title: ChIP-Seq analysis of H3K36me3 in AdiposeNuclei cells; Lib:XZ:20100107:09--ChIP:XZ:20100104:07: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:20100107:09--ChIP:XZ:20100104:07:AdiposeNuclei:H3K36Me3
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.3801
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.3891
****************
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: GSM621461_BI.Adipose_Nuclei.H3K36me3.7.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100107:09--ChIP:XZ:20100104:07:AdiposeNuclei:H3K36Me3.hg19.level.1
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 7 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.4588
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: 0.353
FINDPEAKS_PERCENTILE: 72
HOTSPOT_SCORE: 0.3075
HOTSPOT_PERCENTILE: 64
IROC_SCORE: 0.9942
IROC_PERCENTILE: 91
POISSON_SCORE: 0.5926
POISSON_PERCENTILE: 70

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

ANALYSIS FILE NAME: GSM621461_BI.Adipose_Nuclei.H3K36me3.7.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100107:09--ChIP:XZ:20100104:07:AdiposeNuclei:H3K36Me3.hg19.level.2
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 7 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.4862
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: AN H3K36me3 7
BROWSER_TRACK_DESCRIPTION: BI Adipose Nuclei Histone H3K36me3 Donor 7 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED: 54
FINDPEAKS_SCORE: 0.353
FINDPEAKS_PERCENTILE: 72
HOTSPOT_SCORE: 0.3075
HOTSPOT_PERCENTILE: 64
IROC_SCORE: 0.9942
IROC_PERCENTILE: 91
POISSON_SCORE: 0.5926
POISSON_PERCENTILE: 70

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

source_name: Nuclei derived from crude preps of adipose tissue; Lib:XZ:20100107:09--ChIP:XZ:20100104:07:AdiposeNuclei:H3K36Me3

value: surgery

value: Adipose Nuclei

value: Female

value: Primary Tissue

value: abdomen

value: Harvard University


title: ChIP-Seq analysis of H3K4me1 in Skeletal muscle cells; Lib:XZ:20100423:03--ChIP:XZ:20100331:03:Skeletal muscle:H3K4Me1

status: Public on Nov 12 2010

type: SRA

city: Cambridge

first: BROAD

last: INSTITUTE

state: MA

country: USA

institute: Broad Institute

description:
sample_term_id: UBERON_0001134
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib:XZ:20100423:03--ChIP:XZ:20100331:03:Skeletal muscle:H3K4Me1
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.3224
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.3347
****************
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

library_source: genomic

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

ANALYSIS FILE NAME: GSM621640_BI.Skeletal_Muscle.H3K4me1.19.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100423:03--ChIP:XZ:20100331:03:Skeletal muscle:H3K4Me1.hg19.level.1
ANALYSIS TITLE: Mapping of Skeletal Muscle Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me1 ChIP-Seq on Skeletal Muscle, Donor 19 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.4590
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: 0.4017
FINDPEAKS_PERCENTILE: 65
HOTSPOT_SCORE: 0.4091
HOTSPOT_PERCENTILE: 65
IROC_SCORE: 0.9899
IROC_PERCENTILE: 60
POISSON_SCORE: 0.6257
POISSON_PERCENTILE: 79

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

ANALYSIS FILE NAME: GSM621640_BI.Skeletal_Muscle.H3K4me1.19.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100423:03--ChIP:XZ:20100331:03:Skeletal muscle:H3K4Me1.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Skeletal Muscle Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me1 ChIP-Seq read mappings from Skeletal Muscle, Donor 19 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.4864
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: SM H3K4me1 19
BROWSER_TRACK_DESCRIPTION: BI Skeletal Muscle Histone H3K4me1 Donor 19 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED: 43
FINDPEAKS_SCORE: 0.4017
FINDPEAKS_PERCENTILE: 65
HOTSPOT_SCORE: 0.4091
HOTSPOT_PERCENTILE: 65
IROC_SCORE: 0.9899
IROC_PERCENTILE: 60
POISSON_SCORE: 0.6257
POISSON_PERCENTILE: 79

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

molecule: genomic DNA

organism: Homo sapiens

source_name: Primary skeletal muscle tissue; Lib:XZ:20100423:03--ChIP:XZ:20100331:03:Skeletal muscle:H3K4Me1

extract_protocol: Library construction protocol: Single read - Illumina

tag: molecule

value: genomic DNA

tag: disease

value: Skeletal muscle

value: Unknown

value: unknown

value: MGH Pathology

value: Protein A-Sepharose 4B

value: 10 million cells

value: SDS lysis

value: 70 ul bed volume

value: Abcam

value: Histone H3K4me1

value: Bioruptor


title: ChIP-Seq analysis of H3K9me3 in human Th17 cells; Lib:RI:20100422:11--ChIP:MA:20100416:11:Th17:H3K9Me3

description:
sample_term_id: CL_0000899
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib:RI:20100422:11--ChIP:MA:20100416:11:Th17:H3K9Me3
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.3768
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.3883
****************
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: GSM621428_BI.Th17_Primary_Cells.H3K9me3.20.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:RI:20100422:11--ChIP:MA:20100416:11:Th17:H3K9Me3.hg19.level.1
ANALYSIS TITLE: Mapping of Th17 Primary Cells Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K9me3 ChIP-Seq on Th17 Primary Cells, Donor 20 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.4684
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: 0.0892
FINDPEAKS_PERCENTILE: 51
HOTSPOT_SCORE: 0.1903
HOTSPOT_PERCENTILE: 63
IROC_SCORE: 0.7868
IROC_PERCENTILE: 37
POISSON_SCORE: 0.3515
POISSON_PERCENTILE: 42

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

ANALYSIS FILE NAME: GSM621428_BI.Th17_Primary_Cells.H3K9me3.20.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:RI:20100422:11--ChIP:MA:20100416:11:Th17:H3K9Me3.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Th17 Primary Cells Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K9me3 ChIP-Seq read mappings from Th17 Primary Cells, Donor 20 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.4958
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: Th17 H3K9me3 20
BROWSER_TRACK_DESCRIPTION: BI Th17 Primary Cells Histone H3K9me3 Donor 20 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED: 59
FINDPEAKS_SCORE: 0.0892
FINDPEAKS_PERCENTILE: 51
HOTSPOT_SCORE: 0.1903
HOTSPOT_PERCENTILE: 63
IROC_SCORE: 0.7868
IROC_PERCENTILE: 37
POISSON_SCORE: 0.3515
POISSON_PERCENTILE: 42

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

source_name: "Th17 cells derived from fom pooled leukopacks by Ficoll sedimentation, magnetic bead purification, PMA/ionomycin stimulation, and FACS"; Lib:RI:20100422:11--ChIP:MA:20100416:11:Th17:H3K9Me3

tag: markers

value: Primary Cell

value: Whitehead Institute

value: Histone H3K9me3


title: ChIP-Seq analysis of H3K4me1 in human AdiposeNuclei cells; Lib:XZ:20100423:07--ChIP:XZ:20100331:07:AdiposeNuclei:H3K4Me1

description:
sample_term_id: UBERON_0014455
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib:XZ:20100423:07--ChIP:XZ:20100331:07:AdiposeNuclei:H3K4Me1
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.3765
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.3891
****************
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: GSM621425_BI.Adipose_Nuclei.H3K4me1.7.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100423:07--ChIP:XZ:20100331:07:AdiposeNuclei:H3K4Me1.hg19.level.1
ANALYSIS TITLE: Mapping of Adipose Nuclei Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me1 ChIP-Seq on Adipose Nuclei, Donor 7 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.4810
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: 0.0125
FINDPEAKS_PERCENTILE: 2
HOTSPOT_SCORE: 0.0885
HOTSPOT_PERCENTILE: 2
IROC_SCORE: 0.7057
IROC_PERCENTILE: 2
POISSON_SCORE: 0.3592
POISSON_PERCENTILE: 2

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

ANALYSIS FILE NAME: GSM621425_BI.Adipose_Nuclei.H3K4me1.7.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100423:07--ChIP:XZ:20100331:07:AdiposeNuclei:H3K4Me1.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Adipose Nuclei Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me1 ChIP-Seq read mappings from Adipose Nuclei, Donor 7 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.5084
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: AN H3K4me1 7
BROWSER_TRACK_DESCRIPTION: BI Adipose Nuclei Histone H3K4me1 Donor 7 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED: 43
FINDPEAKS_SCORE: 0.0125
FINDPEAKS_PERCENTILE: 2
HOTSPOT_SCORE: 0.0885
HOTSPOT_PERCENTILE: 2
IROC_SCORE: 0.7057
IROC_PERCENTILE: 2
POISSON_SCORE: 0.3592
POISSON_PERCENTILE: 2

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

source_name: Nuclei derived from crude preps of adipose tissue; Lib:XZ:20100423:07--ChIP:XZ:20100331:07:AdiposeNuclei:H3K4Me1

value: surgery

value: Adipose Nuclei

value: Female

value: Primary Tissue

value: abdomen


title: WD fibroblasts

status: Public on Dec 01 2010

type: RNA

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 fibroblasts(dermal, male)

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.

label: biotin

molecule: total RNA

source_name: WD fibroblasts (passage 5)

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 fibroblasts


title: ChIP-Seq analysis of WCE in human Th17 cells; Lib:RI:20100422:08--ChIP:MA:20100416:08:Th17:WCE

description:
sample_term_id: CL_0000899
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib:RI:20100422:08--ChIP:MA:20100416:08:Th17:WCE
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.3795
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.3883
****************
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: GSM621455_BI.Th17_Primary_Cells.Input.20.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:RI:20100422:08--ChIP:MA:20100416:08:Th17:WCE.hg19.level.1
ANALYSIS TITLE: Mapping of Th17 Primary Cells ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina reads produced by ChIP-Seq Input on Th17 Primary Cells, Donor 20 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.4802
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: 0.0101
FINDPEAKS_PERCENTILE: 54
HOTSPOT_SCORE: 0.0863
HOTSPOT_PERCENTILE: 70
IROC_SCORE: 0.393
IROC_PERCENTILE: 29
POISSON_SCORE: 0.2039
POISSON_PERCENTILE: 31

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

ANALYSIS FILE NAME: GSM621455_BI.Th17_Primary_Cells.Input.20.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:RI:20100422:08--ChIP:MA:20100416:08:Th17:WCE.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Th17 Primary Cells ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina ChIP-Seq Input read mappings from Th17 Primary Cells, Donor 20 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.5076
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: Th17 Input 20
BROWSER_TRACK_DESCRIPTION: BI Th17 Primary Cells ChIP-Seq Input Donor 20 EA Release 2

QUALITY SCORES:
NUMBER_OF_Input_EXPERIMENTS_SCORED: 67
FINDPEAKS_SCORE: 0.0101
FINDPEAKS_PERCENTILE: 54
HOTSPOT_SCORE: 0.0863
HOTSPOT_PERCENTILE: 70
IROC_SCORE: 0.393
IROC_PERCENTILE: 29
POISSON_SCORE: 0.2039
POISSON_PERCENTILE: 31

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

source_name: "Th17 cells derived from fom pooled leukopacks by Ficoll sedimentation, magnetic bead purification, PMA/ionomycin stimulation, and FACS"; Lib:RI:20100422:08--ChIP:MA:20100416:08:Th17:WCE

value: genomic DNA

value: Unknown

value: standard

value: ChIP-Seq Input

value: Input


title: ChIP-Seq analysis of H3K4me3 in Duodenum mucosa cells; Lib:XZ:20100628:02--ChIP:XZ:20100621:02:Duodenum mucosa:H3K4Me3

description:
sample_term_id: UBERON_0000320
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib:XZ:20100628:02--ChIP:XZ:20100621:02:Duodenum mucosa:H3K4Me3
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.3772
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.3882
****************
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: GSM621432_BI.Duodenum_Mucosa.H3K4me3.61.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100628:02--ChIP:XZ:20100621:02:Duodenum mucosa:H3K4Me3.hg19.level.1
ANALYSIS TITLE: Mapping of Duodenum Mucosa Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me3 ChIP-Seq on Duodenum Mucosa, Donor 61 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.4766
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_H3K4me3_EXPERIMENTS_SCORED: 62
FINDPEAKS_SCORE: 0.3057
FINDPEAKS_PERCENTILE: 34
HOTSPOT_SCORE: 0.3018
HOTSPOT_PERCENTILE: 30
IROC_SCORE: 0.9987
IROC_PERCENTILE: 47
POISSON_SCORE: 0.4282
POISSON_PERCENTILE: 40

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

ANALYSIS FILE NAME: GSM621432_BI.Duodenum_Mucosa.H3K4me3.61.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100628:02--ChIP:XZ:20100621:02:Duodenum mucosa:H3K4Me3.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Duodenum Mucosa Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me3 ChIP-Seq read mappings from Duodenum Mucosa, Donor 61 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.5040
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: DM H3K4me3 61
BROWSER_TRACK_DESCRIPTION: BI Duodenum Mucosa Histone H3K4me3 Donor 61 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED: 62
FINDPEAKS_SCORE: 0.3057
FINDPEAKS_PERCENTILE: 34
HOTSPOT_SCORE: 0.3018
HOTSPOT_PERCENTILE: 30
IROC_SCORE: 0.9987
IROC_PERCENTILE: 47
POISSON_SCORE: 0.4282
POISSON_PERCENTILE: 40

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

source_name: Primary duodenum mucosa tissue; Lib:XZ:20100628:02--ChIP:XZ:20100621:02:Duodenum mucosa:H3K4Me3

value: "NL mucosa,... Pancreatitis/IPMN"

value: mucosa

value: white

value: Male

value: duodenum

value: MGH Pathology

value: 76 years

value: Protein A-Sepharose 4B

value: 10 million cells

value: SDS lysis

value: 70 ul bed volume

value: Millipore

value: Histone H3K4me3


title: ChIP-Seq analysis of H3K36me3 in Duodenum mucosa cells; Lib:XZ:20100628:03--ChIP:XZ:20100621:03:Duodenum mucosa:H3K36Me3

description:
sample_term_id: UBERON_0000320
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib:XZ:20100628:03--ChIP:XZ:20100621:03:Duodenum mucosa:H3K36Me3
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.3761
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.3882
****************
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: GSM621421_BI.Duodenum_Mucosa.H3K36me3.61.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100628:03--ChIP:XZ:20100621:03:Duodenum mucosa:H3K36Me3.hg19.level.1
ANALYSIS TITLE: Mapping of Duodenum Mucosa Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K36me3 ChIP-Seq on Duodenum Mucosa, Donor 61 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.4761
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: 0.2649
FINDPEAKS_PERCENTILE: 57
HOTSPOT_SCORE: 0.2461
HOTSPOT_PERCENTILE: 47
IROC_SCORE: 0.9849
IROC_PERCENTILE: 80
POISSON_SCORE: 0.5617
POISSON_PERCENTILE: 67

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

ANALYSIS FILE NAME: GSM621421_BI.Duodenum_Mucosa.H3K36me3.61.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100628:03--ChIP:XZ:20100621:03:Duodenum mucosa:H3K36Me3.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Duodenum Mucosa Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K36me3 ChIP-Seq read mappings from Duodenum Mucosa, Donor 61 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.5035
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: DM H3K36me3 61
BROWSER_TRACK_DESCRIPTION: BI Duodenum Mucosa Histone H3K36me3 Donor 61 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED: 54
FINDPEAKS_SCORE: 0.2649
FINDPEAKS_PERCENTILE: 57
HOTSPOT_SCORE: 0.2461
HOTSPOT_PERCENTILE: 47
IROC_SCORE: 0.9849
IROC_PERCENTILE: 80
POISSON_SCORE: 0.5617
POISSON_PERCENTILE: 67

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

source_name: Primary duodenum mucosa tissue; Lib:XZ:20100628:03--ChIP:XZ:20100621:03:Duodenum mucosa:H3K36Me3

value: surgery

value: genomic DNA

value: Primary Tissue

value: Abcam

value: Histone H3K36me3

value: Bioruptor


title: ChIP-Seq analysis of H3K9ac in Duodenum mucosa cells; Lib:XZ:20100628:05--ChIP:XZ:20100621:05:Duodenum mucosa:H3K9Ac

description:
sample_term_id: UBERON_0000320
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib:XZ:20100628:05--ChIP:XZ:20100621:05:Duodenum mucosa:H3K9Ac
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.3785
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.3882
****************
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: GSM621445_BI.Duodenum_Mucosa.H3K9ac.61.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100628:05--ChIP:XZ:20100621:05:Duodenum mucosa:H3K9Ac.hg19.level.1
ANALYSIS TITLE: Mapping of Duodenum Mucosa Histone H3K9ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K9ac ChIP-Seq on Duodenum Mucosa, Donor 61 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.4626
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: 0.1109
FINDPEAKS_PERCENTILE: 29
HOTSPOT_SCORE: 0.1351
HOTSPOT_PERCENTILE: 11
IROC_SCORE: 0.9956
IROC_PERCENTILE: 77
POISSON_SCORE: 0.3235
POISSON_PERCENTILE: 26

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

ANALYSIS FILE NAME: GSM621445_BI.Duodenum_Mucosa.H3K9ac.61.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100628:05--ChIP:XZ:20100621:05:Duodenum mucosa:H3K9Ac.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Duodenum Mucosa Histone H3K9ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K9ac ChIP-Seq read mappings from Duodenum Mucosa, Donor 61 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.4900
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: DM H3K9ac 61
BROWSER_TRACK_DESCRIPTION: BI Duodenum Mucosa Histone H3K9ac Donor 61 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K9ac_EXPERIMENTS_SCORED: 35
FINDPEAKS_SCORE: 0.1109
FINDPEAKS_PERCENTILE: 29
HOTSPOT_SCORE: 0.1351
HOTSPOT_PERCENTILE: 11
IROC_SCORE: 0.9956
IROC_PERCENTILE: 77
POISSON_SCORE: 0.3235
POISSON_PERCENTILE: 26

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

source_name: Primary duodenum mucosa tissue; Lib:XZ:20100628:05--ChIP:XZ:20100621:05:Duodenum mucosa:H3K9Ac

value: "NL mucosa,... Pancreatitis/IPMN"

value: mucosa

value: white

value: Histone H3K9ac


title: ChIP-Seq analysis of H3K9me3 in Duodenum mucosa cells; Lib:XZ:20100628:06--ChIP:XZ:20100621:06:Duodenum mucosa:H3K9Me3

description:
sample_term_id: UBERON_0000320
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib:XZ:20100628:06--ChIP:XZ:20100621:06:Duodenum mucosa:H3K9Me3
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.3735
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.3882
****************
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: GSM621395_BI.Duodenum_Mucosa.H3K9me3.61.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100628:06--ChIP:XZ:20100621:06:Duodenum mucosa:H3K9Me3.hg19.level.1
ANALYSIS TITLE: Mapping of Duodenum Mucosa Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K9me3 ChIP-Seq on Duodenum Mucosa, Donor 61 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.4725
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: 0.0466
FINDPEAKS_PERCENTILE: 34
HOTSPOT_SCORE: 0.0935
HOTSPOT_PERCENTILE: 32
IROC_SCORE: 0.7126
IROC_PERCENTILE: 17
POISSON_SCORE: 0.4295
POISSON_PERCENTILE: 63

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

ANALYSIS FILE NAME: GSM621395_BI.Duodenum_Mucosa.H3K9me3.61.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100628:06--ChIP:XZ:20100621:06:Duodenum mucosa:H3K9Me3.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Duodenum Mucosa Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K9me3 ChIP-Seq read mappings from Duodenum Mucosa, Donor 61 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.4999
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: DM H3K9me3 61
BROWSER_TRACK_DESCRIPTION: BI Duodenum Mucosa Histone H3K9me3 Donor 61 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED: 59
FINDPEAKS_SCORE: 0.0466
FINDPEAKS_PERCENTILE: 34
HOTSPOT_SCORE: 0.0935
HOTSPOT_PERCENTILE: 32
IROC_SCORE: 0.7126
IROC_PERCENTILE: 17
POISSON_SCORE: 0.4295
POISSON_PERCENTILE: 63

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

source_name: Primary duodenum mucosa tissue; Lib:XZ:20100628:06--ChIP:XZ:20100621:06:Duodenum mucosa:H3K9Me3

value: Male

value: duodenum

value: MGH Pathology

value: 76 years

value: Histone H3K9me3


title: ChIP-Seq analysis of H3K4me3 in human AdiposeNuclei cells; Lib:XZ:20100107:11--ChIP:XZ:20100104:09:AdiposeNuclei:H3K4Me3

description:
sample_term_id: UBERON_0014455
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib:XZ:20100107:11--ChIP:XZ:20100104:09:AdiposeNuclei:H3K4Me3
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.3775
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.3891
****************
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: GSM621435_BI.Adipose_Nuclei.H3K4me3.7.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100107:11--ChIP:XZ:20100104:09:AdiposeNuclei:H3K4Me3.hg19.level.1
ANALYSIS TITLE: Mapping of Adipose Nuclei Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me3 ChIP-Seq on Adipose Nuclei, Donor 7 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.4728
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_H3K4me3_EXPERIMENTS_SCORED: 62
FINDPEAKS_SCORE: 0.3567
FINDPEAKS_PERCENTILE: 48
HOTSPOT_SCORE: 0.3453
HOTSPOT_PERCENTILE: 39
IROC_SCORE: 0.9994
IROC_PERCENTILE: 56
POISSON_SCORE: 0.4538
POISSON_PERCENTILE: 48

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

ANALYSIS FILE NAME: GSM621435_BI.Adipose_Nuclei.H3K4me3.7.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100107:11--ChIP:XZ:20100104:09:AdiposeNuclei:H3K4Me3.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Adipose Nuclei Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me3 ChIP-Seq read mappings from Adipose Nuclei, Donor 7 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.5002
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: AN H3K4me3 7
BROWSER_TRACK_DESCRIPTION: BI Adipose Nuclei Histone H3K4me3 Donor 7 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED: 62
FINDPEAKS_SCORE: 0.3567
FINDPEAKS_PERCENTILE: 48
HOTSPOT_SCORE: 0.3453
HOTSPOT_PERCENTILE: 39
IROC_SCORE: 0.9994
IROC_PERCENTILE: 56
POISSON_SCORE: 0.4538
POISSON_PERCENTILE: 48

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

source_name: Nuclei derived from crude preps of adipose tissue; Lib:XZ:20100107:11--ChIP:XZ:20100104:09:AdiposeNuclei:H3K4Me3

value: Adipose Nuclei

value: Female

value: abdomen

value: Harvard University

value: Protein A-Sepharose 4B

value: 10 million cells

value: SDS lysis

value: 70 ul bed volume

value: Millipore


title: Bisulfite-Seq analysis of RRBS820 derived from human stomach smooth muscle cells; RRBS820

status: Public on Nov 11 2010

description:
sample_term_id: UBERON_0008856
assay_term_id: OBI_0001862
nucleic_acid_term_id: SO_0000352
Design description: RRBS REMC Sequencing on Illumina
Library name: RRBS820
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.3951
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.3346
****************
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: GSM621732_BI.Stomach_Smooth_Muscle.RRBS.28.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: RRBS820.hg19.level.2
ANALYSIS TITLE: Methylation Proportion Graphs of Stomach Smooth Muscle RRBS Data
ANALYSIS DESCRIPTION: Illumina RRBS read mappings from Stomach Smooth Muscle, Donor 28 were processed into graphs of methylation proportions. Methylation proportions were calculated as (methylated calls / (methylated calls + unmethylated calls)) for all CpGs covered by at least 4 reads.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.5212
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Reduced Representation Bisulfite-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19 MspI restriction fragments 40-220bp
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
GENOMIC_WINDOW: 2bp containing CpGs
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: SSM RRBS 28
BROWSER_TRACK_DESCRIPTION: BI Stomach Smooth Muscle RRBS Donor 28 EA Release 2
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 98.83

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

source_name: Primary gastric smooth muscle tissue; RRBS820

extract_protocol: Library construction protocol: Smith et al., Methods 48, 226-232

value: surgery

value: normal smooth muscle

value: genomic DNA

value: smooth muscle

value: Primary Tissue

value: stomach

value: 2x5hrs Epitect Kit

value: 20 ng

value: T4 Ligase (2,000U/ul) 16C o/n

value: 5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT

value: 5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT

value: Standard Protocol (Smith et al., Methods 48, 226-232)

value: DNA Methylation

value: Smith et al., Methods 48, 226-232

value: Gel size selection

value: Pfu Turbo Cx hot start


title: ChIP-Seq analysis of H3K9me3 in human AdiposeNuclei cells; Lib:XZ:20100107:13--ChIP:XZ:20100104:11:AdiposeNuclei:H3K9Me3

description:
sample_term_id: UBERON_0014455
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib:XZ:20100107:13--ChIP:XZ:20100104:11:AdiposeNuclei:H3K9Me3
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.3731
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.3891
****************
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: GSM621391_BI.Adipose_Nuclei.H3K9me3.7.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100107:13--ChIP:XZ:20100104:11:AdiposeNuclei:H3K9Me3.hg19.level.1
ANALYSIS TITLE: Mapping of Adipose Nuclei Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K9me3 ChIP-Seq on Adipose Nuclei, Donor 7 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.4756
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: 0.0228
FINDPEAKS_PERCENTILE: 15
HOTSPOT_SCORE: 0.0488
HOTSPOT_PERCENTILE: 10
IROC_SCORE: 0.801
IROC_PERCENTILE: 42
POISSON_SCORE: 0.3415
POISSON_PERCENTILE: 37

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

ANALYSIS FILE NAME: GSM621391_BI.Adipose_Nuclei.H3K9me3.7.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100107:13--ChIP:XZ:20100104:11:AdiposeNuclei:H3K9Me3.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Adipose Nuclei Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K9me3 ChIP-Seq read mappings from Adipose Nuclei, Donor 7 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.5030
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: AN H3K9me3 7
BROWSER_TRACK_DESCRIPTION: BI Adipose Nuclei Histone H3K9me3 Donor 7 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED: 59
FINDPEAKS_SCORE: 0.0228
FINDPEAKS_PERCENTILE: 15
HOTSPOT_SCORE: 0.0488
HOTSPOT_PERCENTILE: 10
IROC_SCORE: 0.801
IROC_PERCENTILE: 42
POISSON_SCORE: 0.3415
POISSON_PERCENTILE: 37

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

source_name: Nuclei derived from crude preps of adipose tissue; Lib:XZ:20100107:13--ChIP:XZ:20100104:11:AdiposeNuclei:H3K9Me3

value: Adipose Nuclei

value: Female

value: abdomen

value: Harvard University

value: Protein A-Sepharose 4B

value: 10 million cells

value: SDS lysis

value: 70 ul bed volume

value: Abcam

value: Histone H3K9me3

value: Bioruptor


title: ChIP-Seq analysis of WCE in human Duodenum mucosa cells; Lib:XZ:20100628:07--ChIP:XZ:20100621:07:Duodenum mucosa:WCE

description:
sample_term_id: UBERON_0000320
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib:XZ:20100628:07--ChIP:XZ:20100621:07:Duodenum mucosa:WCE
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.3746
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.3882
****************
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: GSM621406_BI.Duodenum_Mucosa.Input.61.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100628:07--ChIP:XZ:20100621:07:Duodenum mucosa:WCE.hg19.level.1
ANALYSIS TITLE: Mapping of Duodenum Mucosa ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina reads produced by ChIP-Seq Input on Duodenum Mucosa, Donor 61 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.4720
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: 0.0054
FINDPEAKS_PERCENTILE: 10
HOTSPOT_SCORE: 0.0033
HOTSPOT_PERCENTILE: 5
IROC_SCORE: 0.0
IROC_PERCENTILE: 18
POISSON_SCORE: 0.2126
POISSON_PERCENTILE: 37

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

ANALYSIS FILE NAME: GSM621406_BI.Duodenum_Mucosa.Input.61.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100628:07--ChIP:XZ:20100621:07:Duodenum mucosa:WCE.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Duodenum Mucosa ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina ChIP-Seq Input read mappings from Duodenum Mucosa, Donor 61 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.4994
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: DM Input 61
BROWSER_TRACK_DESCRIPTION: BI Duodenum Mucosa ChIP-Seq Input Donor 61 EA Release 2

QUALITY SCORES:
NUMBER_OF_Input_EXPERIMENTS_SCORED: 67
FINDPEAKS_SCORE: 0.0054
FINDPEAKS_PERCENTILE: 10
HOTSPOT_SCORE: 0.0033
HOTSPOT_PERCENTILE: 5
IROC_SCORE: 0.0
IROC_PERCENTILE: 18
POISSON_SCORE: 0.2126
POISSON_PERCENTILE: 37

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

source_name: Primary duodenum mucosa tissue; Lib:XZ:20100628:07--ChIP:XZ:20100621:07:Duodenum mucosa:WCE

value: surgery

value: "NL mucosa,... Pancreatitis/IPMN"

value: genomic DNA

value: mucosa

value: white

value: Male

value: Primary Tissue

value: duodenum

value: MGH Pathology

value: 76 years

value: standard

value: ChIP-Seq Input

value: Input


title: Bisulfite-Seq analysis of RRBS825 derived from human Duodenum mucosa cells; RRBS825

description:
sample_term_id: UBERON_0000320
assay_term_id: OBI_0001862
nucleic_acid_term_id: SO_0000352
Design description: RRBS REMC Sequencing on Illumina
Library name: RRBS825
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.3948
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.3882
****************
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: GSM621729_BI.Duodenum_Mucosa.RRBS.61.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: RRBS825.hg19.level.2
ANALYSIS TITLE: Methylation Proportion Graphs of Duodenum Mucosa RRBS Data
ANALYSIS DESCRIPTION: Illumina RRBS read mappings from Duodenum Mucosa, Donor 61 were processed into graphs of methylation proportions. Methylation proportions were calculated as (methylated calls / (methylated calls + unmethylated calls)) for all CpGs covered by at least 4 reads.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.5209
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Reduced Representation Bisulfite-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19 MspI restriction fragments 40-220bp
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
GENOMIC_WINDOW: 2bp containing CpGs
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: DM RRBS 61
BROWSER_TRACK_DESCRIPTION: BI Duodenum Mucosa RRBS Donor 61 EA Release 2
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 98.68

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

source_name: Primary duodenum mucosa tissue; RRBS825

value: 2x5hrs Epitect Kit

value: 20 ng

value: T4 Ligase (2,000U/ul) 16C o/n

value: 5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT

value: 5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT

value: Standard Protocol (Smith et al., Methods 48, 226-232)

value: DNA Methylation

value: Smith et al., Methods 48, 226-232

value: Gel size selection

value: Pfu Turbo Cx hot start


title: ChIP-Seq analysis of WCE in human AdiposeNuclei cells; Lib:XZ:20100107:14--ChIP:XZ:20100104:12:AdiposeNuclei:WCE

description:
sample_term_id: UBERON_0014455
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib:XZ:20100107:14--ChIP:XZ:20100104:12:AdiposeNuclei:WCE
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.3741
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.3891
****************
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: GSM621401_BI.Adipose_Nuclei.Input.7.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100107:14--ChIP:XZ:20100104:12:AdiposeNuclei:WCE.hg19.level.1
ANALYSIS TITLE: Mapping of Adipose Nuclei ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina reads produced by ChIP-Seq Input on Adipose Nuclei, Donor 7 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.4817
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: 0.0085
FINDPEAKS_PERCENTILE: 40
HOTSPOT_SCORE: 0.0063
HOTSPOT_PERCENTILE: 21
IROC_SCORE: 0.9938
IROC_PERCENTILE: 95
POISSON_SCORE: 0.241
POISSON_PERCENTILE: 58

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

ANALYSIS FILE NAME: GSM621401_BI.Adipose_Nuclei.Input.7.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100107:14--ChIP:XZ:20100104:12:AdiposeNuclei:WCE.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Adipose Nuclei ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina ChIP-Seq Input read mappings from Adipose Nuclei, Donor 7 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.5091
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: AN Input 7
BROWSER_TRACK_DESCRIPTION: BI Adipose Nuclei ChIP-Seq Input Donor 7 EA Release 2

QUALITY SCORES:
NUMBER_OF_Input_EXPERIMENTS_SCORED: 67
FINDPEAKS_SCORE: 0.0085
FINDPEAKS_PERCENTILE: 40
HOTSPOT_SCORE: 0.0063
HOTSPOT_PERCENTILE: 21
IROC_SCORE: 0.9938
IROC_PERCENTILE: 95
POISSON_SCORE: 0.241
POISSON_PERCENTILE: 58

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

source_name: Nuclei derived from crude preps of adipose tissue; Lib:XZ:20100107:14--ChIP:XZ:20100104:12:AdiposeNuclei:WCE

value: surgery

value: genomic DNA

value: Adipose Nuclei

value: Female

value: Primary Tissue

value: abdomen

value: Harvard University

value: SDS lysis

value: Bioruptor


title: Bisulfite-Seq analysis of RRBS822 derived from human rectal smooth muscle cells; RRBS822

description:
sample_term_id: NTR_0001404
assay_term_id: OBI_0001862
nucleic_acid_term_id: SO_0000352
Design description: RRBS REMC Sequencing on Illumina
Library name: RRBS822
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.3949
EDACC Genboree Sample Page:

****************
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: GSM621730_BI.Rectal_Smooth_Muscle.RRBS.30.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: RRBS822.hg19.level.2
ANALYSIS TITLE: Methylation Proportion Graphs of Rectal Smooth Muscle RRBS Data
ANALYSIS DESCRIPTION: Illumina RRBS read mappings from Rectal Smooth Muscle, Donor 30 were processed into graphs of methylation proportions. Methylation proportions were calculated as (methylated calls / (methylated calls + unmethylated calls)) for all CpGs covered by at least 4 reads.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.5211
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Reduced Representation Bisulfite-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19 MspI restriction fragments 40-220bp
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
GENOMIC_WINDOW: 2bp containing CpGs
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: RSM RRBS 30
BROWSER_TRACK_DESCRIPTION: BI Rectal Smooth Muscle RRBS Donor 30 EA Release 2
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 98.97

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

source_name: Primary rectal smooth muscle tissue; RRBS822

value: normal smooth muscle

value: smooth muscle

value: white

value: rectum

value: MGH Pathology

value: 2x5hrs Epitect Kit

value: 20 ng

value: T4 Ligase (2,000U/ul) 16C o/n


title: ChIP-Seq analysis of WCE in human Treg cells; Lib:RI:20100422:14--ChIP:MA:20100416:14:Treg:WCE

description:
sample_term_id: CL_0000815
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib:RI:20100422:14--ChIP:MA:20100416:14:Treg:WCE
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.3793
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.3893
****************
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: GSM621453_BI.Treg_Primary_Cells.Input.20.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:RI:20100422:14--ChIP:MA:20100416:14:Treg:WCE.hg19.level.1
ANALYSIS TITLE: Mapping of Treg Primary Cells ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina reads produced by ChIP-Seq Input on Treg Primary Cells, Donor 20 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.4566
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: 0.0079
FINDPEAKS_PERCENTILE: 37
HOTSPOT_SCORE: 0.0046
HOTSPOT_PERCENTILE: 11
IROC_SCORE: 0.9924
IROC_PERCENTILE: 92
POISSON_SCORE: 0.2778
POISSON_PERCENTILE: 70

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

ANALYSIS FILE NAME: GSM621453_BI.Treg_Primary_Cells.Input.20.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:RI:20100422:14--ChIP:MA:20100416:14:Treg:WCE.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Treg Primary Cells ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina ChIP-Seq Input read mappings from Treg Primary Cells, Donor 20 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.4840
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: Treg Input 20
BROWSER_TRACK_DESCRIPTION: BI Treg Primary Cells ChIP-Seq Input Donor 20 EA Release 2

QUALITY SCORES:
NUMBER_OF_Input_EXPERIMENTS_SCORED: 67
FINDPEAKS_SCORE: 0.0079
FINDPEAKS_PERCENTILE: 37
HOTSPOT_SCORE: 0.0046
HOTSPOT_PERCENTILE: 11
IROC_SCORE: 0.9924
IROC_PERCENTILE: 92
POISSON_SCORE: 0.2778
POISSON_PERCENTILE: 70

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

source_name: "Treg cells derived from fom pooled leukopacks by Ficoll sedimentation, magnetic bead purification, and FACS"; Lib:RI:20100422:14--ChIP:MA:20100416:14:Treg:WCE

value: CD4+ CD25high IL7R-

value: Treg

value: Unknown

value: Primary Cell

value: Whitehead Institute

value: standard

value: ChIP-Seq Input

value: Input


title: ChIP-Seq analysis of H3K4me1 in Duodenum mucosa cells; Lib:XZ:20100628:01--ChIP:XZ:20100621:01:Duodenum mucosa:H3K4Me1

description:
sample_term_id: UBERON_0000320
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib:XZ:20100628:01--ChIP:XZ:20100621:01:Duodenum mucosa:H3K4Me1
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.3743
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.3882
****************
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: GSM621403_BI.Duodenum_Mucosa.H3K4me1.61.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100628:01--ChIP:XZ:20100621:01:Duodenum mucosa:H3K4Me1.hg19.level.1
ANALYSIS TITLE: Mapping of Duodenum Mucosa Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me1 ChIP-Seq on Duodenum Mucosa, Donor 61 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.4571
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: 0.1111
FINDPEAKS_PERCENTILE: 19
HOTSPOT_SCORE: 0.2163
HOTSPOT_PERCENTILE: 16
IROC_SCORE: 0.9475
IROC_PERCENTILE: 17
POISSON_SCORE: 0.4757
POISSON_PERCENTILE: 21

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

ANALYSIS FILE NAME: GSM621403_BI.Duodenum_Mucosa.H3K4me1.61.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100628:01--ChIP:XZ:20100621:01:Duodenum mucosa:H3K4Me1.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Duodenum Mucosa Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me1 ChIP-Seq read mappings from Duodenum Mucosa, Donor 61 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.4845
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: DM H3K4me1 61
BROWSER_TRACK_DESCRIPTION: BI Duodenum Mucosa Histone H3K4me1 Donor 61 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED: 43
FINDPEAKS_SCORE: 0.1111
FINDPEAKS_PERCENTILE: 19
HOTSPOT_SCORE: 0.2163
HOTSPOT_PERCENTILE: 16
IROC_SCORE: 0.9475
IROC_PERCENTILE: 17
POISSON_SCORE: 0.4757
POISSON_PERCENTILE: 21

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

source_name: Primary duodenum mucosa tissue; Lib:XZ:20100628:01--ChIP:XZ:20100621:01:Duodenum mucosa:H3K4Me1

value: surgery

value: "NL mucosa,... Pancreatitis/IPMN"

value: genomic DNA

value: mucosa

value: Male

value: Primary Tissue

value: duodenum

value: 76 years

value: Protein A-Sepharose 4B

value: 10 million cells

value: SDS lysis

value: 70 ul bed volume

value: Abcam

value: Histone H3K4me1

value: Bioruptor


title: ChIP-Seq analysis of H3K4me3 in human Treg cells; Lib:RI:20100422:16--ChIP:MA:20100416:16:Treg:H3K4Me3

description:
sample_term_id: CL_0000815
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib:RI:20100422:16--ChIP:MA:20100416:16:Treg:H3K4Me3
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.3728
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.3893
****************
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: GSM621388_BI.Treg_Primary_Cells.H3K4me3.20.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:RI:20100422:16--ChIP:MA:20100416:16:Treg:H3K4Me3.hg19.level.1
ANALYSIS TITLE: Mapping of Treg Primary Cells Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me3 ChIP-Seq on Treg Primary Cells, Donor 20 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.4599
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_H3K4me3_EXPERIMENTS_SCORED: 62
FINDPEAKS_SCORE: 0.537
FINDPEAKS_PERCENTILE: 77
HOTSPOT_SCORE: 0.4929
HOTSPOT_PERCENTILE: 69
IROC_SCORE: 0.9994
IROC_PERCENTILE: 56
POISSON_SCORE: 0.5939
POISSON_PERCENTILE: 74

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

ANALYSIS FILE NAME: GSM621388_BI.Treg_Primary_Cells.H3K4me3.20.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:RI:20100422:16--ChIP:MA:20100416:16:Treg:H3K4Me3.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Treg Primary Cells Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me3 ChIP-Seq read mappings from Treg Primary Cells, Donor 20 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.4873
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: Treg H3K4me3 20
BROWSER_TRACK_DESCRIPTION: BI Treg Primary Cells Histone H3K4me3 Donor 20 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED: 62
FINDPEAKS_SCORE: 0.537
FINDPEAKS_PERCENTILE: 77
HOTSPOT_SCORE: 0.4929
HOTSPOT_PERCENTILE: 69
IROC_SCORE: 0.9994
IROC_PERCENTILE: 56
POISSON_SCORE: 0.5939
POISSON_PERCENTILE: 74

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

source_name: "Treg cells derived from fom pooled leukopacks by Ficoll sedimentation, magnetic bead purification, and FACS"; Lib:RI:20100422:16--ChIP:MA:20100416:16:Treg:H3K4Me3

value: CD4+ CD25high IL7R-

value: Treg

value: Unknown

value: Primary Cell

value: Whitehead Institute

value: Millipore

value: Histone H3K4me3


title: Bisulfite-Seq analysis of RRBS824 derived from human colonic mucosa cells; RRBS824

description:
sample_term_id: UBERON_0000317
assay_term_id: OBI_0001862
nucleic_acid_term_id: SO_0000352
Design description: RRBS REMC Sequencing on Illumina
Library name: RRBS824
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.3947
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.3354
****************
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: GSM621728_BI.Colonic_Mucosa.RRBS.32.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: RRBS824.hg19.level.2
ANALYSIS TITLE: Methylation Proportion Graphs of Colonic Mucosa RRBS Data
ANALYSIS DESCRIPTION: Illumina RRBS read mappings from Colonic Mucosa, Donor 32 were processed into graphs of methylation proportions. Methylation proportions were calculated as (methylated calls / (methylated calls + unmethylated calls)) for all CpGs covered by at least 4 reads.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.5218
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Reduced Representation Bisulfite-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19 MspI restriction fragments 40-220bp
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
GENOMIC_WINDOW: 2bp containing CpGs
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: CM RRBS 32
BROWSER_TRACK_DESCRIPTION: BI Colonic Mucosa RRBS Donor 32 EA Release 2
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 98.86

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

source_name: Primary colonic mucosal tissue; RRBS824

value: surgery

value: "normal mucosa, adeno. CA of Cecum"

value: genomic DNA

value: mucosa

value: white

value: Female

value: Primary Tissue

value: colon

value: MGH Pathology

value: 2x5hrs Epitect Kit

value: 20 ng

value: T4 Ligase (2,000U/ul) 16C o/n

value: 5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT

value: 5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT

value: Standard Protocol (Smith et al., Methods 48, 226-232)

value: DNA Methylation

value: Smith et al., Methods 48, 226-232

value: Gel size selection

value: Pfu Turbo Cx hot start


title: Bisulfite-Seq analysis of RRBS827 derived from human Skeletal muscle cells; RRBS827

description:
sample_term_id: UBERON_0001134
assay_term_id: OBI_0001862
nucleic_acid_term_id: SO_0000352
Design description: RRBS REMC Sequencing on Illumina
Library name: RRBS827
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.3946
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.3355
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

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

ANALYSIS FILE NAME: GSM621727_BI.Skeletal_Muscle.RRBS.63.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: RRBS827.hg19.level.2
ANALYSIS TITLE: Methylation Proportion Graphs of Skeletal Muscle RRBS Data
ANALYSIS DESCRIPTION: Illumina RRBS read mappings from Skeletal Muscle, Donor 63 were processed into graphs of methylation proportions. Methylation proportions were calculated as (methylated calls / (methylated calls + unmethylated calls)) for all CpGs covered by at least 4 reads.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.5219
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Reduced Representation Bisulfite-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19 MspI restriction fragments 40-220bp
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
GENOMIC_WINDOW: 2bp containing CpGs
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: SM RRBS 63
BROWSER_TRACK_DESCRIPTION: BI Skeletal Muscle RRBS Donor 63 EA Release 2
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 99.08

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

source_name: Primary skeletal muscle tissue; RRBS827

value: surgery

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

value: genomic DNA

value: Skeletal muscle

value: Male

value: unknown

value: 54 years


title: Bisulfite-Seq analysis of RRBS534 derived from human H1 cells; RRBS534

description:
sample_term_id: EFO_0003042
assay_term_id: OBI_0001862
nucleic_acid_term_id: SO_0000352
Design description: RRBS REMC Sequencing on Illumina
Library name: RRBS534/RRBS535
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.3899
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.3906
****************
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: GSM621763_BI.H1.RRBS.RRBS534-535.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: RRBS534-RRBS535.hg19.level.2
ANALYSIS TITLE: Methylation Proportion Graphs of H1 Cell Line RRBS Data
ANALYSIS DESCRIPTION: Illumina RRBS read mappings from the H1 Cell Line, Libraries RRBS534-535 were processed into graphs of methylation proportions. Methylation proportions were calculated as (methylated calls / (methylated calls + unmethylated calls)) for all CpGs covered by at least 4 reads.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.5236
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Reduced Representation Bisulfite-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19 MspI restriction fragments 40-220bp
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
GENOMIC_WINDOW: 2bp containing CpGs
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: H1 RRBS 34
BROWSER_TRACK_DESCRIPTION: BI H1 Cell Line RRBS Libraries RRBS534-535 EA Release 2
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 97.56

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

source_name: H1 (WA01) embryonic stem cells; NIH Approval # NIHhESC-10-0043; RRBS534

tag: lineage

value: embrionic stem cell

tag: medium

value: TESR

tag: passage

tag: line

tag: batch

value: Cell Line

value: undifferentiated

tag: Sex

value: Cellular Dynamics

value: 2x5hrs Epitect Kit


title: Bisulfite-Seq analysis of RRBS768 derived from human HUES1 cells; RRBS768

description:
sample_term_id: NTR_0000839
assay_term_id: OBI_0001862
nucleic_acid_term_id: SO_0000352
Design description: RRBS REMC Sequencing on Illumina
Library name: RRBS768/RRBS769/RRBS770/RRBS771
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.3953
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.3961
****************
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: GSM621734_BI.HUES1.RRBS.RRBS768-771.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: RRBS768-RRBS769-RRBS770-RRBS771.hg19.level.2
ANALYSIS TITLE: Methylation Proportion Graphs of HUES1 Cell Line RRBS Data
ANALYSIS DESCRIPTION: Illumina RRBS read mappings from the HUES1 Cell Line, Libraries RRBS768-771 were processed into graphs of methylation proportions. Methylation proportions were calculated as (methylated calls / (methylated calls + unmethylated calls)) for all CpGs covered by at least 4 reads.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.5248
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Reduced Representation Bisulfite-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19 MspI restriction fragments 40-220bp
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
GENOMIC_WINDOW: 2bp containing CpGs
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: HUES1 RRBS 68
BROWSER_TRACK_DESCRIPTION: BI HUES1 Cell Line RRBS Libraries RRBS768-771 EA Release 2
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 97.9

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

source_name: Harvard University Embryonic Stem Cells; RRBS768

value: KSR

value: p28 or p29

value: HUES_1p28 ES

value: Female

value: Harvard University

value: 20 ng

value: T4 Ligase (2,000U/ul) 16C o/n

value: 5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT

value: 5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT

value: Standard Protocol (Smith et al., Methods 48, 226-232)

value: DNA Methylation


title: Bisulfite-Seq analysis of RRBS826 derived from human Skeletal muscle cells; RRBS826

description:
sample_term_id: UBERON_0001134
assay_term_id: OBI_0001862
nucleic_acid_term_id: SO_0000352
Design description: RRBS REMC Sequencing on Illumina
Library name: RRBS826
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.3945
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.3356
****************
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: GSM621726_BI.Skeletal_Muscle.RRBS.62.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: RRBS826.hg19.level.2
ANALYSIS TITLE: Methylation Proportion Graphs of Skeletal Muscle RRBS Data
ANALYSIS DESCRIPTION: Illumina RRBS read mappings from Skeletal Muscle, Donor 62 were processed into graphs of methylation proportions. Methylation proportions were calculated as (methylated calls / (methylated calls + unmethylated calls)) for all CpGs covered by at least 4 reads.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.5217
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Reduced Representation Bisulfite-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19 MspI restriction fragments 40-220bp
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
GENOMIC_WINDOW: 2bp containing CpGs
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: SM RRBS 62
BROWSER_TRACK_DESCRIPTION: BI Skeletal Muscle RRBS Donor 62 EA Release 2
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 98.77

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

source_name: Primary skeletal muscle tissue; RRBS826

value: surgery

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

value: genomic DNA

value: Skeletal muscle

value: white

value: Primary Tissue

value: unknown

value: MGH Pathology

value: 72 years

value: Smith et al., Methods 48, 226-232

value: Gel size selection

value: Pfu Turbo Cx hot start


title: Bisulfite-Seq analysis of RRBS354 derived from human hiPS-11a cells; RRBS354

description:
sample_term_id: NTR_0001159
assay_term_id: OBI_0001862
nucleic_acid_term_id: SO_0000352
Design description: RRBS REMC Sequencing on Illumina
Library name: RRBS354/RRBS355
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.3938
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.3972
****************
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: GSM621719_BI.iPS-11a.RRBS.RRBS354-355.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: RRBS354-RRBS355.hg19.level.2
ANALYSIS TITLE: Methylation Proportion Graphs of iPS-11a Cell Line RRBS Data
ANALYSIS DESCRIPTION: Illumina RRBS read mappings from the iPS-11a Cell Line, Libraries RRBS354-355 were processed into graphs of methylation proportions. Methylation proportions were calculated as (methylated calls / (methylated calls + unmethylated calls)) for all CpGs covered by at least 4 reads.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.5223
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Reduced Representation Bisulfite-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19 MspI restriction fragments 40-220bp
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
GENOMIC_WINDOW: 2bp containing CpGs
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: iPS11a RRBS 54
BROWSER_TRACK_DESCRIPTION: BI iPS-11a Cell Line RRBS Libraries RRBS354-355 EA Release 2
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 97.34

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

source_name: IPS cell line 11a; RRBS354

value: induced pluripotent cells

value: KSR

value: hiPS cells(3F)/11a(1)-P22

value: Cell Line

value: undifferentiated

value: Male

value: Harvard University

value: 2x5hrs Epitect Kit

value: 20 ng

value: T4 Ligase (2,000U/ul) 16C o/n


title: Bisulfite-Seq analysis of RRBS540 derived from human HUES9 cells; RRBS540

description:
sample_term_id: NTR_0000843
assay_term_id: OBI_0001862
nucleic_acid_term_id: SO_0000352
Design description: RRBS REMC Sequencing on Illumina
Library name: RRBS540/RRBS541
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.3937
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.3966
****************
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: GSM621718_BI.HUES9.RRBS.RRBS540-541.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: RRBS540-RRBS541.hg19.level.2
ANALYSIS TITLE: Methylation Proportion Graphs of HUES9 Cell Line RRBS Data
ANALYSIS DESCRIPTION: Illumina RRBS read mappings from the HUES9 Cell Line, Libraries RRBS540-541 were processed into graphs of methylation proportions. Methylation proportions were calculated as (methylated calls / (methylated calls + unmethylated calls)) for all CpGs covered by at least 4 reads.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.5241
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Reduced Representation Bisulfite-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19 MspI restriction fragments 40-220bp
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
GENOMIC_WINDOW: 2bp containing CpGs
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: HUES9 RRBS 40
BROWSER_TRACK_DESCRIPTION: BI HUES9 Cell Line RRBS Libraries RRBS540-541 EA Release 2
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 97.86

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

source_name: Harvard University Embryonic Stem Cells; RRBS540

value: embrionic stem cell

value: genomic DNA

value: Female

value: 5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT

value: 5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT

value: Standard Protocol (Smith et al., Methods 48, 226-232)

value: DNA Methylation


title: Bisulfite-Seq analysis of RRBS356 derived from human hiPS-15b cells; RRBS356

description:
sample_term_id: NTR_0001162
assay_term_id: OBI_0001862
nucleic_acid_term_id: SO_0000352
Design description: RRBS REMC Sequencing on Illumina
Library name: RRBS356/RRBS357/Solexa-11964
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.3940
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.3965
****************
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: GSM621721_BI.iPS-15b.RRBS.RRBS356-357.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: 30HD2AAXX090607-1-S-RRBS356-RRBS357.hg19.level.2
ANALYSIS TITLE: Methylation Proportion Graphs of iPS-15b Cell Line RRBS Data
ANALYSIS DESCRIPTION: Illumina RRBS read mappings from the iPS-15b Cell Line, Libraries RRBS356-357 were processed into graphs of methylation proportions. Methylation proportions were calculated as (methylated calls / (methylated calls + unmethylated calls)) for all CpGs covered by at least 4 reads.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.5237
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Reduced Representation Bisulfite-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19 MspI restriction fragments 40-220bp
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
GENOMIC_WINDOW: 2bp containing CpGs
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: iPS15b RRBS 56
BROWSER_TRACK_DESCRIPTION: BI iPS-15b Cell Line RRBS Libraries RRBS356-357 EA Release 2
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 97.97

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

source_name: IPS cell line 15b; RRBS356

value: induced pluripotent cells

value: Smith et al., Methods 48, 226-232

value: Gel size selection

value: Pfu Turbo Cx hot start