:13--ChIP:MC:20100216:13:hSKM:H3K9Ac

value: hSKM

value: in vivo

value: Cell Line

value: differentiated

value: Unknown

value: Histone H3K9ac


title: AB15823_H4K8AC487128_N2_L3_2 extraction2_array1

status: Public on Nov 18 2010

type: genomic

city: Toronto

first: DCC

last: modENCODE

state: Ontario

address: MaRS Centre, South Tower, 101 College Street, Suite 800

country: Canada

institute: Ontario Institute for Cancer Research

description:
channel ch1 is input DNA;
channel ch2 is ChIP DNA; Antibody information listed below: official name: H4K8ac;target name: H4K8ac;host: Rabbit;antigen: Synthetic peptide conjugated to KLH derived from within residues 1 - 100 of Human Histone H4 acetylated at K8.;clonal: Polyclonal;purified: Affinity;company: Abcam;catalog: ab15823;reference: http://www.abcam.com/Histone-H4-acetyl-K8-antibody-ChIP-Grade-ab15823.html;short description: Rabbit polyclonal to Histone H4 (acetyl K8) - ChIP Grade;

hyb_protocol: ChIP-chip_label_hyb_nimblegen_v2. DNA was labeled and hybridized to NimbleGen C. elegans tiling array (HD2) according to the protocol described in chapter 3 and 4 of the NimbleGen Arrays User's Guide ChIP-chip Analysis, Version 3.1, 27 May 2008 with slight modifications. Briefly, amplified IP or input DNA was either labeled with Cy5 or Cy3 in the presence of Klenow fragment. The reaction was stopped by the addition of EDTA. Labeled DNA was recovered by isopropanol precipitation, and dried. The labeled DNA was hybridized to C. elegans tiling array for 16 - 20 hours at 42°C.

scan_protocol: ChIP-chip_scanning_nimblegen_v2. Array scanning and raw data extraction were performed according to the protocol described in chapter 5 and 6 of the NimbleGen Arrays User's Guide ChIP-chip Analysis, Version 3.1, 27 May 2008. Briefly, array signal was scanned by using a GenePix 4000B Scanner with associated software and saved as .tif files of the 532nm and 635nm images individually. Raw signal intensities of the images were extracted and saved as .pair files by using NimbleScan software v2.5 according to the NimbleScan User's Guide.

data_processing: ChIP-chip normalization standard nimblegen:JL:1 protocol. ChIP-chip_normalization_standard_nimblegen_v1. The log2-ratio ratio of intensity from sample/reference channel was scaled to center the ratio data around zero by subtracting the bi-weight mean for the log2-ratio values for all features on the array from each log2-ratio value. This was performed using NimbleScan software according to the NimbleScan v2.4 User's Guide and chapter 6 of the NimbleGen Arrays User's Guide ChIP-chip Analysis (version 3.1, 27 May 2008) at Roche NimbleGen.  Processed data are obtained using following parameters: genome version is WS180

label: Cy3 dye

organism: Caenorhabditis elegans

growth_protocol: Worm_L3_growth_and_harvest_vPK1. About 2-7 million of worms are bleached and then hatched in M9 for 24-42 hrs. About 100 embryos are seeded onto the plate to test for contamination and hatching efficiency. Remaining hatched L1 larvae are inoculated in a proper volume of liquid culture. Next day when larvae reach the L3 stage they are cleaned by M9 washes and sucrose gradient and collected by freezing in liquid nitrogen. Just before collection DIC pictures are taken and about 50ul of worms are stained for DAPI to assess the stage.

extract_protocol:
Worm_L3_extraction_vPK1. Worms are frozen, ground, and crosslinked for 10 minutes in 1% formaldehyde. Later, washed pellets are resuspended in FA buffer and subjected to sonication in Bioruptor (14 pulses of 30 seconds with 1 minute rests in between). Extracts are then spun down and soluble fraction is stored for quality tests and future ChIP.
Worm_chromatin_immunoprecipitation_vIL2. Appropriate amount of extract is incubated overnight with a proper amount of antibody (exceptional antibodies due to better results are incubated 2hrs). Afterwards, 40ul of equilibrated magnetic beads (either protein A or G, depending on antibody) are added and incubated for 2 hrs. Later, washes with FA, 500mM-salt FA, 1M salt FA, TEL, and TE buffer are performed and DNA is eluted in elution buffer (1% SDS in TE with 250 mM NaCl) two times with 57 ul volume each, at 65°C. Samples are treated with RNAse, proteinase K and then crosslinks are reversed overnight at 65°C. DNA is purified on Qiagen PCR purification columns, tested by q-PCR for ChIP quality, and stored at -20°C for future applications.
Worm_LM-PCR_Amplification_for_ChIP-chip_vIL1. 1/3 of ChIP and 10ng of input are blunted (T4 polymerase), ligated (concentrated T4 ligase) to annealed linkers and amplified by PCR using longer oligonucleotide as a primer. Generally two rounds of amplification are used to get the amount needed for microarray. Amplified DNA is tested by q-PCR and DNA gel is run to ensure small size and lack of degradation.

tag: strain

tag: developmental stage

value: L3 Larva

value: wild type

value: mixed Male and Hermaphrodite population

label: Cy5 dye


title: Exon arrays of Roadmap cell types; Fetal Brain primary tissue, day 112; DS15453-exon

description:
sample_term_id: UBERON_0000955
assay_term_id: OBI_0001463
nucleic_acid_term_id: SO_0000356
Exon profiling of NREMC cell types, these coincide with chromatin accessibility sequencing assays.
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.5432
sample alias: fBrain.H-23399d112
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.5295
EDACC Genboree Run Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FRUN%2FEDACC.5433

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

value: Primary Tissue

value: Fetal Brain

value: UW

value: fetal

value: day 112


title: AB15823_H4K8AC487128_N2_L3_1 extraction1_array1

label_protocol: ChIP-chip_label_hyb_nimblegen_v2. DNA was labeled and hybridized to NimbleGen C. elegans tiling array (HD2) according to the protocol described in chapter 3 and 4 of the NimbleGen Arrays User's Guide ChIP-chip Analysis, Version 3.1, 27 May 2008 with slight modifications. Briefly, amplified IP or input DNA was either labeled with Cy5 or Cy3 in the presence of Klenow fragment. The reaction was stopped by the addition of EDTA. Labeled DNA was recovered by isopropanol precipitation, and dried. The labeled DNA was hybridized to C. elegans tiling array for 16 - 20 hours at 42°C.

tag: genotype


title: Exon arrays of Roadmap cell types; iPS DF 19.11 Cell Line, Induced pluripotent stem cells; DS15153-exon

description:
sample_term_id: NTR_0001173
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.5454
sample alias: iPS_19_11
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.5333
EDACC Genboree Run Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FRUN%2FEDACC.5455

source_name: iPS DF 19.11 Cell Line, Induced pluripotent stem cel, derived from fibroblast. the first set of numbers before the period refer to different clones, the number after the period indicates the sub-clone.; DS15153-exon

value: James Thomson, Morgridge Institute for Research, University of Wisconsin-Madison

value: iPS DF 19.11 Cell Line

value: Derived from newborn foreskin fibroblast:Cat# CRL-2097TM, ATCC

value: Induced pluripotent stem cell


title: Exon arrays of Roadmap cell types; Fetal Lung, Right primary tissue, day 110; DS16566-exon

description:
sample_term_id: UBERON_0002167
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.5446
sample alias: fLung_Right.H-23604d110
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.5373
EDACC Genboree Run Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FRUN%2FEDACC.5447

value: Fetal Lung, Right

value: day 110

value: Female


title: ChIP-Seq analysis of H3K36me3 in human hSKM cells; Lib:MC:20100222:11--ChIP:MC:20100216:11:hSKM:H3K36Me3

description:
sample_term_id: CL_0000594
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib:MC:20100222:11--ChIP:MC:20100216:11:hSKM:H3K36Me3
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.3178
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.3211
****************
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: GSM621754_BI.Muscle_Satellite_Cultured_Cells.H3K36me3.hSKM-3.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:MC:20100222:11--ChIP:MC:20100216:11:hSKM:H3K36Me3.hg19.level.1
ANALYSIS TITLE: Mapping of Muscle Satellite Cultured Cells Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K36me3 ChIP-Seq on Muscle Satellite Cultured Cells, Donor hSKM-3 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.4659
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 2

QUALITY SCORES:
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED: 54
FINDPEAKS_SCORE: 0.0567
FINDPEAKS_PERCENTILE: 11
HOTSPOT_SCORE: 0.1494
HOTSPOT_PERCENTILE: 9
IROC_SCORE: 0.9062
IROC_PERCENTILE: 28
POISSON_SCORE: 0.4412
POISSON_PERCENTILE: 31

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

ANALYSIS FILE NAME: GSM621754_BI.Muscle_Satellite_Cultured_Cells.H3K36me3.hSKM-3.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:MC:20100222:11--ChIP:MC:20100216:11:hSKM:H3K36Me3.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Muscle Satellite Cultured Cells Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K36me3 ChIP-Seq read mappings from Muscle Satellite Cultured Cells, Donor hSKM-3 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.4933
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 2
BROWSER_TRACK_NAME: MS H3K36me3 3
BROWSER_TRACK_DESCRIPTION: BI Muscle Satellite Cultured Cells Histone H3K36me3 Donor hSKM-3 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED: 54
FINDPEAKS_SCORE: 0.0567
FINDPEAKS_PERCENTILE: 11
HOTSPOT_SCORE: 0.1494
HOTSPOT_PERCENTILE: 9
IROC_SCORE: 0.9062
IROC_PERCENTILE: 28
POISSON_SCORE: 0.4412
POISSON_PERCENTILE: 31

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

source_name: "Expanded from muscle spindle cells (Muoio et al; Diabetes 51, 901 (2002))"; Lib:MC:20100222:11--ChIP:MC:20100216:11:hSKM:H3K36Me3

value: mesoderm

value: DMEM

value: genomic DNA

value: unknown

value: hSKM

value: in vivo

value: Cell Line

value: differentiated

value: Unknown

value: Duke University

value: Protein A-Sepharose 4B

value: 10 million cells

value: SDS lysis

value: 70 ul bed volume

value: Abcam

value: Histone H3K36me3

value: Bioruptor


title: Exon arrays of Roadmap cell types; Fetal Lung, Left primary tissue, day 110; DS16570-exon

description:
sample_term_id: UBERON_0002168
assay_term_id: OBI_0001463
nucleic_acid_term_id: SO_0000356
Exon profiling of NREMC cell types, these coincide with chromatin accessibility sequencing assays.
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.5456
sample alias: fLung_Left.H-23604d110
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.5369
EDACC Genboree Run Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FRUN%2FEDACC.5457

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

value: Primary Tissue

value: Fetal Lung, Left

value: UW

value: fetal

value: day 110

value: Female


title: WD iPSC-2

status: Public on Dec 01 2010

city: Guangzhou

first: shiqiang

last: zhang

address: 190 Kai Yuan Avenue, Science Park

country: China

institute: Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences

description: WD iPSC-2(dFBS+Vc+VPA)

hyb_protocol: Following fragmentation and labeling, 10 ug of cDNA were hybridized for 16 hr at 45C on GeneChip HuGene 1.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix Scanner 3000 7G.

data_processing: The data were analyzed with Robust Multichip Average (RMA) using Partek software.

source_name: WD iPSC (passage 8)

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA (Whole Transcript (WT) Sense Target   Labeling Assay Manual, 2007, Affymetrix).

growth_protocol: WD fibroblasts were maintained in DMEM plus 10% fetal bovine serum (FBS),  WD iPSCs and H9 were maintained on Matrigel with mTESR1 culture medium

extract_protocol: Cells were collected by Accutase treatment. Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: WD fibroblasts (passage 5),  WD iPSCs (passage 8) and H9 (passage 40) were used for RNA extraction, spontaneously differentiated cells in WD iPSCs and H9 were removed manually before Trizol treatment.

tag: cell type

value: Wilson’s disease iPSC


title: Exon arrays of Roadmap cell types; Fetal Lung primary tissue, day 108; DS15227-exon

description:
sample_term_id: UBERON_0002048
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.5460
sample alias: fLung.H-23365d108
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.3140
EDACC Genboree Run Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FRUN%2FEDACC.5461

value: fetal lung

value: day 108

value: Male


title: WD iPSC-1

description: WD iPSC-1(KSR+VPA)


title: ChIP-Seq analysis of H3K9me3 in human hSKM cells; Lib:MC:20100222:14--ChIP:MC:20100216:14:hSKM:H3K9Me3

description:
sample_term_id: CL_0000594
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib:MC:20100222:14--ChIP:MC:20100216:14:hSKM:H3K9Me3
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.3177
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.3211
****************
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: GSM621753_BI.Muscle_Satellite_Cultured_Cells.H3K9me3.hSKM-3.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:MC:20100222:14--ChIP:MC:20100216:14:hSKM:H3K9Me3.hg19.level.1
ANALYSIS TITLE: Mapping of Muscle Satellite Cultured Cells Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K9me3 ChIP-Seq on Muscle Satellite Cultured Cells, Donor hSKM-3 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.4783
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 2

QUALITY SCORES:
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED: 59
FINDPEAKS_SCORE: 0.0238
FINDPEAKS_PERCENTILE: 19
HOTSPOT_SCORE: 0.0852
HOTSPOT_PERCENTILE: 29
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.3636
POISSON_PERCENTILE: 46

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

ANALYSIS FILE NAME: GSM621753_BI.Muscle_Satellite_Cultured_Cells.H3K9me3.hSKM-3.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:MC:20100222:14--ChIP:MC:20100216:14:hSKM:H3K9Me3.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Muscle Satellite Cultured Cells Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K9me3 ChIP-Seq read mappings from Muscle Satellite Cultured Cells, Donor hSKM-3 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.5057
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 2
BROWSER_TRACK_NAME: MS H3K9me3 3
BROWSER_TRACK_DESCRIPTION: BI Muscle Satellite Cultured Cells Histone H3K9me3 Donor hSKM-3 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED: 59
FINDPEAKS_SCORE: 0.0238
FINDPEAKS_PERCENTILE: 19
HOTSPOT_SCORE: 0.0852
HOTSPOT_PERCENTILE: 29
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.3636
POISSON_PERCENTILE: 46

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

source_name: "Expanded from muscle spindle cells (Muoio et al; Diabetes 51, 901 (2002))"; Lib:MC:20100222:14--ChIP:MC:20100216:14:hSKM:H3K9Me3

value: mesoderm

value: DMEM

value: genomic DNA

value: unknown

value: hSKM

value: in vivo

value: Cell Line

value: differentiated

value: Unknown

value: Duke University

value: Protein A-Sepharose 4B

value: 10 million cells

value: Histone H3K9me3


title: ChIP-Seq analysis of H3K9ac in human hSKM cells; Lib:MC:20100511:14--ChIP:MC:20100505:14:hSKM:H3K9Ac

description:
sample_term_id: CL_0000594
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib:MC:20100511:14--ChIP:MC:20100505:14:hSKM:H3K9Ac
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.3172
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.3210
****************
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: GSM621748_BI.Muscle_Satellite_Cultured_Cells.H3K9ac.hSKM-2.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:MC:20100511:14--ChIP:MC:20100505:14:hSKM:H3K9Ac.hg19.level.1
ANALYSIS TITLE: Mapping of Muscle Satellite Cultured Cells Histone H3K9ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K9ac ChIP-Seq on Muscle Satellite Cultured Cells, Donor hSKM-2 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.4786
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 2

QUALITY SCORES:
NUMBER_OF_H3K9ac_EXPERIMENTS_SCORED: 35
FINDPEAKS_SCORE: 0.5173
FINDPEAKS_PERCENTILE: 83
HOTSPOT_SCORE: 0.4984
HOTSPOT_PERCENTILE: 83
IROC_SCORE: 0.9983
IROC_PERCENTILE: 89
POISSON_SCORE: 0.604
POISSON_PERCENTILE: 77

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

ANALYSIS FILE NAME: GSM621748_BI.Muscle_Satellite_Cultured_Cells.H3K9ac.hSKM-2.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:MC:20100511:14--ChIP:MC:20100505:14:hSKM:H3K9Ac.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Muscle Satellite Cultured Cells Histone H3K9ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K9ac ChIP-Seq read mappings from Muscle Satellite Cultured Cells, Donor hSKM-2 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.5060
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 2
BROWSER_TRACK_NAME: MS H3K9ac 2
BROWSER_TRACK_DESCRIPTION: BI Muscle Satellite Cultured Cells Histone H3K9ac Donor hSKM-2 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K9ac_EXPERIMENTS_SCORED: 35
FINDPEAKS_SCORE: 0.5173
FINDPEAKS_PERCENTILE: 83
HOTSPOT_SCORE: 0.4984
HOTSPOT_PERCENTILE: 83
IROC_SCORE: 0.9983
IROC_PERCENTILE: 89
POISSON_SCORE: 0.604
POISSON_PERCENTILE: 77

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

source_name: "Expanded from muscle spindle cells (Muoio et al; Diabetes 51, 901 (2002))"; Lib:MC:20100511:14--ChIP:MC:20100505:14:hSKM:H3K9Ac

value: SDS lysis

value: 70 ul bed volume

value: Abcam

value: Histone H3K9ac

value: Bioruptor


title: ChIP-Seq analysis of H3K4me1 in human hSKM cells; Lib:MC:20100511:09--ChIP:MC:20100505:09:hSKM:H3K4Me1

description:
sample_term_id: CL_0000594
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib:MC:20100511:09--ChIP:MC:20100505:09:hSKM:H3K4Me1
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.3176
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.3210
****************
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: GSM621752_BI.Muscle_Satellite_Cultured_Cells.H3K4me1.hSKM-2.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:MC:20100511:09--ChIP:MC:20100505:09:hSKM:H3K4Me1.hg19.level.1
ANALYSIS TITLE: Mapping of Muscle Satellite Cultured Cells Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me1 ChIP-Seq on Muscle Satellite Cultured Cells, Donor hSKM-2 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.4632
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 2

QUALITY SCORES:
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED: 43
FINDPEAKS_SCORE: 0.6184
FINDPEAKS_PERCENTILE: 88
HOTSPOT_SCORE: 0.5688
HOTSPOT_PERCENTILE: 91
IROC_SCORE: 0.9986
IROC_PERCENTILE: 88
POISSON_SCORE: 0.7173
POISSON_PERCENTILE: 88

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

ANALYSIS FILE NAME: GSM621752_BI.Muscle_Satellite_Cultured_Cells.H3K4me1.hSKM-2.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:MC:20100511:09--ChIP:MC:20100505:09:hSKM:H3K4Me1.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Muscle Satellite Cultured Cells Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me1 ChIP-Seq read mappings from Muscle Satellite Cultured Cells, Donor hSKM-2 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.4906
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 2
BROWSER_TRACK_NAME: MS H3K4me1 2
BROWSER_TRACK_DESCRIPTION: BI Muscle Satellite Cultured Cells Histone H3K4me1 Donor hSKM-2 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED: 43
FINDPEAKS_SCORE: 0.6184
FINDPEAKS_PERCENTILE: 88
HOTSPOT_SCORE: 0.5688
HOTSPOT_PERCENTILE: 91
IROC_SCORE: 0.9986
IROC_PERCENTILE: 88
POISSON_SCORE: 0.7173
POISSON_PERCENTILE: 88

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

source_name: "Expanded from muscle spindle cells (Muoio et al; Diabetes 51, 901 (2002))"; Lib:MC:20100511:09--ChIP:MC:20100505:09:hSKM:H3K4Me1

value: mesoderm

value: DMEM

value: Histone H3K4me1