title: Bisulfite-Seq analysis of RRBS420 derived from human hiPS-11b cells; RRBS420

description:
sample_term_id: NTR_0001160
assay_term_id: OBI_0001862
nucleic_acid_term_id: SO_0000352
Design description: RRBS REMC Sequencing on Illumina
Library name: RRBS420/RRBS421
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.3934
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.3964
****************
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: GSM621715_BI.iPS-11b.RRBS.RRBS420-421.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: RRBS420-RRBS421.hg19.level.2
ANALYSIS TITLE: Methylation Proportion Graphs of iPS-11b Cell Line RRBS Data
ANALYSIS DESCRIPTION: Illumina RRBS read mappings from the iPS-11b Cell Line, Libraries RRBS420-421 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.5246
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: iPS11b RRBS 20
BROWSER_TRACK_DESCRIPTION: BI iPS-11b Cell Line RRBS Libraries RRBS420-421 EA Release 2
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 98.82

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

source_name: induced pleuripotent 11b stem cell line; RRBS420

value: KSR

value: Cell Line

value: undifferentiated


title: Bisulfite-Seq analysis of RRBS589 derived from human hiPS-17b cells; RRBS589

status: Public on Nov 11 2010

type: SRA

city: Cambridge

first: BROAD

last: INSTITUTE

state: MA

country: USA

institute: Broad Institute

description:
sample_term_id: NTR_0001164
assay_term_id: OBI_0001862
nucleic_acid_term_id: SO_0000352
Design description: RRBS REMC Sequencing on Illumina
Library name: RRBS589/RRBS590
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.3933
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.3957
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

library_source: genomic

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

ANALYSIS FILE NAME: GSM621714_BI.iPS-17b.RRBS.RRBS589-590.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: RRBS589-RRBS590.hg19.level.2
ANALYSIS TITLE: Methylation Proportion Graphs of iPS-17b Cell Line RRBS Data
ANALYSIS DESCRIPTION: Illumina RRBS read mappings from the iPS-17b Cell Line, Libraries RRBS589-590 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.5225
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: iPS17b RRBS 89
BROWSER_TRACK_DESCRIPTION: BI iPS-17b Cell Line RRBS Libraries RRBS589-590 EA Release 2
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 98.16

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

molecule: genomic DNA

organism: Homo sapiens

source_name: induced pleuripotent 17b stem cell line; RRBS589

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

tag: lineage

value: induced pluripotent cells

tag: medium

tag: molecule

value: genomic DNA

tag: disease

tag: passage

tag: line

tag: batch

tag: Sex

value: Female

value: Harvard University

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 RRBS569 derived from human HUES3 cells; RRBS569

description:
sample_term_id: NTR_0000840
assay_term_id: OBI_0001862
nucleic_acid_term_id: SO_0000352
Design description: RRBS REMC Sequencing on Illumina
Library name: RRBS569/RRBS571
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.3903
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.3905
****************
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: GSM621767_BI.HUES3.RRBS.RRBS569-571.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: RRBS569-RRBS571.hg19.level.2
ANALYSIS TITLE: Methylation Proportion Graphs of HUES3 Cell Line RRBS Data
ANALYSIS DESCRIPTION: Illumina RRBS read mappings from the HUES3 Cell Line, Libraries RRBS569-571 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.5249
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: HUES3 RRBS 69
BROWSER_TRACK_DESCRIPTION: BI HUES3 Cell Line RRBS Libraries RRBS569-571 EA Release 2
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 97.86

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

source_name: Harvard University Embryonic Stem Cells; RRBS569

value: embrionic stem cell

value: KSR

value: Male


title: ChIP-Seq analysis of H3K9me3 in human Treg cells; Lib:RI:20100422:18--ChIP:MA:20100416:18:Treg:H3K9Me3

status: Public on Nov 12 2010

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:20100422:18--ChIP:MA:20100416:18:Treg:H3K9Me3
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.3729
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: GSM621389_BI.Treg_Primary_Cells.H3K9me3.20.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:RI:20100422:18--ChIP:MA:20100416:18:Treg:H3K9Me3.hg19.level.1
ANALYSIS TITLE: Mapping of Treg Primary Cells Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K9me3 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.4565
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: 0.1284
FINDPEAKS_PERCENTILE: 63
HOTSPOT_SCORE: 0.1752
HOTSPOT_PERCENTILE: 53
IROC_SCORE: 0.8499
IROC_PERCENTILE: 58
POISSON_SCORE: 0.5746
POISSON_PERCENTILE: 95

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

ANALYSIS FILE NAME: GSM621389_BI.Treg_Primary_Cells.H3K9me3.20.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:RI:20100422:18--ChIP:MA:20100416:18:Treg:H3K9Me3.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Treg Primary Cells Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K9me3 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.4839
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 H3K9me3 20
BROWSER_TRACK_DESCRIPTION: BI Treg Primary Cells Histone H3K9me3 Donor 20 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED: 59
FINDPEAKS_SCORE: 0.1284
FINDPEAKS_PERCENTILE: 63
HOTSPOT_SCORE: 0.1752
HOTSPOT_PERCENTILE: 53
IROC_SCORE: 0.8499
IROC_PERCENTILE: 58
POISSON_SCORE: 0.5746
POISSON_PERCENTILE: 95

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

source_name: "Treg cells derived from fom pooled leukopacks by Ficoll sedimentation, magnetic bead purification, and FACS"; Lib:RI:20100422:18--ChIP:MA:20100416:18:Treg:H3K9Me3

extract_protocol: Library construction protocol: Single read - Illumina

tag: markers

value: CD4+ CD25high IL7R-

value: Treg

value: Unknown

value: Primary Cell

value: Whitehead Institute

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: Bisulfite-Seq analysis of RRBS823 derived from human rectal mucosa cells; RRBS823

description:
sample_term_id: UBERON_0003346
assay_term_id: OBI_0001862
nucleic_acid_term_id: SO_0000352
Design description: RRBS REMC Sequencing on Illumina
Library name: RRBS823
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.3921
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.3351
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

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

ANALYSIS FILE NAME: GSM621702_BI.Rectal_Mucosa.RRBS.31.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: RRBS823.hg19.level.2
ANALYSIS TITLE: Methylation Proportion Graphs of Rectal Mucosa RRBS Data
ANALYSIS DESCRIPTION: Illumina RRBS read mappings from Rectal Mucosa, Donor 31 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.5215
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: RM RRBS 31
BROWSER_TRACK_DESCRIPTION: BI Rectal Mucosa RRBS Donor 31 EA Release 2
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 98.89

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

source_name: Primary rectal mucosal tissue; RRBS823

value: surgery

value: "normal mucosa, diverticular disease"

value: genomic DNA

value: mucosa

value: white

value: Female

value: Primary Tissue

value: rectum

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


title: Bisulfite-Seq analysis of RRBS418 derived from human hiPS-17a cells; RRBS418

description:
sample_term_id: NTR_0001163
assay_term_id: OBI_0001862
nucleic_acid_term_id: SO_0000352
Design description: RRBS REMC Sequencing on Illumina
Library name: RRBS418/RRBS419
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.3918
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.3969
****************
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: GSM621699_BI.iPS-17a.RRBS.RRBS418-419.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: RRBS418-RRBS419.hg19.level.2
ANALYSIS TITLE: Methylation Proportion Graphs of iPS-17a Cell Line RRBS Data
ANALYSIS DESCRIPTION: Illumina RRBS read mappings from the iPS-17a Cell Line, Libraries RRBS418-419 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.5250
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: iPS17a RRBS 18
BROWSER_TRACK_DESCRIPTION: BI iPS-17a Cell Line RRBS Libraries RRBS418-419 EA Release 2
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 98.1

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

source_name: induced pleuripotent 17a stem cell line; RRBS418

value: induced pluripotent cells

value: KSR

value: Cell Line

value: undifferentiated

value: Harvard University

value: Pfu Turbo Cx hot start


title: Bisulfite-Seq analysis of RRBS819 derived from human adult kidney cells; RRBS819

description:
sample_term_id: UBERON_0002113
assay_term_id: OBI_0001862
nucleic_acid_term_id: SO_0000352
Design description: RRBS REMC Sequencing on Illumina
Library name: RRBS819
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.3932
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.3349
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

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

ANALYSIS FILE NAME: GSM621713_BI.Adult_Kidney.RRBS.27.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: RRBS819-RRBS821.hg19.level.2
ANALYSIS TITLE: Methylation Proportion Graphs of Adult Kidney RRBS Data
ANALYSIS DESCRIPTION: Illumina RRBS read mappings from Adult Kidney, Donor 27 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.6834
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 3
BROWSER_TRACK_NAME: AK RRBS 27
BROWSER_TRACK_DESCRIPTION: BI Adult Kidney RRBS Donor 27 EA Release 3
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 99.53

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

source_name: Primary kidney tissue; RRBS819

value: surgery

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

value: genomic DNA

value: Adult Kidney

value: white

value: Male

value: Primary Tissue

value: kidney


title: Bisulfite-Seq analysis of RRBS536 derived from human HUES6 cells; RRBS536

description:
sample_term_id: NTR_0000841
assay_term_id: OBI_0001862
nucleic_acid_term_id: SO_0000352
Design description: RRBS REMC Sequencing on Illumina
Library name: RRBS536/RRBS537
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.3919
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.3967
****************
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: GSM621700_BI.HUES6.RRBS.RRBS536-537.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: RRBS536-RRBS537.hg19.level.2
ANALYSIS TITLE: Methylation Proportion Graphs of HUES6 Cell Line RRBS Data
ANALYSIS DESCRIPTION: Illumina RRBS read mappings from the HUES6 Cell Line, Libraries RRBS536-537 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.5230
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: HUES6 RRBS 36
BROWSER_TRACK_DESCRIPTION: BI HUES6 Cell Line RRBS Libraries RRBS536-537 EA Release 2
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 97.85

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

source_name: Harvard University Embryonic Stem Cells; RRBS536

value: embrionic stem cell

value: HUES 6

value: Female

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


title: Bisulfite-Seq analysis of RRBS556 derived from human HUES49 cells; RRBS556

description:
sample_term_id: NTR_0000849
assay_term_id: OBI_0001862
nucleic_acid_term_id: SO_0000352
Design description: RRBS REMC Sequencing on Illumina
Library name: RRBS556/RRBS557
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.4028
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.4033
****************
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: GSM621603_BI.HUES49.RRBS.RRBS556-557.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: RRBS556-RRBS557.hg19.level.2
ANALYSIS TITLE: Methylation Proportion Graphs of HUES49 Cell Line RRBS Data
ANALYSIS DESCRIPTION: Illumina RRBS read mappings from the HUES49 Cell Line, Libraries RRBS556-557 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.5238
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: HUES49 RRBS 56
BROWSER_TRACK_DESCRIPTION: BI HUES49 Cell Line RRBS Libraries RRBS556-557 EA Release 2
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 97.35

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

source_name: Harvard University Embryonic Stem Cells; RRBS556

value: KSR

value: Cell Line

value: undifferentiated

value: Harvard University

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

value: Gel size selection

value: Pfu Turbo Cx hot start


title: Bisulfite-Seq analysis of RRBS542 derived from human HUES28 cells; RRBS542

description:
sample_term_id: NTR_0000845
assay_term_id: OBI_0001862
nucleic_acid_term_id: SO_0000352
Design description: RRBS REMC Sequencing on Illumina
Library name: RRBS542/RRBS543
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.4031
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.4032
****************
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: GSM621606_BI.HUES28.RRBS.RRBS542-543.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: RRBS542-RRBS543.hg19.level.2
ANALYSIS TITLE: Methylation Proportion Graphs of HUES28 Cell Line RRBS Data
ANALYSIS DESCRIPTION: Illumina RRBS read mappings from the HUES28 Cell Line, Libraries RRBS542-543 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.5229
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: HUES28 RRBS 42
BROWSER_TRACK_DESCRIPTION: BI HUES28 Cell Line RRBS Libraries RRBS542-543 EA Release 2
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 98.08

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

source_name: Harvard University Embryonic Stem Cells; RRBS542

value: embrionic stem cell

value: genomic DNA


title: Bisulfite-Seq analysis of RRBS368 derived from human hES I3 TESR cells; 42LNLAAXX090804-1-S

description:
sample_term_id: NTR_0000836
assay_term_id: OBI_0001862
nucleic_acid_term_id: SO_0000352
Design description: RRBS REMC Sequencing on Illumina
Library name: Solexa-13317/Solexa-13235
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.2355
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.2350
****************
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: GSM621345_BI.ES-I3.RRBS.RRBS368-369.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: 42LNLAAXX090804-1-S-42M0DAAXX090728-8-S.hg19.level.2
ANALYSIS TITLE: Methylation Proportion Graphs of ES-I3 Cell Line RRBS Data
ANALYSIS DESCRIPTION: Illumina RRBS read mappings from the ES-I3 Cell Line, Libraries RRBS368-369 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.5226
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: ESI3  RRBS 68
BROWSER_TRACK_DESCRIPTION: BI ES-I3  Cell Line RRBS Libraries RRBS368-369 EA Release 2
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 98.89

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

source_name: I3(eye three) stem cells; 42LNLAAXX090804-1-S

value: hES I3 TESR

value: TESR

value: Female


title: Bisulfite-Seq analysis of RRBS360 derived from human H1 cells; 42R88AAXX091028-3-S

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: Solexa-13232/Solexa-13233
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.1904
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.1903
****************
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: GSM621357_BI.H1.RRBS.RRBS360-361.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: 42R88AAXX091028-3-S-617F7AAXX091106-2-S-42M0DAAXX090728-6-S-617F7AAXX091106-3-S.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 RRBS360-361 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.5243
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 60
BROWSER_TRACK_DESCRIPTION: BI H1 Cell Line RRBS Libraries RRBS360-361 EA Release 2
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 98.75

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

source_name: H1 stem cells from Cellular Dynamics; 42R88AAXX091028-3-S

extract_protocol: Library construction protocol: Standard Protocol (Smith et al., Methods 48, 226-232)

value: Cellular Dynamics

value: Male

value: 20 ng

value: 5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG

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

value: 2x5hrs Epitect Kit


title: Bisulfite-Seq analysis of RRBS772 derived from human HUES8 cells; RRBS772

description:
sample_term_id: NTR_0000842
assay_term_id: OBI_0001862
nucleic_acid_term_id: SO_0000352
Design description: RRBS REMC Sequencing on Illumina
Library name: RRBS772/RRBS772/RRBS775
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.3928
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.3958
****************
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: GSM621709_BI.HUES8.RRBS.RRBS772-775.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: RRBS772-RRBS773-RRBS774-RRBS775.hg19.level.2
ANALYSIS TITLE: Methylation Proportion Graphs of HUES8 Cell Line RRBS Data
ANALYSIS DESCRIPTION: Illumina RRBS read mappings from the HUES8 Cell Line, Libraries RRBS772-775 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.5235
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: HUES8 RRBS 72
BROWSER_TRACK_DESCRIPTION: BI HUES8 Cell Line RRBS Libraries RRBS772-775 EA Release 2
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 98.19

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

source_name: Harvard University Embryonic Stem Cells; RRBS772

value: KSR

value: p29 or p30

value: HUES_8p29 ES

value: Cell Line

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 RRBS350 derived from human WA-7 cells; 30J03AAXX090718-7-S

description:
sample_term_id: NTR_0000837
assay_term_id: OBI_0001862
nucleic_acid_term_id: SO_0000352
Design description: RRBS REMC Sequencing on Illumina
Library name: Solexa-11958/Solexa-11959
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.2357
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.2351
****************
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: GSM621347_BI.ES-WA7.RRBS.RRBS350-351.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: 30J03AAXX090718-7-S-30HD2AAXX090607-3-S-30J03AAXX090718-2-S.hg19.level.2
ANALYSIS TITLE: Methylation Proportion Graphs of ES-WA7 Cell Line RRBS Data
ANALYSIS DESCRIPTION: Illumina RRBS read mappings from the ES-WA7 Cell Line, Libraries RRBS350-351 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.5224
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: ESWA7 RRBS 50
BROWSER_TRACK_DESCRIPTION: BI ES-WA7 Cell Line RRBS Libraries RRBS350-351 EA Release 2
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 98.3

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

source_name: WA7 stem cells; 30J03AAXX090718-7-S

value: genomic DNA

value: Harvard University

value: embrionic stem cell

value: undifferentiated

value: Pfu Turbo Cx hot start

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

value: Gel size selection


title: Bisulfite-Seq analysis of RRBS550 derived from human HUES53 cells; RRBS550

description:
sample_term_id: NTR_0000850
assay_term_id: OBI_0001862
nucleic_acid_term_id: SO_0000352
Design description: RRBS REMC Sequencing on Illumina
Library name: RRBS550/RRBS551
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.4026
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.4036
****************
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: GSM621601_BI.HUES53.RRBS.RRBS550-551.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: RRBS550-RRBS551.hg19.level.2
ANALYSIS TITLE: Methylation Proportion Graphs of HUES53 Cell Line RRBS Data
ANALYSIS DESCRIPTION: Illumina RRBS read mappings from the HUES53 Cell Line, Libraries RRBS550-551 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.5254
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: HUES53 RRBS 50
BROWSER_TRACK_DESCRIPTION: BI HUES53 Cell Line RRBS Libraries RRBS550-551 EA Release 2
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 98.0

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

source_name: Harvard University Embryonic Stem Cells; RRBS550

value: Male

value: 20 ng

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


title: Bisulfite-Seq analysis of RRBS479 derived from human pancreatic islets normal cells; 42ND9AAXX091218-8-S

description:
sample_term_id: UBERON_0000016
assay_term_id: OBI_0001862
nucleic_acid_term_id: SO_0000352
Design description: RRBS REMC Sequencing on Illumina
Library name: Solexa-16805/Solexa-16804
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.2326
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.2307
****************
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: GSM621567_BI.Pancreatic_Islets.RRBS.pancreatic_islets_normal_0_0_00.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: 42ND9AAXX091218-8-S-42ND9AAXX091218-7-S.hg19.level.2
ANALYSIS TITLE: Methylation Proportion Graphs of Pancreatic Islets RRBS Data
ANALYSIS DESCRIPTION: Illumina RRBS read mappings from Pancreatic Islets, Donor pancreatic islets normal_0/0/00 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.5214
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: PI RRBS 0
BROWSER_TRACK_DESCRIPTION: BI Pancreatic Islets RRBS Donor pancreatic islets normal_0/0/00 EA Release 2
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 99.45

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

source_name: pancreatic islets from a normal donor; 42ND9AAXX091218-8-S

value: Islet Cell Resource Center

value: Primary Cell

value: Pancreatic Islets

value: pancreatic islets normal_0/0/00

value: not passaged

value: 2x5hrs Epitect Kit


title: Bisulfite-Seq analysis of RRBS514 derived from human CD34 cells; 42TY1AAXX100126-5-S

description:
sample_term_id: CL_0000837
assay_term_id: OBI_0001862
nucleic_acid_term_id: SO_0000352
Design description: RRBS REMC Sequencing on Illumina
Library name: Solexa-17915/Solexa-17942
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.2320
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.2299
****************
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: GSM621561_BI.CD34_Primary_Cells.RRBS.CD34_0_0_00.RRBS514-515.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: 42TY1AAXX100126-5-S-42TWHAAXX100222-2-S.hg19.level.2
ANALYSIS TITLE: Methylation Proportion Graphs of CD34 Primary Cells RRBS Data
ANALYSIS DESCRIPTION: Illumina RRBS read mappings from CD34 Primary Cells, Donor CD34_0/0/00, Libraries RRBS514-515 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.5210
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: CD34 RRBS 14
BROWSER_TRACK_DESCRIPTION: BI CD34 Primary Cells RRBS Donor CD34_0/0/00 Libraries RRBS514-515 EA Release 2
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 99.52

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

source_name: flow sorted CD34+ cells from cord blood; 42TY1AAXX100126-5-S

value: FHCRC

value: CD34 Primary Cells

value: Unknown

value: DNA Methylation

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

value: 5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT

value: 5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT


title: Bisulfite-Seq analysis of RRBS519 derived from human HUES63 cells; RRBS519

description:
sample_term_id: NTR_0000852
assay_term_id: OBI_0001862
nucleic_acid_term_id: SO_0000352
Design description: RRBS REMC Sequencing on Illumina
Library name: RRBS519
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.4016
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.4039
****************
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: GSM621591_BI.HUES63.RRBS.RRBS519.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: RRBS519.hg19.level.2
ANALYSIS TITLE: Methylation Proportion Graphs of HUES63 Cell Line RRBS Data
ANALYSIS DESCRIPTION: Illumina RRBS read mappings from the HUES63 Cell Line, Library RRBS519 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.5231
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: HUES63 RRBS 19
BROWSER_TRACK_DESCRIPTION: BI HUES63 Cell Line RRBS Library RRBS519 EA Release 2
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 98.56

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

source_name: Harvard University Embryonic Stem Cells; RRBS519

value: embrionic stem cell

value: KSR

value: genomic DNA

value: Cell Line

value: undifferentiated

value: Harvard University

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

value: Gel size selection

value: Pfu Turbo Cx hot start


title: Bisulfite-Seq analysis of RRBS554 derived from human HUES66 cells; RRBS554

description:
sample_term_id: NTR_0000855
assay_term_id: OBI_0001862
nucleic_acid_term_id: SO_0000352
Design description: RRBS REMC Sequencing on Illumina
Library name: RRBS554
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.4017
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.4038
****************
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: GSM621592_BI.HUES66.RRBS.RRBS554.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: RRBS554.hg19.level.2
ANALYSIS TITLE: Methylation Proportion Graphs of HUES66 Cell Line RRBS Data
ANALYSIS DESCRIPTION: Illumina RRBS read mappings from the HUES66 Cell Line, Library RRBS554 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.5227
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: HUES66 RRBS 54
BROWSER_TRACK_DESCRIPTION: BI HUES66 Cell Line RRBS Library RRBS554 EA Release 2
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 97.65

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

source_name: Harvard University Embryonic Stem Cells; RRBS554

value: Female

value: 2x5hrs Epitect Kit

value: 20 ng

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


title: Bisulfite-Seq analysis of RRBS512 derived from human CD19 cells; 42TY1AAXX100126-6-S

description:
sample_term_id: CL_0000236
assay_term_id: OBI_0001862
nucleic_acid_term_id: SO_0000352
Design description: RRBS REMC Sequencing on Illumina
Library name: Solexa-17913/Solexa-17940
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.2319
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.2303
****************
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: GSM621560_BI.CD19_Primary_Cells.RRBS.CD19_0_0_00.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: 42TY1AAXX100126-6-S-42TWHAAXX100222-1-S.hg19.level.2
ANALYSIS TITLE: Methylation Proportion Graphs of CD19 Primary Cells RRBS Data
ANALYSIS DESCRIPTION: Illumina RRBS read mappings from CD19 Primary Cells, Donor CD19_0/0/00 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.5213
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: CD19 RRBS 0
BROWSER_TRACK_DESCRIPTION: BI CD19 Primary Cells RRBS Donor CD19_0/0/00 EA Release 2
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 99.37

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

source_name: flow sorted CD19+ cells from cord blood; 42TY1AAXX100126-6-S

value: FHCRC

value: Primary Cell

value: CD19 Primary Cells

value: not passaged

value: DNA Methylation


title: Bisulfite-Seq analysis of RRBS533 derived from human CD34 cells; 42U16AAXX100205-7-S

description:
sample_term_id: CL_0000837
assay_term_id: OBI_0001862
nucleic_acid_term_id: SO_0000352
Design description: RRBS REMC Sequencing on Illumina
Library name: Solexa-17943/Solexa-17919
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.2318
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.2302
****************
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: GSM621559_BI.CD34_Primary_Cells.RRBS.CD34_0_0_00.RRBS532-533.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: 42U16AAXX100205-7-S-42TY1AAXX100126-2-S.hg19.level.2
ANALYSIS TITLE: Methylation Proportion Graphs of CD34 Primary Cells RRBS Data
ANALYSIS DESCRIPTION: Illumina RRBS read mappings from CD34 Primary Cells, Donor CD34_0/0/00, Libraries RRBS532-533 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.5216
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: CD34 RRBS 32
BROWSER_TRACK_DESCRIPTION: BI CD34 Primary Cells RRBS Donor CD34_0/0/00 Libraries RRBS532-533 EA Release 2
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 99.28

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

source_name: flow sorted CD34+ cells from cord blood; 42U16AAXX100205-7-S

value: CD34 Primary Cells

value: Unknown

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

value: 5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT

value: 5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT


title: Bisulfite-Seq analysis of RRBS516 derived from human HUES62 cells; RRBS516

description:
sample_term_id: NTR_0000851
assay_term_id: OBI_0001862
nucleic_acid_term_id: SO_0000352
Design description: RRBS REMC Sequencing on Illumina
Library name: RRBS516/RRBS517
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.4020
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.4035
****************
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: GSM621595_BI.HUES62.RRBS.RRBS516-517.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: RRBS516-RRBS517.hg19.level.2
ANALYSIS TITLE: Methylation Proportion Graphs of HUES62 Cell Line RRBS Data
ANALYSIS DESCRIPTION: Illumina RRBS read mappings from the HUES62 Cell Line, Libraries RRBS516-517 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.5232
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: HUES62 RRBS 16
BROWSER_TRACK_DESCRIPTION: BI HUES62 Cell Line RRBS Libraries RRBS516-517 EA Release 2
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 98.37

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

source_name: Harvard University Embryonic Stem Cells; RRBS516

value: embrionic stem cell

value: KSR

value: genomic DNA

value: Cell Line

value: undifferentiated

value: Harvard University

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


title: Bisulfite-Seq analysis of RRBS348 derived from human hES-I3 cells; 30J03AAXX090718-6-S

description:
sample_term_id: NTR_0000836
assay_term_id: OBI_0001862
nucleic_acid_term_id: SO_0000352
Design description: RRBS REMC Sequencing on Illumina
Library name: Solexa-11956/Solexa-11957
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.2358
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.2352
****************
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: GSM621348_BI.ES-I3.RRBS.RRBS348-349.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: 30J03AAXX090718-6-S-42R88AAXX091028-2-S-30H5VAAXX090528-2-S.hg19.level.2
ANALYSIS TITLE: Methylation Proportion Graphs of ES-I3 Cell Line RRBS Data
ANALYSIS DESCRIPTION: Illumina RRBS read mappings from the ES-I3 Cell Line, Libraries RRBS348-349 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.5234
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: ESI3 RRBS 48
BROWSER_TRACK_DESCRIPTION: BI ES-I3 Cell Line RRBS Libraries RRBS348-349 EA Release 2
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 98.96

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

source_name: I3(eye three) stem cells; 30J03AAXX090718-6-S

value: KSR or TESR

value: Female

value: 20 ng

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

value: 2x5hrs Epitect Kit

value: Pfu Turbo Cx hot start

value: Gel size selection


title: Bisulfite-Seq analysis of RRBS520 derived from human HUES64 cells; RRBS520

description:
sample_term_id: NTR_0000853
assay_term_id: OBI_0001862
nucleic_acid_term_id: SO_0000352
Design description: RRBS REMC Sequencing on Illumina
Library name: RRBS520/RRBS521
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.4019
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.4034
****************
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: GSM621594_BI.HUES64.RRBS.RRBS520-521.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: RRBS520-RRBS521.hg19.level.2
ANALYSIS TITLE: Methylation Proportion Graphs of HUES64 Cell Line RRBS Data
ANALYSIS DESCRIPTION: Illumina RRBS read mappings from the HUES64 Cell Line, Libraries RRBS520-521 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.5240
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: HUES64 RRBS 20
BROWSER_TRACK_DESCRIPTION: BI HUES64 Cell Line RRBS Libraries RRBS520-521 EA Release 2
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 98.11

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

source_name: Harvard University Embryonic Stem Cells; RRBS520

value: Male

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

value: DNA Methylation


title: Bisulfite-Seq analysis of RRBS522 derived from human hiPS-15b cells; 42TY1AAXX100126-3-S

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: Solexa-17917/Solexa-17944
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.2316
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.2300
****************
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: GSM621557_BI.iPS-15b.RRBS.RRBS522-523.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: 42TY1AAXX100126-3-S-42TWHAAXX100222-3-S.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 RRBS522-523 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.5255
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 22
BROWSER_TRACK_DESCRIPTION: BI iPS-15b Cell Line RRBS Libraries RRBS522-523 EA Release 2
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 98.1

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

source_name: IPS cell line 15b; 42TY1AAXX100126-3-S

value: induced pluripotent cells

value: 5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT

value: 5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT


title: JC-11 Benign nevus

status: Public on Oct 30 2010

type: RNA

city: Kingston

first: Harriet

last: Feilotter

state: Ontario

address: 88 Stuart St

department: Pathology and molecular department

country: Canada

institute: Queen's University

hyb_protocol: Labeled RNA was hybridized to Agilent miRNA array (8 arrays per slide) at 55°C for 22h in rotisserie in a hybridization oven. Disassembled arrays were washed in GE wash buffer 1&2 for 5 minutes each.

scan_protocol: Images were scanned with Agilent scanner at 5µm resolution.

data_processing: Raw data (probe view file) from feature extracted file was imported into GeneSpring, raw data summarized per miRNA in GeneSpring was used to plot miRNA193-b expression levels in all samples. No interarray normalization method was employed

molecule: total RNA

source_name: FFPE benign nevus

label_protocol: 100ng total RNA was dephosphorylated in the presence of calf intestine alkaline phsphatase, then a Cy3-pCp molecule was ligated to the 3' end of the RNA molecule according to Agilent miRNA protocol version 1.5.

extract_protocol: The RecoverAll total RNA Isolation kit (Ambion, Streetsville, Canada) was used to extract total RNA (including miRNA) from FFPE samples.

treatment_protocol: Formalin-fixed paraffin-embedded (FFPE) tissues

tag: tissue

value: benign nevus


title: JC-7 Metastatic melanoma

source_name: FFPE metastatic melanoma

value: metastatic melanoma


title: JC-10 Benign nevus


title: JC-8 Metastatic melanoma


title: JC-47 Primary melanoma

source_name: FFPE primary melanoma

value: primary melanoma


title: JC-45 Primary melanoma


title: JC-53 Primary melanoma


title: JC-46 Primary melanoma


title: JC-44 Primary melanoma


title: JC-2 Metastatic melanoma


title: Bisulfite-Seq analysis of RRBS552 derived from human HUES65 cells; RRBS552

description:
sample_term_id: NTR_0000854
assay_term_id: OBI_0001862
nucleic_acid_term_id: SO_0000352
Design description: RRBS REMC Sequencing on Illumina
Library name: RRBS552/RRBS553
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.4024
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.4037
****************
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: GSM621599_BI.HUES65.RRBS.RRBS552-553.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: RRBS552-RRBS553.hg19.level.2
ANALYSIS TITLE: Methylation Proportion Graphs of HUES65 Cell Line RRBS Data
ANALYSIS DESCRIPTION: Illumina RRBS read mappings from the HUES65 Cell Line, Libraries RRBS552-553 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.5228
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: HUES65 RRBS 52
BROWSER_TRACK_DESCRIPTION: BI HUES65 Cell Line RRBS Libraries RRBS552-553 EA Release 2
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 97.87

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

source_name: Harvard University Embryonic Stem Cells; RRBS552

value: embrionic stem cell

value: KSR

value: genomic DNA

value: Cell Line

value: undifferentiated

value: Harvard University

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


title: JC-22 Primary melanoma


title: JC-3 Metastatic melanoma


title: JC-9 Metastatic melanoma


title: JC-50 Primary melanoma


title: JC-20 Primary melanoma


title: JC-4 Metastatic melanoma


title: JC-25 Primary melanoma


title: JC-23 Primary melanoma


title: JC-6 Metastatic melanoma


title: JC-5 Metastatic melanoma


title: JC-42 Primary melanoma


title: JC-51 Primary melanoma


title: JC-19 Primary melanoma


title: JC-14 Benign nevus


title: JC-15 Benign nevus


title: JC-16 Benign nevus


title: JC-17 Benign nevus


title: JC-24 Primary melanoma


title: JC-12 Benign nevus


title: JC-18 Primary melanoma


title: JC-13 Benign nevus


title: br1_statin_tr1

status: Public on Oct 29 2010

city: Seattle

first: Douglas

middle: McKay

last: Fowler

state: WA

address: 1705 NE Pacific St, Foege Building S313

department: Genome Sciences

institute: University of Washington

description:
Biological replicate 1.
Technical replicate 1.

hyb_protocol: RNA was hybridized to Agilent S. cerevisiae v2 (8 x 15k) microarrays following the Agilent two-color gene expression protocol v5.7 (Agilent Technologies, Santa Clara, CA).  Slides were washed according to the Agilent protocol.  There were two randomly chosen conditions that were replicated per slide; these technical replicates were used to assess RNA labeling and hybridization quality.  Three independent biological replicates were performed according to the procedure outlined above.

scan_protocol: Slides were scanned on an Agilent G2505C scanner.  Images were quantified using Agilent Feature Extraction Software (version 10.5.1.1).

data_processing: Agilent Feature Extraction Software (version 10.5.1.1) was used for background subtraction and LOWESS normalization.

organism: Saccharomyces cerevisiae

source_name: statin

label_protocol: For dye labeling, 5 μg of RNA were purified using the Qiagen RNeasy kit (Qiagen, Valencia, CA), and a reference RNA sample was created by pooling RNA from all 6 conditions. RNA was labeled following the Agilent two-color gene expression protocol v5.7 (Agilent Technologies, Santa Clara, CA), although only 25% of the recommended amounts of Cy3 and Cy5 dyes were used in each reaction.

growth_protocol: Yeast (BY4741a) carrying the pdr5Δ mutation was grown to saturation in SC media + 2% glucose for 20-24 hr at 30°C with constant agitation. The culture was back diluted to 0.01 OD600 (-statin) or 0.09 OD600 (+statin, 5 μg/mL), and these pretreatment cultures were grown for an additional 18-20 hr, at which point an OD600 of approximately 0.4-0.6 was reached.

extract_protocol: Cultures were collected using a 0.45 μm vacuum filter with nylon filter membranes and the cell cake was rapidly frozen in liquid nitrogen and stored at -80 °C.  RNA isolation was initiated by adding 4 mL lysis buffer (0.1 M EDTA, 0.5% SDS, 0.01 M Tris pH 7.5) to the frozen filter membrane and vortexing thoroughly. Then, 3 mL acid phenol was added and the tube was vortexed and placed in a 65 °C water bath for 1 hr with additional vortexing every 20 min. The filter paper was removed with tweezers and the liquid poured into a phase lock gel tube (5Prime, Gaithersburg, GA), incubated at 4 °C for 10 min and centrifuged for 10 min at 1880 RCF. 3 mL of chloroform was added, and the tube was inverted 3 times to mix and then centrifuged at 1880 RCF for 10 min. The chloroform extraction was repeated and the aqueous layer was poured into a new 15 mL conical tube.  The RNA was precipitated by adding 1/10 volume 3 M sodium acetate and 2 volumes of 100% ethanol followed by mixing and incubation overnight at -20 °C. The precipitated RNA was pelleted and washed twice with 70% ethanol, then reconstituted in 250 μL deionized, RNAse-free H2O.

treatment_protocol: Cultures were spun down and resuspended in fresh media (SC, 2% glucose, 0.25 mM EDTA) either with or without statin (5 μg/mL) at an OD600 of 0.1. Metabolites were added as indicated and the vehicle (DMSO) concentration was adjusted to 0.1% (v/v) in all cases.  The yeast were harvested at approximately 50% of the eventual maximum OD600 (~0.4 for +statin, ~0.8 for –statin).

tag: strain/background

tag: genotype

tag: statin treated

value: yes

tag: cuso4 treated

value: no

tag: znso4 treated

source_name: Reference RNA

tag: composition

value: mix of RNA from all 6 experimental conditions


title: br1_untreated_cu_tr1


title: RAG1KO-H3K4me3-ChIP-Seq

status: Public on Jun 13 2010

city: La Jolla

first: Christopher

last: Benner

state: California

address: 9500 Gilman Dr. MC 0640

department: Medicine

institute: University of California, San Diego (UCSD)

description: Chromatin IP against H3K4me3 in RAG1-/- pro-B cells

data_processing:
Alignment: Reads were truncated to 25 bp and aligned to the mouse mm8 genome (NCBI Build 36) using eland. Only reads that mapped to a single, unique position were used for downstream analysis.
Peak Identification: Peaks were identified using custom software (HOMER, available at http://biowhat.ucsd.edu/homer/). For transcription factors, peaks were found by identifying 200 bp regions with tag density exceeding a threshold set at a 0.1% false discovery rate (determined by tag randomization). Only peaks with >4x normalized tag density relative to control sequencing and >4x normlaized tag density to the sourrounding 10kb of region were considered for analysis.

organism: Mus musculus

source_name: RAG1-/- pro-B cell

growth_protocol: Pro-B cells were isolated from femoral bone marrow of Rag1 knockout mice by positive enrichment of B220+ cells using magnetic separation (Miltenyi) and expanded for 10 d in Opti-MEM medium containing 10% FCS, 2x penicillin/streptomycin/glutamine, and 50 µM ß-mercaptoethanol supplemented with IL-7 and SCF.

extract_protocol: Lysates were clarified from sonicated cells or nuclei and protein-DNA complexes were isolated with antibody. Libraries were prepared according to Illumina's instructions. Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation, ChIP DNA was PCR-amplified with Illumina primers for 12-18 cycles and library fragments (ChIP) (insert plus adaptor and PCR primer sequences) were size selected from a 2% agarose gel or a 8% polyacrylamide gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer I or Genome Analyzer II following the manufacturer's protocols.

tag: strain

tag: cell type

value: pro-B cell

tag: chip antibody

tag: transgenes

tag: genetic background


title: RAG1KO-H3K27me3-ChIP-Seq

description: Chromatin IP against H3K27me3 in RAG1-/- pro-B cells


title: JL00002_SDC3_YPT47_MXemb_1 extraction1_array1

status: Public on Jul 07 2010

type: genomic

city: Toronto

first: DCC

last: modENCODE

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

institute: Ontario Institute for Cancer Research

description:
channel ch1 is ChIP DNA; Antibody information listed below: official name: JL00002 SDC3;target name: SDC-3;host: Rabbit;antigen: 1067-1340;clonal: Polyclonal;purified: Affinity;company: Covance;catalog: JL00002 SDC3;reference: PMID: 17293863;
channel ch2 is input DNA;

hyb_protocol: ChIP-chip_label_hyb_nimblegen_v1. DNA was labeled and hybridized to C. elegans tiling array by Roche NimbleGen according to the protocol described in chapter 3 and 4 of the NimbleGen Arrays User?s Guide ChIP-chip Analysis, Version 3.1, 27 May 2008. Briefly, Amplified IP or input DNA was either labeled with Cy5 or Cy3 in the presence of Klenow fragment. The reaction was stopped by the addition of EDTA. Labeled DNA was recovered by isopropanol precipitation, and dried. The labeled DNA was hybridized to C. elegans tiling array for 16 - 20 hours at 42°C.

scan_protocol: ChIP-chip_scanning_nimblegen_v1. Array scanning and raw data extraction were performed at Roche NimbleGen, according to the protocol described in chapter 5 and 6 of the NimbleGen Arrays User?s Guide ChIP-chip Analysis, Version 3.1, 27 May 2008. Briefly, array signal was scanned by using a GenePix 4000B Scanner with associated software and saved as .tif files of the 532nm and 635nm images individually. Raw signal intensities of the images were extracted  and saved as .pair files by using NimbleScan software according to the NimbleScan v2.4 User?s Guide.

data_processing:
ChIP-chip normalization standard zscore:JL:2 protocol. ChIP-chip_normalization_standard_zscore_v2   First, the ratio of intensity from sample/reference channel was transformed to log2 space. Second, z-scores were obtained for each probe by standardizing the data by subtracting the mean and dividing by the standard deviation of all probes.  Processed data are obtained using following parameters: genome version is WS180
ChIP-chip normalization standard zscore:JL:2 protocol. ChIP-chip_normalization_standard_zscore_v2   First, the ratio of intensity from sample/reference channel was transformed to log2 space. Second, z-scores were obtained for each probe by standardizing the data by subtracting the mean and dividing by the standard deviation of all probes.  Processed data are obtained using following parameters: genome version is WS180

label: Cy5 dye

organism: Caenorhabditis elegans

growth_protocol: Worm_embryo_growth_and_harvest_vSE1. Embryos were prepared by bleaching from gravid N2 adults grown in standard S-basal media liquid culture. Live embryos were cross-linked in M9 + 2% formaldehyde for 30 minutes at room temperature. Embryos were then washed once with 100 mM Tris, twice with M9 Buffer and once by FA buffer (50 mM HEPES/KOH pH 7.5, 1 mM EDTA, 1% Triton X-100, 0.1 % sodium deoxycholate; 150 mM NaCl).  Pellets were frozen at -80C. For a detailed protocol see http://www.modencode.org/.

extract_protocol:
Worm_embryo_extraction_v1. Embryos were resuspended in FA buffer (50 mM HEPES/KOH pH 7.5, 1 mM EDTA, 1% Triton X-100, 0.1 % sodium deoxycholate; 150 mM NaCl) + protease inhibitors (Calbiochem Cat# 539131). Using a Branson sonifier microtip, samples were sonicated on ice at the following settings: 35% amplitude, 0.9 sec on, 0.1 sec off, 12 pulses, 7 times. Cell debris was removed by centrifuging at 13,000 g for 15 minutes at 4ºC and taking the supernatant. Protein concentration was determined by Bradford Assay and extracts were aliquoted at stored at -80C.
Worm_chromatin_immunoprecipitation_v4.1. 2.2 mg extract was taken and sarkosyl was added to 1% final concentration. 0.2 mg was used for each ChIP with 10% taken as input directly into elution buffer (1% SDS in TE, 250 mM NaCl) and treated with RNAse. Antibody was added to each IP sample and incubated overnight at 4C. Immune complexes were incubated (2hrs at 4C) with 20 uL protein A sepharose (Amersham) and washed 5 minutes with 1 mL of each of the following solutions: ChIP Buffer, ChIP Buffer+1M NaCl, ChIP Buffer+500mM NaCl, TEL Buffer (10mM Tris-HCl pH 8.0, 250mM LiCl, 1% NP-40, 1% sodium deoxycholate, 1mM EDTA), and 2X TE (10mM Tris-HCl pH 8.0, 1mM EDTA). Samples were eluted twice with 150uL elution buffer for 15minutes at 65C. Samples were treated with proteinase K at 55C for 1-2hrs then transfer to 65C overnight to reverse crosslinks. DNA was cleaned up Qiagen PCR purification kit.
Worm_LM-PCR_Amplification_for_ChIP-chip_v1. ChIP DNA was amplified with a modified ligation mediated PCR (LM-PCR) protocol derived from Ren, R et al (2000) Science 290, 2306-9.

tag: developmental stage

value: Mixed Embryo

tag: sex

value: mixed Male and Hermaphrodite population

label: Cy3 dye


title: EL667 (MicMa086) Replicate 1

status: Public on Oct 28 2010

city: Cold Spring Harbor

first: Jude

last: Kendall

state: NY

address: 1 Bungtown Road

institute: Cold Spring Harbor Laboratory

description: These samples were hybridized to two color-reversal arrays

hyb_protocol: Hybridizations consisted of 35 uL of hybridization solution (37% formamide, 4x SSC, 0.1%SDS, and labeled DNA). Samples were denatured in an MJ Research Tetrad (Bio-Rad, Hercules, CA) at 95 degrees C for 5 min, and then pre-annealed at 37 degrees C for no more than 30 min. The solution was then applied to the microarray and hybridized under a coverslip in an oven at 42 degrees C for 14 to 16 h. Thereafter, slides were washed 1 min in 0.2% SDS/0.2x SSC, 30 sec in 0.2x SSC, and 30 sec in 0.05x SSC. Slides were dried by centrifugation and scanned immediately.

scan_protocol: Scanned on an Axon GenePix 4000B scanner using a pixel size of 5 um. Microarrays were scanned and gridded using GenePix Pro 4.0 software (MDS Analytical Technologies, Toronto, Canada).

data_processing: The data were normalized using a lowess curve-fitting algorithm, followed by a local normalization (previously described in Hicks et al.). After placement in genome order, the mean of log ratios was computed for color reversal experiments for each sample. Segmentation was performed on the above-described data. Segments are defined as non-overlapping, genomic regions where copy number has changed. Our segmentation method is based on the minimization of the square-sum of differences between log-ratios and means (squared deviation) over segments larger than 6 probes in size. Initially, the segmenter searches for breakpoints that might be boundaries of segments. The first known breakpoint on a given chromosome is its first probe. For a given breakpoint, a 100-probe window to its right is selected. The sum of squared deviations of the flanking probes is calculated for each probe within this window. A probe whose squared deviation value produces a local minimum with respect to its neighbors, and is below a threshold of 95% of the square deviation within a window, is accepted as a new, known breakpoint. Whenever a probe is found below the threshold in the newly defined region, the segmenter recursively breaks said region into two pieces until it cannot find any further breakpoints therein. If no breakpoints are found, the 100- probe window is shifted by half its size and this procedure continues until a chromosome end is reached. Initial segments are constructed using found breakpoints. Each segment and its neighbors are validated for significance by the Kolmogorov-Smirnov (K-S) algorithm. If the p-value of compared segments is less than 10-5, then said segment is accepted as real. If not, the segments are merged. The segmenter also reports statistics such as mean, standard deviation, and median for each segment.

label_protocol: Complexity-reduced representations, consisting of small (200-1200 bp) fragments were amplified by adapter-mediated PCR of genomic DNA. DNA samples (2 ug) were labeled either with Cy5-dCTP or Cy3-dCTP using Amersham-Pharmacia MegaPrimelabeling kit (Amersham Biosciences, Piscataway, NJ), and competitively hybridized to each other on the same slide.

extract_protocol: Qiagen Genomic DNA Isolation Kit

value: Ductal Breast Carcinoma

tag: cell line

value: EBV Immortalized Fibroblast Reference


title: EL668 (MicMa086) Replicate 2


title: RAG1KO-H3K9/14ac-ChIP-Seq

description: Chromatin IP against H3K9/14ac in RAG1-/- pro-B cells


title: RAG1KO-H3K4me2-ChIP-Seq

description: Chromatin IP against H3K4me2 in RAG1-/- pro-B cells


title: br1_statin_cu_tr1

source_name: statin + CuSO4


title: EBFKO-H3K4me3-ChIP-Seq

description: Chromatin IP against H3K4me3 in EBF-/- pre-pro-B cells

source_name: EBF-/- pre-pro-B cell

growth_protocol: EBF-/- pre-pro-B cells were cultured on S17 stromal cells in the presence of IL7, SCF, and FLT3 ligand in Iscove’s Modified Dulbecco’s medium and in the presence of 10% FCS, penicillin, streptomycin and L-glutamine.

value: pre-pro-B cell

value: EBF-/-


title: JL00001_DPY27_YPT47_MXemb_2 extraction2_array1

description:
channel ch1 is input DNA;
channel ch2 is ChIP DNA; Antibody information listed below: official name: JL00001 DPY27;target name: DPY-27;host: Mouse;antigen: 1-409;clonal: Polyclonal;purified: Affinity;company: Covance;catalog: JL00001 DPY27;reference: PMID: 17293863;short description: *  recombinant proteins were cloned and expressed with Novagen's Pet30-EkLIC system
* rabbit polyclonal antibodies were produced at Covance Immunology Services
* DNA encoding epitopes were cloned into pGEX-5X-2 vector (Amersham Biosciences) and used to affinity-purify antibodies.;

label_protocol: ChIP-chip_label_hyb_nimblegen_v1. DNA was labeled and hybridized to C. elegans tiling array by Roche NimbleGen according to the protocol described in chapter 3 and 4 of the NimbleGen Arrays User?s Guide ChIP-chip Analysis, Version 3.1, 27 May 2008. Briefly, Amplified IP or input DNA was either labeled with Cy5 or Cy3 in the presence of Klenow fragment. The reaction was stopped by the addition of EDTA. Labeled DNA was recovered by isopropanol precipitation, and dried. The labeled DNA was hybridized to C. elegans tiling array for 16 - 20 hours at 42°C.


title: br1_statin_cu_tr2

description:
Biological replicate 1.
Technical replicate 2.


title: EBFKO-H3K4me2-ChIP-Seq

description: Chromatin IP against H3K4me2 in EBF-/- pre-pro-B cells


title: RAG1KO-H3K4me1-ChIP-Seq

description: Chromatin IP against H3K4me1 in RAG1-/- pro-B cells


title: EBFKO-H3K27me3-ChIP-Seq

description: Chromatin IP against H3K27me3 in EBF-/- pre-pro-B cells


title: PUER-CEBPb-48h-ChIP-Seq

status: Public on May 27 2010

description: Chromatin IP against C/EBPb in PUER cells after 48h Tamoxifen treatment

source_name: PUER cells

growth_protocol: PUER cells were propagated in 10 % FCS/Iscove's Modified Dulbecco's Medium (IMDM) supplemented with 100 U/ml penicillin/streptomycin, 1 µg/ml puromycin, 2 mM L-glutamine and 5 ng/ml recombinant mIL-4. The PU.1-ER fusion protein was activated by adding 4-hydroxy-tamoxifen at a final concentration of 100 nM to the media.

extract_protocol: Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody. Alternatively, DNA was phenol/chloroform-extracted from MNase-treated nuclei, and 134-154 bp long fragments were extractred from a 2% agarose gel. Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation, ChIP DNA was PCR-amplified with Illumina primers for 12-16 cycles and library fragments of 200-300 bp (ChIP) (insert plus adaptor and PCR primer sequences) were isolated from a 2% agarose gel. For MNase-Seq, size-selected mononucleosome-derived DNA fragments were ligated to modified adapters that incorporate both the adapter sequence as well as the primer landing sites for the flow cell-conjugated primers. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer or Genome Analyzer II following the manufacturer's protocols.

treatment_protocol: Tamoxifen, 48h

value: PUER cells

value: C/EBPb (sc-150)

tag: treatment

value: Tamoxifen, 48h

tag: genotype/variation

value: C/EBPb (Vendor:Santa Cruz, cat# sc-150, lot# D0808)


title: PU.1KO-PU.1-ChIP-Seq

description: Chromatin IP against PU.1 in PU.1-/- myloid cells

source_name: PU.1-/- myloid cell

growth_protocol: PU.1-/- were propagated in 10 % FCS/Iscove's Modified Dulbecco's Medium (IMDM) supplemented with 100 U/ml penicillin/streptomycin, 2 mM L-glutamine and 5 ng/ml recombinant mIL-4.

value: PU.1-/- myloid cell

value: PU.1 (Vendor:Santa Cruz, cat# sc-352, lot# F1808)


title: PU.1KO-CEBPb-ChIP-Seq

description: Chromatin IP against C/EBPb in PU.1-/- myloid cells


title: EBFKO-H3K9/14ac-ChIP-Seq

description: Chromatin IP against H3K9/14ac in EBF-/- pre-pro-B cells


title: PUER-PU.1-48h-ChIP-Seq

description: Chromatin IP against PU.1 in PUER cells after 48h Tamoxifen treatment


title: E2AKO-PU.1-E2A-ER-ChIP-Seq

description: Chromatin IP against PU.1 in E2A-/- pre-pro-B cells expressing an Tamoxifen activated E2A (E2A-ER)

source_name: E2A-/- pre-pro-B cell

growth_protocol: E2A-/-and EBF-/- pre-pro-B cells were cultured on S17 stromal cells in the presence of IL7 (10 ng/ml), SCF (10 ng/ml), and FLT3 ligand (10 ng/ml) in Iscove’s Dulbecco’s medium and in the presence of 10% FCS, 200 U/ml penicillin, 200 mg/ml streptomycin and 4 mM L-glutamine.

treatment_protocol: The cells were spin-infected with a retrovirus expressing full length E2A fused to the estrogen receptor ligand binding domain, as well as hCD25 from a second cistron. After 16 h in culture, cells were treated with tamoxifen (1 µM final concentration) for 6 h. Cells expressing hCD25 were then enriched magnetically (Miltenyi).


title: ChIP-Seq analysis of H3K36me3 in human hLiver cells; 61GKJAAXX100226-7-S

status: Public on Apr 28 2010

description:
sample_term_id: UBERON_0002107
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Solexa-20750
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.2532
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.2563
****************
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: GSM537708_BI.Adult_Liver.H3K36me3.5.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: 61GKJAAXX100226-7-S.hg19.level.1
ANALYSIS TITLE: Mapping of Adult Liver Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K36me3 ChIP-Seq on Adult Liver, Donor 5.0 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.4733
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: 0.2772
FINDPEAKS_PERCENTILE: 61
HOTSPOT_SCORE: 0.2738
HOTSPOT_PERCENTILE: 53
IROC_SCORE: 0.9766
IROC_PERCENTILE: 63
POISSON_SCORE: 0.5008
POISSON_PERCENTILE: 50

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

ANALYSIS FILE NAME: GSM537708_BI.Adult_Liver.H3K36me3.5.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: 61GKJAAXX100226-7-S.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Adult Liver Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K36me3 ChIP-Seq read mappings from Adult Liver, Donor 5.0 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.5007
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: AL H3K36me3 5.0
BROWSER_TRACK_DESCRIPTION: BI Adult Liver Histone H3K36me3 Donor 5.0 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED: 54
FINDPEAKS_SCORE: 0.2772
FINDPEAKS_PERCENTILE: 61
HOTSPOT_SCORE: 0.2738
HOTSPOT_PERCENTILE: 53
IROC_SCORE: 0.9766
IROC_PERCENTILE: 63
POISSON_SCORE: 0.5008
POISSON_PERCENTILE: 50

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

source_name: normal adult liver; 61GKJAAXX100226-7-S

tag: molecule

value: genomic DNA

tag: disease

value: MGH Pathology

value: Primary Tissue

value: liver

value: surgery

value: Male

value: Histone H3K36me3

value: SDS lysis

value: Bioruptor

value: 10 million cells

value: Protein A-Sepharose 4B

value: 70 ul bed volume

value: Abcam


title: ChIP-Seq analysis of H3K9me3 in human hLiver cells; 61GKJAAXX100226-5-S

description:
sample_term_id: UBERON_0002107
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Solexa-20746
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.2534
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.2563
****************
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: GSM537710_BI.Adult_Liver.H3K9me3.5.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: 61GKJAAXX100226-5-S.hg19.level.1
ANALYSIS TITLE: Mapping of Adult Liver Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K9me3 ChIP-Seq on Adult Liver, Donor 5.0 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.4633
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: 0.1007
FINDPEAKS_PERCENTILE: 54
HOTSPOT_SCORE: 0.1618
HOTSPOT_PERCENTILE: 49
IROC_SCORE: 0.8158
IROC_PERCENTILE: 49
POISSON_SCORE: 0.4706
POISSON_PERCENTILE: 78

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

ANALYSIS FILE NAME: GSM537710_BI.Adult_Liver.H3K9me3.5.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: 61GKJAAXX100226-5-S.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Adult Liver Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K9me3 ChIP-Seq read mappings from Adult Liver, Donor 5.0 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.4907
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: AL H3K9me3 5.0
BROWSER_TRACK_DESCRIPTION: BI Adult Liver Histone H3K9me3 Donor 5.0 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED: 59
FINDPEAKS_SCORE: 0.1007
FINDPEAKS_PERCENTILE: 54
HOTSPOT_SCORE: 0.1618
HOTSPOT_PERCENTILE: 49
IROC_SCORE: 0.8158
IROC_PERCENTILE: 49
POISSON_SCORE: 0.4706
POISSON_PERCENTILE: 78

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

source_name: normal adult liver; 61GKJAAXX100226-5-S

value: Histone H3K9me3


title: RAG1KO-PU.1-ChIP-Seq

description: Chromatin IP against PU.1 in RAG1-/- pre-pro-B cells

growth_protocol: Pro-B cells were isolated from femoral bone marrow of Rag1 knockout mice by positive enrichment of B220+ cells using magnetic separation (Miltenyi) and expanded for 10 d in Opti-MEM medium containing 10% FCS, 2x penicillin/streptomycin/glutamine, and 50 µM ß-mercaptoethanol supplemented with 1:100 IL-7 and 1:500 SCF.

value: pro-B cell


title: EBFKO-E2A-ChIP-Seq

description: Chromatin IP against E2A in EBF-/- pre-pro-B cells

value: pre-pro-B cell

value: EBF-/-


title: E2AKO-PU.1-bHLH-ER-ChIP-Seq

description: Chromatin IP against PU.1 in E2A-/- pre-pro-B cells expressing an Tamoxifen activated E2A mutatant lacking both transactivation domains (bHLH-ER)

treatment_protocol: The cells were spin-infected with a retrovirus expressing truncated E2A (lacking both activation domains) fused to the estrogen receptor ligand binding domain, as well as hCD25 from a second cistron. After 16 h in culture, cells were treated with tamoxifen (1 µM final concentration) for 6 h. Cells expressing hCD25 were then enriched magnetically (Miltenyi).

value: bHLH-ER

value: PU.1 (Vendor:Santa Cruz, cat# sc-352, lot# F1808)