title: ChIP-Seq analysis of H3K27me3 in human CD3 cells; 30B91AAXX080917-2-S

status: Public on May 03 2010

description:
sample_term_id: CL_0000084
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Solexa-7456/Solexa-7461
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.1920
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.1919
****************
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: GSM537613_BI.CD3_Primary_Cells.H3K27me3.CD3_39661.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: 30B91AAXX080917-2-S-30BN3AAXX080918-3-S.hg19.level.1
ANALYSIS TITLE: Mapping of CD3 Primary Cells Histone H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K27me3 ChIP-Seq on CD3 Primary Cells, Donor CD3_39661 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.4765
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_H3K27me3_EXPERIMENTS_SCORED: 52
FINDPEAKS_SCORE: 0.2902
FINDPEAKS_PERCENTILE: 83
HOTSPOT_SCORE: 0.3042
HOTSPOT_PERCENTILE: 81
IROC_SCORE: 0.951
IROC_PERCENTILE: 73
POISSON_SCORE: 0.5403
POISSON_PERCENTILE: 81

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

ANALYSIS FILE NAME: GSM537613_BI.CD3_Primary_Cells.H3K27me3.CD3_39661.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: 30B91AAXX080917-2-S-30BN3AAXX080918-3-S.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of CD3 Primary Cells Histone H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K27me3 ChIP-Seq read mappings from CD3 Primary Cells, Donor CD3_39661 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.5039
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: CD3 H3K27me3 61
BROWSER_TRACK_DESCRIPTION: BI CD3 Primary Cells Histone H3K27me3 Donor CD3_39661 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED: 52
FINDPEAKS_SCORE: 0.2902
FINDPEAKS_PERCENTILE: 83
HOTSPOT_SCORE: 0.3042
HOTSPOT_PERCENTILE: 81
IROC_SCORE: 0.951
IROC_PERCENTILE: 73
POISSON_SCORE: 0.5403
POISSON_PERCENTILE: 81

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

source_name: flow sorted CD3+ cells from cord blood; 30B91AAXX080917-2-S

value: genomic DNA

value: FHCRC

value: Primary Cell

value: CD3 Primary Cells

tag: markers

value: Unknown

value: Histone H3K27me3

value: Upstate


title: ChIP-Seq analysis of H3K36me3 in human hLiver cells; 61C9RAAXX100224-7-S

status: Public on Apr 28 2010

type: SRA

city: Cambridge

first: BROAD

last: INSTITUTE

state: MA

country: USA

institute: Broad Institute

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-20739
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.2523
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.2561
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************
BED and WIG files were replaced on April 29, 2014

library_source: genomic

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

ANALYSIS FILE NAME: GSM537699_BI.Adult_Liver.H3K36me3.3.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: 61C9RAAXX100224-7-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 3.0 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.4816
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: 0.2964
FINDPEAKS_PERCENTILE: 69
HOTSPOT_SCORE: 0.2812
HOTSPOT_PERCENTILE: 57
IROC_SCORE: 0.984
IROC_PERCENTILE: 76
POISSON_SCORE: 0.5379
POISSON_PERCENTILE: 63

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

ANALYSIS FILE NAME: GSM537699_BI.Adult_Liver.H3K36me3.3.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: 61C9RAAXX100224-7-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 3.0 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.5090
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 3.0
BROWSER_TRACK_DESCRIPTION: BI Adult Liver Histone H3K36me3 Donor 3.0 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED: 54
FINDPEAKS_SCORE: 0.2964
FINDPEAKS_PERCENTILE: 69
HOTSPOT_SCORE: 0.2812
HOTSPOT_PERCENTILE: 57
IROC_SCORE: 0.984
IROC_PERCENTILE: 76
POISSON_SCORE: 0.5379
POISSON_PERCENTILE: 63

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

molecule: genomic DNA

organism: Homo sapiens

source_name: normal adult liver; 61C9RAAXX100224-7-S

extract_protocol: Library construction protocol: Single read - Illumina

tag: molecule

tag: disease

value: MGH Pathology

value: Primary Tissue

value: liver

value: surgery

value: Female

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 H3K36me3 in human CD3 cells; 30B91AAXX080917-1-S

description:
sample_term_id: CL_0000084
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Solexa-7457/Solexa-7462
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.1911
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.1910
****************
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: GSM537612_BI.CD3_Primary_Cells.H3K36me3.CD3_39661.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: 30B91AAXX080917-1-S-30B91AAXX080917-5-S.hg19.level.1
ANALYSIS TITLE: Mapping of CD3 Primary Cells Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K36me3 ChIP-Seq on CD3 Primary Cells, Donor CD3_39661 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.4764
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: 0.2315
FINDPEAKS_PERCENTILE: 48
HOTSPOT_SCORE: 0.2994
HOTSPOT_PERCENTILE: 62
IROC_SCORE: 0.9322
IROC_PERCENTILE: 35
POISSON_SCORE: 0.527
POISSON_PERCENTILE: 57

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

ANALYSIS FILE NAME: GSM537612_BI.CD3_Primary_Cells.H3K36me3.CD3_39661.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: 30B91AAXX080917-1-S-30B91AAXX080917-5-S.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of CD3 Primary Cells Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K36me3 ChIP-Seq read mappings from CD3 Primary Cells, Donor CD3_39661 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.5038
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: CD3 H3K36me3 61
BROWSER_TRACK_DESCRIPTION: BI CD3 Primary Cells Histone H3K36me3 Donor CD3_39661 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED: 54
FINDPEAKS_SCORE: 0.2315
FINDPEAKS_PERCENTILE: 48
HOTSPOT_SCORE: 0.2994
HOTSPOT_PERCENTILE: 62
IROC_SCORE: 0.9322
IROC_PERCENTILE: 35
POISSON_SCORE: 0.527
POISSON_PERCENTILE: 57

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

source_name: flow sorted CD3+ cells from cord blood; 30B91AAXX080917-1-S

value: genomic DNA

value: FHCRC

value: Primary Cell


title: ChIP-Seq analysis of H3K9me3 in human pancreatic islets normal cells; 61ETBAAXX100322-4-S

description:
sample_term_id: UBERON_0000016
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Solexa-17433
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.2510
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
****************
BED and WIG files were replaced on April 29, 2014

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

ANALYSIS FILE NAME: GSM537686_BI.Pancreatic_Islets.H3K9me3.pancreatic_islets_normal_0_0_00.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: 61ETBAAXX100322-4-S.hg19.level.1
ANALYSIS TITLE: Mapping of Pancreatic Islets Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K9me3 ChIP-Seq on Pancreatic Islets, Donor pancreatic islets normal_0/0/00 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.4567
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: 0.1004
FINDPEAKS_PERCENTILE: 53
HOTSPOT_SCORE: 0.1883
HOTSPOT_PERCENTILE: 61
IROC_SCORE: 0.8654
IROC_PERCENTILE: 66
POISSON_SCORE: 0.471
POISSON_PERCENTILE: 81

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

ANALYSIS FILE NAME: GSM537686_BI.Pancreatic_Islets.H3K9me3.pancreatic_islets_normal_0_0_00.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: 61ETBAAXX100322-4-S.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Pancreatic Islets Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K9me3 ChIP-Seq read mappings from Pancreatic Islets, Donor pancreatic islets normal_0/0/00 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.4841
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: PI H3K9me3 0
BROWSER_TRACK_DESCRIPTION: BI Pancreatic Islets Histone H3K9me3 Donor pancreatic islets normal_0/0/00 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED: 59
FINDPEAKS_SCORE: 0.1004
FINDPEAKS_PERCENTILE: 53
HOTSPOT_SCORE: 0.1883
HOTSPOT_PERCENTILE: 61
IROC_SCORE: 0.8654
IROC_PERCENTILE: 66
POISSON_SCORE: 0.471
POISSON_PERCENTILE: 81

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

source_name: pancreatic islets from a normal donor; 61ETBAAXX100322-4-S

value: Islet Cell Resource Center

value: Pancreatic Islets

value: pancreatic islets normal_0/0/00

value: Male

value: not passaged

value: Histone H3K9me3


title: ChIP-Seq analysis of H3K36me3 in human pancreatic islets normal cells; 42LTMAAXX090725-8-S

description:
sample_term_id: UBERON_0000016
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Solexa-13150
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.2248
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.2247
****************
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: GSM537661_BI.Pancreatic_Islets.H3K36me3.pancreatic_islets_normal_3_27_09.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: 42LTMAAXX090725-8-S.hg19.level.1
ANALYSIS TITLE: Mapping of Pancreatic Islets Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K36me3 ChIP-Seq on Pancreatic Islets, Donor pancreatic islets normal_3/27/09 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.4662
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: 0.1727
FINDPEAKS_PERCENTILE: 33
HOTSPOT_SCORE: 0.27
HOTSPOT_PERCENTILE: 49
IROC_SCORE: 0.9213
IROC_PERCENTILE: 31
POISSON_SCORE: 0.3701
POISSON_PERCENTILE: 13

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

ANALYSIS FILE NAME: GSM537661_BI.Pancreatic_Islets.H3K36me3.pancreatic_islets_normal_3_27_09.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: 42LTMAAXX090725-8-S.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Pancreatic Islets Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K36me3 ChIP-Seq read mappings from Pancreatic Islets, Donor pancreatic islets normal_3/27/09 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.4936
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: PI H3K36me3 27
BROWSER_TRACK_DESCRIPTION: BI Pancreatic Islets Histone H3K36me3 Donor pancreatic islets normal_3/27/09 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED: 54
FINDPEAKS_SCORE: 0.1727
FINDPEAKS_PERCENTILE: 33
HOTSPOT_SCORE: 0.27
HOTSPOT_PERCENTILE: 49
IROC_SCORE: 0.9213
IROC_PERCENTILE: 31
POISSON_SCORE: 0.3701
POISSON_PERCENTILE: 13

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

source_name: pancreatic islets from a normal donor; 42LTMAAXX090725-8-S

value: pancreatic islets normal_3/27/09


title: ChIP-Seq analysis of H3K9ac in human pancreatic islets normal cells; 42LTMAAXX090725-6-S

description:
sample_term_id: UBERON_0000016
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Solexa-13148
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.2254
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.2253
****************
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: GSM537660_BI.Pancreatic_Islets.H3K9ac.pancreatic_islets_normal_3_27_09.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: 42LTMAAXX090725-6-S.hg19.level.1
ANALYSIS TITLE: Mapping of Pancreatic Islets Histone H3K9ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K9ac ChIP-Seq on Pancreatic Islets, Donor pancreatic islets normal_3/27/09 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.4605
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 2

QUALITY SCORES:
NUMBER_OF_H3K9ac_EXPERIMENTS_SCORED: 35
FINDPEAKS_SCORE: 0.2975
FINDPEAKS_PERCENTILE: 69
HOTSPOT_SCORE: 0.3653
HOTSPOT_PERCENTILE: 69
IROC_SCORE: 0.9713
IROC_PERCENTILE: 34
POISSON_SCORE: 0.4374
POISSON_PERCENTILE: 66

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

ANALYSIS FILE NAME: GSM537660_BI.Pancreatic_Islets.H3K9ac.pancreatic_islets_normal_3_27_09.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: 42LTMAAXX090725-6-S.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Pancreatic Islets Histone H3K9ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K9ac ChIP-Seq read mappings from Pancreatic Islets, Donor pancreatic islets normal_3/27/09 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.4879
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: PI H3K9ac 27
BROWSER_TRACK_DESCRIPTION: BI Pancreatic Islets Histone H3K9ac Donor pancreatic islets normal_3/27/09 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K9ac_EXPERIMENTS_SCORED: 35
FINDPEAKS_SCORE: 0.2975
FINDPEAKS_PERCENTILE: 69
HOTSPOT_SCORE: 0.3653
HOTSPOT_PERCENTILE: 69
IROC_SCORE: 0.9713
IROC_PERCENTILE: 34
POISSON_SCORE: 0.4374
POISSON_PERCENTILE: 66

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

source_name: pancreatic islets from a normal donor; 42LTMAAXX090725-6-S

value: Histone H3K9ac


title: ChIP-Seq analysis of H3K36me3 in human CD3 cells; 42M0GAAXX091022-8-S

description:
sample_term_id: CL_0000084
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Solexa-15476
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.1917
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.1916
****************
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: GSM537666_BI.CD3_Primary_Cells.H3K36me3.CD3_39804.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: 42M0GAAXX091022-8-S.hg19.level.1
ANALYSIS TITLE: Mapping of CD3 Primary Cells Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K36me3 ChIP-Seq on CD3 Primary Cells, Donor CD3_39804 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.4652
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: 0.6545
FINDPEAKS_PERCENTILE: 98
HOTSPOT_SCORE: 0.4455
HOTSPOT_PERCENTILE: 92
IROC_SCORE: 0.995
IROC_PERCENTILE: 93
POISSON_SCORE: 0.7065
POISSON_PERCENTILE: 94

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

ANALYSIS FILE NAME: GSM537666_BI.CD3_Primary_Cells.H3K36me3.CD3_39804.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: 42M0GAAXX091022-8-S.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of CD3 Primary Cells Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K36me3 ChIP-Seq read mappings from CD3 Primary Cells, Donor CD3_39804 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.4926
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: CD3 H3K36me3 04
BROWSER_TRACK_DESCRIPTION: BI CD3 Primary Cells Histone H3K36me3 Donor CD3_39804 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED: 54
FINDPEAKS_SCORE: 0.6545
FINDPEAKS_PERCENTILE: 98
HOTSPOT_SCORE: 0.4455
HOTSPOT_PERCENTILE: 92
IROC_SCORE: 0.995
IROC_PERCENTILE: 93
POISSON_SCORE: 0.7065
POISSON_PERCENTILE: 94

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

source_name: flow sorted CD3+ cells from cord blood; 42M0GAAXX091022-8-S

value: CD3 Primary Cells

value: Unknown

value: Histone H3K36me3

value: SDS lysis


title: ChIP-Seq analysis of WCE in human pancreatic islets normal cells; 42LTMAAXX090725-5-S

description:
sample_term_id: UBERON_0000016
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Solexa-13151
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.2152
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.2151
****************
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: GSM537659_BI.Pancreatic_Islets.Input.pancreatic_islets_normal_3_27_09.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: 42LTMAAXX090725-5-S.hg19.level.1
ANALYSIS TITLE: Mapping of Pancreatic Islets ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina reads produced by ChIP-Seq Input on Pancreatic Islets, Donor pancreatic islets normal_3/27/09 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.4768
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 2

QUALITY SCORES:
NUMBER_OF_Input_EXPERIMENTS_SCORED: 67
FINDPEAKS_SCORE: 0.0193
FINDPEAKS_PERCENTILE: 76
HOTSPOT_SCORE: 0.1354
HOTSPOT_PERCENTILE: 80
IROC_SCORE: 0.6455
IROC_PERCENTILE: 42
POISSON_SCORE: 0.2587
POISSON_PERCENTILE: 69

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

ANALYSIS FILE NAME: GSM537659_BI.Pancreatic_Islets.Input.pancreatic_islets_normal_3_27_09.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: 42LTMAAXX090725-5-S.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Pancreatic Islets ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina ChIP-Seq Input read mappings from Pancreatic Islets, Donor pancreatic islets normal_3/27/09 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.5042
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: PI Input 27
BROWSER_TRACK_DESCRIPTION: BI Pancreatic Islets ChIP-Seq Input Donor pancreatic islets normal_3/27/09 EA Release 2

QUALITY SCORES:
NUMBER_OF_Input_EXPERIMENTS_SCORED: 67
FINDPEAKS_SCORE: 0.0193
FINDPEAKS_PERCENTILE: 76
HOTSPOT_SCORE: 0.1354
HOTSPOT_PERCENTILE: 80
IROC_SCORE: 0.6455
IROC_PERCENTILE: 42
POISSON_SCORE: 0.2587
POISSON_PERCENTILE: 69

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

source_name: pancreatic islets from a normal donor; 42LTMAAXX090725-5-S

value: ChIP-Seq Input

value: Bioruptor

value: Input

value: standard


title: ChIP-Seq analysis of H3K27me3 in human WA-7 cells; 42LR0AAXX091002-2-S

description:
sample_term_id: NTR_0000837
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Solexa-12609
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.2143
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.2142
****************
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: GSM537657_BI.ES-WA7.H3K27me3.Solexa-12609.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: 42LR0AAXX091002-2-S.hg19.level.1
ANALYSIS TITLE: Mapping of ES-WA7 Cell Line Histone H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K27me3 ChIP-Seq on the ES-WA7 Cell Line, Library Solexa-12609 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.4612
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_H3K27me3_EXPERIMENTS_SCORED: 52
FINDPEAKS_SCORE: 0.278
FINDPEAKS_PERCENTILE: 79
HOTSPOT_SCORE: 0.2923
HOTSPOT_PERCENTILE: 75
IROC_SCORE: 0.9281
IROC_PERCENTILE: 60
POISSON_SCORE: 0.4255
POISSON_PERCENTILE: 40

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

ANALYSIS FILE NAME: GSM537657_BI.ES-WA7.H3K27me3.Solexa-12609.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: 42LR0AAXX091002-2-S.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of ES-WA7 Cell Line Histone H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K27me3 ChIP-Seq read mappings from the ES-WA7 Cell Line, Library Solexa-12609 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.4886
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: ESWA7 H3K27me3 09
BROWSER_TRACK_DESCRIPTION: BI ES-WA7 Cell Line Histone H3K27me3 Library Solexa-12609 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED: 52
FINDPEAKS_SCORE: 0.278
FINDPEAKS_PERCENTILE: 79
HOTSPOT_SCORE: 0.2923
HOTSPOT_PERCENTILE: 75
IROC_SCORE: 0.9281
IROC_PERCENTILE: 60
POISSON_SCORE: 0.4255
POISSON_PERCENTILE: 40

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

source_name: WA7 stem cells; 42LR0AAXX091002-2-S

value: genomic DNA

value: Harvard University

value: Cell Line

tag: line

tag: lineage

value: embrionic stem cell

value: undifferentiated

tag: passage

tag: medium

value: KSR

tag: sex

value: Female

tag: batch

value: Histone H3K27me3

value: 10 million cells

value: Protein A-Sepharose 4B

value: 70 ul bed volume

value: Millipore


title: ChIP-Seq analysis of H3K9me3 in human CD3 cells; 314K1AAXX090315-8-S

description:
sample_term_id: CL_0000084
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Solexa-10225
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.1955
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.1946
****************
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: GSM537645_BI.CD3_Primary_Cells.H3K9me3.CD3_39840.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: 314K1AAXX090315-8-S-314G4AAXX090310-7-S.hg19.level.1
ANALYSIS TITLE: Mapping of CD3 Primary Cells Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K9me3 ChIP-Seq on CD3 Primary Cells, Donor CD3_39840 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.4726
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: 0.1598
FINDPEAKS_PERCENTILE: 75
HOTSPOT_SCORE: 0.2465
HOTSPOT_PERCENTILE: 80
IROC_SCORE: 0.859
IROC_PERCENTILE: 59
POISSON_SCORE: 0.4485
POISSON_PERCENTILE: 69

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

ANALYSIS FILE NAME: GSM537645_BI.CD3_Primary_Cells.H3K9me3.CD3_39840.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: 314K1AAXX090315-8-S-314G4AAXX090310-7-S.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of CD3 Primary Cells Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K9me3 ChIP-Seq read mappings from CD3 Primary Cells, Donor CD3_39840 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.5000
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: CD3 H3K9me3 40
BROWSER_TRACK_DESCRIPTION: BI CD3 Primary Cells Histone H3K9me3 Donor CD3_39840 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED: 59
FINDPEAKS_SCORE: 0.1598
FINDPEAKS_PERCENTILE: 75
HOTSPOT_SCORE: 0.2465
HOTSPOT_PERCENTILE: 80
IROC_SCORE: 0.859
IROC_PERCENTILE: 59
POISSON_SCORE: 0.4485
POISSON_PERCENTILE: 69

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

source_name: flow sorted CD3+ cells from cord blood; 314K1AAXX090315-8-S

value: FHCRC

value: Primary Cell

value: CD3 Primary Cells

value: Unknown

value: Histone H3K9me3

value: SDS lysis

value: Abcam


title: Exon arrays of Roadmap cell types; flow sorted CD34+ cells from cord blood; DS12785-exon

status: Public on Oct 06 2010

type: RNA

city: Seattle

first: Northwest

last: REMC

state: WA

institute: University of Washington

description:
sample_term_id: CL_0000837
assay_term_id: OBI_0001463
nucleic_acid_term_id:
Exon profiling of NREMC cell types, these coincide with chromatin accessibility sequencing assays.
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.3484
sample alias: RO 01520
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.2417

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

scan_protocol: Affymetrix Gene Chip Scanner 3000

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

label: biotin

molecule: total RNA

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

growth_protocol: Followed vendor recommendations for growth protocol/media

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

value: FHCRC HEIMFELD

value: CD34 Primary Cells

value: 50 years


title: ChIP-Seq analysis of H3K9me3 in human CD3 cells; 30EDEAAXX090127-8-S

description:
sample_term_id: CL_0000084
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Solexa-9768
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.1932
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.1931
****************
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: GSM537637_BI.CD3_Primary_Cells.H3K9me3.CD3_39811.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: 30EDEAAXX090127-8-S.hg19.level.1
ANALYSIS TITLE: Mapping of CD3 Primary Cells Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K9me3 ChIP-Seq on CD3 Primary Cells, Donor CD3_39811 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.4718
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: 0.0871
FINDPEAKS_PERCENTILE: 49
HOTSPOT_SCORE: 0.1669
HOTSPOT_PERCENTILE: 51
IROC_SCORE: 0.7217
IROC_PERCENTILE: 20
POISSON_SCORE: 0.3258
POISSON_PERCENTILE: 31

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

ANALYSIS FILE NAME: GSM537637_BI.CD3_Primary_Cells.H3K9me3.CD3_39811.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: 30EDEAAXX090127-8-S.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of CD3 Primary Cells Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K9me3 ChIP-Seq read mappings from CD3 Primary Cells, Donor CD3_39811 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.4992
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: CD3 H3K9me3 11
BROWSER_TRACK_DESCRIPTION: BI CD3 Primary Cells Histone H3K9me3 Donor CD3_39811 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED: 59
FINDPEAKS_SCORE: 0.0871
FINDPEAKS_PERCENTILE: 49
HOTSPOT_SCORE: 0.1669
HOTSPOT_PERCENTILE: 51
IROC_SCORE: 0.7217
IROC_PERCENTILE: 20
POISSON_SCORE: 0.3258
POISSON_PERCENTILE: 31

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

source_name: flow sorted CD3+ cells from cord blood; 30EDEAAXX090127-8-S

value: genomic DNA

value: Bioruptor


title: Exon arrays of Roadmap cell types; flow sorted CD34+ cells from cord blood; DS13199-exon

description:
sample_term_id: CL_0000837
assay_term_id: OBI_0001463
nucleic_acid_term_id:
Exon profiling of NREMC cell types, these coincide with chromatin accessibility sequencing assays.
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.3482
sample alias: RO 00738
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.2427

value: 49 years

value: Male

value: Caucasian


title: ChIP-Seq analysis of H3K27me3 in human hLiver cells; 61GKJAAXX100226-6-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-20735
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.2531
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: GSM537707_BI.Adult_Liver.H3K27me3.5.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: 61GKJAAXX100226-6-S.hg19.level.1
ANALYSIS TITLE: Mapping of Adult Liver Histone H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K27me3 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.4617
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_H3K27me3_EXPERIMENTS_SCORED: 52
FINDPEAKS_SCORE: 0.0283
FINDPEAKS_PERCENTILE: 15
HOTSPOT_SCORE: 0.1637
HOTSPOT_PERCENTILE: 38
IROC_SCORE: 0.8317
IROC_PERCENTILE: 21
POISSON_SCORE: 0.6773
POISSON_PERCENTILE: 98

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

ANALYSIS FILE NAME: GSM537707_BI.Adult_Liver.H3K27me3.5.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: 61GKJAAXX100226-6-S.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Adult Liver Histone H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K27me3 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.4891
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 H3K27me3 5.0
BROWSER_TRACK_DESCRIPTION: BI Adult Liver Histone H3K27me3 Donor 5.0 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED: 52
FINDPEAKS_SCORE: 0.0283
FINDPEAKS_PERCENTILE: 15
HOTSPOT_SCORE: 0.1637
HOTSPOT_PERCENTILE: 38
IROC_SCORE: 0.8317
IROC_PERCENTILE: 21
POISSON_SCORE: 0.6773
POISSON_PERCENTILE: 98

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

source_name: normal adult liver; 61GKJAAXX100226-6-S

value: MGH Pathology

value: Primary Tissue

value: liver

value: surgery

value: Histone H3K27me3

value: 10 million cells

value: Protein A-Sepharose 4B

value: 70 ul bed volume


title: ChIP-Seq analysis of H3K27me3 in human Mobilized CD34 cells; 42LNGAAXX090916-2-S

description:
sample_term_id: CL_0000837
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Solexa-14520
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.2140
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.2139
****************
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: GSM537649_BI.Mobilized_CD34_Primary_Cells.H3K27me3.Mobilized_CD34_5_28_09.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: 42LNGAAXX090916-2-S.hg19.level.1
ANALYSIS TITLE: Mapping of Mobilized CD34 Primary Cells Histone H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K27me3 ChIP-Seq on Mobilized CD34 Primary Cells, Donor RO 01508 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.4631
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_H3K27me3_EXPERIMENTS_SCORED: 52
FINDPEAKS_SCORE: 0.3372
FINDPEAKS_PERCENTILE: 92
HOTSPOT_SCORE: 0.2825
HOTSPOT_PERCENTILE: 73
IROC_SCORE: 0.9371
IROC_PERCENTILE: 63
POISSON_SCORE: 0.5457
POISSON_PERCENTILE: 87

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

ANALYSIS FILE NAME: GSM537649_BI.Mobilized_CD34_Primary_Cells.H3K27me3.Mobilized_CD34_5_28_09.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: 42LNGAAXX090916-2-S.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Mobilized CD34 Primary Cells Histone H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K27me3 ChIP-Seq read mappings from Mobilized CD34 Primary Cells, Donor RO 01508 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.4905
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: MCD34 H3K27me3 28
BROWSER_TRACK_DESCRIPTION: BI Mobilized CD34 Primary Cells Histone H3K27me3 Donor RO 01508 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED: 52
FINDPEAKS_SCORE: 0.3372
FINDPEAKS_PERCENTILE: 92
HOTSPOT_SCORE: 0.2825
HOTSPOT_PERCENTILE: 73
IROC_SCORE: 0.9371
IROC_PERCENTILE: 63
POISSON_SCORE: 0.5457
POISSON_PERCENTILE: 87

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

source_name: CD34 cells mobilized into peripheral blood; 42LNGAAXX090916-2-S

value: FHCRC

value: Primary Cell

value: Mobilized CD34 Primary Cells

value: Unknown

value: not passaged

value: SDS lysis

value: Upstate


title: Exon arrays of Roadmap cell types; Fetal Kidney primary tissue, day 122; DS12635-exon

description:
sample_term_id: UBERON_0002113
assay_term_id: OBI_0001463
nucleic_acid_term_id:
Exon profiling of NREMC cell types, these coincide with chromatin accessibility sequencing assays.
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.3493
sample alias: fKidney.H-22676d122
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.2461

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

value: fetal kidney

value: UW

value: fetal

value: 122 days


title: Exon arrays of Roadmap cell types; Fetal Heart primary tissue, day 96; DS12531-exon

description:
sample_term_id: UBERON_0000948
assay_term_id: OBI_0001463
nucleic_acid_term_id:
Exon profiling of NREMC cell types, these coincide with chromatin accessibility sequencing assays.
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.3495
sample alias: fHeart.H-22662d96
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.2452

value: Primary Tissue

value: fetal heart

value: 96 days


title: Exon arrays of Roadmap cell types; Fetal Lung primary tissue, day 108; DS13507-exon

description:
sample_term_id: UBERON_0002048
assay_term_id: OBI_0001463
nucleic_acid_term_id:
Exon profiling of NREMC cell types, these coincide with chromatin accessibility sequencing assays.
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.3490
sample alias: fLung.H-22934Bd108
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.3118

value: fetal lung

value: day 108

value: Female


title: Exon arrays of Roadmap cell types; Fetal Lung primary tissue, day 85; DS14724-exon

description:
sample_term_id: UBERON_0002048
assay_term_id: OBI_0001463
nucleic_acid_term_id:
Exon profiling of NREMC cell types, these coincide with chromatin accessibility sequencing assays.
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.3487
sample alias: fLung.H-23266d85
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.3130

value: day 85


title: Exon arrays of Roadmap cell types; Fetal Lung primary tissue, day 67; DS14666-exon

description:
sample_term_id: UBERON_0002048
assay_term_id: OBI_0001463
nucleic_acid_term_id:
Exon profiling of NREMC cell types, these coincide with chromatin accessibility sequencing assays.
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.3488
sample alias: fLung.H-23247d67
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.3127

value: day 67


title: Exon arrays of Roadmap cell types; flow sorted CD34+ cells from cord blood; DS13196-exon

description:
sample_term_id: CL_0000837
assay_term_id: OBI_0001463
nucleic_acid_term_id:
Exon profiling of NREMC cell types, these coincide with chromatin accessibility sequencing assays.
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.3483
sample alias: RO 01562
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.2422

value: FHCRC HEIMFELD

value: Primary Cell

value: CD34 Primary Cells

value: 42 years

value: Male

value: Caucasian


title: ChIP-Seq analysis of WCE in human CD19 cells; 30CAVAAXX081115-3-S

description:
sample_term_id: CL_0000236
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Solexa-8321
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.2212
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.2211
****************
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: GSM537620_BI.CD19_Primary_Cells.Input.CD19_8_1_08.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: 30CAVAAXX081115-3-S.hg19.level.1
ANALYSIS TITLE: Mapping of CD19 Primary Cells ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina reads produced by ChIP-Seq Input on CD19 Primary Cells, Donor CD19_8/1/08 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.4586
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 2

QUALITY SCORES:
NUMBER_OF_Input_EXPERIMENTS_SCORED: 67
FINDPEAKS_SCORE: 0.0176
FINDPEAKS_PERCENTILE: 72
HOTSPOT_SCORE: 0.0634
HOTSPOT_PERCENTILE: 52
IROC_SCORE: 0.0
IROC_PERCENTILE: NA
POISSON_SCORE: 0.1628
POISSON_PERCENTILE: 10

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

ANALYSIS FILE NAME: GSM537620_BI.CD19_Primary_Cells.Input.CD19_8_1_08.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: 30CAVAAXX081115-3-S.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of CD19 Primary Cells ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina ChIP-Seq Input read mappings from CD19 Primary Cells, Donor CD19_8/1/08 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.4860
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: CD19 Input 1
BROWSER_TRACK_DESCRIPTION: BI CD19 Primary Cells ChIP-Seq Input Donor CD19_8/1/08 EA Release 2

QUALITY SCORES:
NUMBER_OF_Input_EXPERIMENTS_SCORED: 67
FINDPEAKS_SCORE: 0.0176
FINDPEAKS_PERCENTILE: 72
HOTSPOT_SCORE: 0.0634
HOTSPOT_PERCENTILE: 52
IROC_SCORE: 0.0
IROC_PERCENTILE: NA
POISSON_SCORE: 0.1628
POISSON_PERCENTILE: 10

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

source_name: flow sorted CD19+ cells from cord blood; 30CAVAAXX081115-3-S

value: genomic DNA

value: FHCRC

value: CD19 Primary Cells

value: Unknown

value: not passaged

value: ChIP-Seq Input

value: SDS lysis

value: Bioruptor

value: Input

value: standard


title: Exon arrays of Roadmap cell types; Fetal Lung primary tissue, day 96; DS14809-exon

description:
sample_term_id: UBERON_0002048
assay_term_id: OBI_0001463
nucleic_acid_term_id:
Exon profiling of NREMC cell types, these coincide with chromatin accessibility sequencing assays.
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.3480
sample alias: fLung.H-23284d96
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.3135

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

value: Primary Tissue

value: fetal lung

value: UW

value: fetal

value: day 96

value: Female


title: Exon arrays of Roadmap cell types; Fetal Lung primary tissue, day 122; DS12646-exon

description:
sample_term_id: UBERON_0002048
assay_term_id: OBI_0001463
nucleic_acid_term_id:
Exon profiling of NREMC cell types, these coincide with chromatin accessibility sequencing assays.
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.3492
sample alias: fLung.H-22676d122
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.2466

value: 122 days


title: ChIP-Seq analysis of H3K4me1 in human CD34 cells, 30EDEAAXX090127-3-S

description:
sample_term_id: CL_0001059
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.1580
Library name: Solexa-9771
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.1581
****************
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: GSM486708_BI.CD34_Primary_Cells.H3K4me1.CD34_39811.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: 30EDEAAXX090127-3-S.hg19.level.1
ANALYSIS TITLE: Mapping of CD34 Primary Cells Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me1 ChIP-Seq on CD34 Primary Cells, Donor CD34_39811 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.4814
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 2

QUALITY SCORES:
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED: 43
FINDPEAKS_SCORE: 0.3175
FINDPEAKS_PERCENTILE: 40
HOTSPOT_SCORE: 0.3781
HOTSPOT_PERCENTILE: 53
IROC_SCORE: 0.9872
IROC_PERCENTILE: 52
POISSON_SCORE: 0.4622
POISSON_PERCENTILE: 16

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

ANALYSIS FILE NAME: GSM486708_BI.CD34_Primary_Cells.H3K4me1.CD34_39811.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: 30EDEAAXX090127-3-S.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of CD34 Primary Cells Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me1 ChIP-Seq read mappings from CD34 Primary Cells, Donor CD34_39811 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.5088
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: CD34 H3K4me1 11
BROWSER_TRACK_DESCRIPTION: BI CD34 Primary Cells Histone H3K4me1 Donor CD34_39811 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED: 43
FINDPEAKS_SCORE: 0.3175
FINDPEAKS_PERCENTILE: 40
HOTSPOT_SCORE: 0.3781
HOTSPOT_PERCENTILE: 53
IROC_SCORE: 0.9872
IROC_PERCENTILE: 52
POISSON_SCORE: 0.4622
POISSON_PERCENTILE: 16

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

source_name: ChIP-Seq analysis ofH3K4me1 in human CD34 cells

value: genomic DNA

value: FHCRC

value: Primary Cell

value: CD34 Primary Cells

value: Histone H3K4me1

value: 10 million cells

value: Protein A-Sepharose 4B

value: 70 ul bed volume

value: Abcam


title: ChIP-Seq analysis of H3K4me3 in human CD34 cells, 30EDEAAXX090127-7-S

description:
sample_term_id: CL_0001059
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.1589
Library name: Solexa-9765
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.1590
****************
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: GSM486711_BI.CD34_Primary_Cells.H3K4me3.CD34_39804.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: 30EDEAAXX090127-7-S.hg19.level.1
ANALYSIS TITLE: Mapping of CD34 Primary Cells Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me3 ChIP-Seq on CD34 Primary Cells, Donor CD34_39804 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.4731
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 2

QUALITY SCORES:
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED: 62
FINDPEAKS_SCORE: 0.284
FINDPEAKS_PERCENTILE: 31
HOTSPOT_SCORE: 0.3749
HOTSPOT_PERCENTILE: 46
IROC_SCORE: 0.9982
IROC_PERCENTILE: 39
POISSON_SCORE: 0.418
POISSON_PERCENTILE: 34

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

ANALYSIS FILE NAME: GSM486711_BI.CD34_Primary_Cells.H3K4me3.CD34_39804.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: 30EDEAAXX090127-7-S.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of CD34 Primary Cells Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me3 ChIP-Seq read mappings from CD34 Primary Cells, Donor CD34_39804 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.5005
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: CD34 H3K4me3 04
BROWSER_TRACK_DESCRIPTION: BI CD34 Primary Cells Histone H3K4me3 Donor CD34_39804 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED: 62
FINDPEAKS_SCORE: 0.284
FINDPEAKS_PERCENTILE: 31
HOTSPOT_SCORE: 0.3749
HOTSPOT_PERCENTILE: 46
IROC_SCORE: 0.9982
IROC_PERCENTILE: 39
POISSON_SCORE: 0.418
POISSON_PERCENTILE: 34

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

source_name: ChIP-Seq analysis ofH3K4me3 in human CD34 cells

value: Unknown

value: Histone H3K4me3

value: SDS lysis

value: Bioruptor


title: ChIP-Seq analysis of WCE in human CD3 cells; 30BN3AAXX080918-8-S

description:
sample_term_id: CL_0000084
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Solexa-7460/Solexa-7455
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.1941
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.1940
****************
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: GSM537619_BI.CD3_Primary_Cells.Input.CD3_39661.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: 30BN3AAXX080918-8-S-30BN3AAXX080918-7-S.hg19.level.1
ANALYSIS TITLE: Mapping of CD3 Primary Cells ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina reads produced by ChIP-Seq Input on CD3 Primary Cells, Donor CD3_39661 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.4701
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 2

QUALITY SCORES:
NUMBER_OF_Input_EXPERIMENTS_SCORED: 67
FINDPEAKS_SCORE: 0.0143
FINDPEAKS_PERCENTILE: 67
HOTSPOT_SCORE: 0.0892
HOTSPOT_PERCENTILE: 71
IROC_SCORE: 0.3574
IROC_PERCENTILE: 24
POISSON_SCORE: 0.2024
POISSON_PERCENTILE: 30

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

ANALYSIS FILE NAME: GSM537619_BI.CD3_Primary_Cells.Input.CD3_39661.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: 30BN3AAXX080918-8-S-30BN3AAXX080918-7-S.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of CD3 Primary Cells ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina ChIP-Seq Input read mappings from CD3 Primary Cells, Donor CD3_39661 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.4975
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: CD3 Input 61
BROWSER_TRACK_DESCRIPTION: BI CD3 Primary Cells ChIP-Seq Input Donor CD3_39661 EA Release 2

QUALITY SCORES:
NUMBER_OF_Input_EXPERIMENTS_SCORED: 67
FINDPEAKS_SCORE: 0.0143
FINDPEAKS_PERCENTILE: 67
HOTSPOT_SCORE: 0.0892
HOTSPOT_PERCENTILE: 71
IROC_SCORE: 0.3574
IROC_PERCENTILE: 24
POISSON_SCORE: 0.2024
POISSON_PERCENTILE: 30

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

source_name: flow sorted CD3+ cells from cord blood; 30BN3AAXX080918-8-S

value: CD3 Primary Cells

value: ChIP-Seq Input

value: Input

value: standard


title: ChIP-Seq analysis of H3K4me3 in human CD34 cells, 30C8WAAXX081104-1-S

description:
sample_term_id: CL_0001059
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.1583
Library name: Solexa-8326
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.1584
****************
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: GSM486709_BI.CD34_Primary_Cells.H3K4me3.CD34_39629.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: 30C8WAAXX081104-1-S.hg19.level.1
ANALYSIS TITLE: Mapping of CD34 Primary Cells Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me3 ChIP-Seq on CD34 Primary Cells, Donor CD34_39629 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.4644
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 2

QUALITY SCORES:
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED: 62
FINDPEAKS_SCORE: 0.5219
FINDPEAKS_PERCENTILE: 76
HOTSPOT_SCORE: 0.5312
HOTSPOT_PERCENTILE: 74
IROC_SCORE: 0.9997
IROC_PERCENTILE: 61
POISSON_SCORE: 0.5996
POISSON_PERCENTILE: 76

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

ANALYSIS FILE NAME: GSM486709_BI.CD34_Primary_Cells.H3K4me3.CD34_39629.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: 30C8WAAXX081104-1-S.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of CD34 Primary Cells Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me3 ChIP-Seq read mappings from CD34 Primary Cells, Donor CD34_39629 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.4918
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: CD34 H3K4me3 29
BROWSER_TRACK_DESCRIPTION: BI CD34 Primary Cells Histone H3K4me3 Donor CD34_39629 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED: 62
FINDPEAKS_SCORE: 0.5219
FINDPEAKS_PERCENTILE: 76
HOTSPOT_SCORE: 0.5312
HOTSPOT_PERCENTILE: 74
IROC_SCORE: 0.9997
IROC_PERCENTILE: 61
POISSON_SCORE: 0.5996
POISSON_PERCENTILE: 76

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

value: genomic DNA


title: ChIP-Seq analysis of H3K27me3 in human CD19 cells; 30EKYAAXX081227-6-S

description:
sample_term_id: CL_0000236
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Solexa-9420
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.2215
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.2214
****************
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: GSM537638_BI.CD19_Primary_Cells.H3K27me3.CD19_6_26_08.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: 30EKYAAXX081227-6-S.hg19.level.1
ANALYSIS TITLE: Mapping of CD19 Primary Cells Histone H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K27me3 ChIP-Seq on CD19 Primary Cells, Donor CD19_6/26/08 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.4654
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_H3K27me3_EXPERIMENTS_SCORED: 52
FINDPEAKS_SCORE: 0.1277
FINDPEAKS_PERCENTILE: 48
HOTSPOT_SCORE: 0.2152
HOTSPOT_PERCENTILE: 48
IROC_SCORE: 0.8722
IROC_PERCENTILE: 33
POISSON_SCORE: 0.4107
POISSON_PERCENTILE: 33

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

ANALYSIS FILE NAME: GSM537638_BI.CD19_Primary_Cells.H3K27me3.CD19_6_26_08.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: 30EKYAAXX081227-6-S.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of CD19 Primary Cells Histone H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K27me3 ChIP-Seq read mappings from CD19 Primary Cells, Donor CD19_6/26/08 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.4928
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: CD19 H3K27me3 26
BROWSER_TRACK_DESCRIPTION: BI CD19 Primary Cells Histone H3K27me3 Donor CD19_6/26/08 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED: 52
FINDPEAKS_SCORE: 0.1277
FINDPEAKS_PERCENTILE: 48
HOTSPOT_SCORE: 0.2152
HOTSPOT_PERCENTILE: 48
IROC_SCORE: 0.8722
IROC_PERCENTILE: 33
POISSON_SCORE: 0.4107
POISSON_PERCENTILE: 33

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

source_name: flow sorted CD19+ cells from cord blood; 30EKYAAXX081227-6-S

value: FHCRC

value: CD19 Primary Cells

value: not passaged

value: Histone H3K27me3


title: Exon arrays of Roadmap cell types; Fetal Lung primary tissue, day 101; DS12817-exon

description:
sample_term_id: UBERON_0002048
assay_term_id: OBI_0001463
nucleic_acid_term_id:
Exon profiling of NREMC cell types, these coincide with chromatin accessibility sequencing assays.
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.3491
sample alias: fLung.H-22727d101
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.2470

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

value: Primary Tissue

value: fetal lung

value: UW

value: fetal

value: 101 days


title: Exon arrays of Roadmap cell types; IMR90 Cell Line; DS13219-exon

description:
sample_term_id: EFO_0001196
assay_term_id: OBI_0001463
nucleic_acid_term_id:
Exon profiling of NREMC cell types, these coincide with chromatin accessibility sequencing assays.
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.3479
sample alias: IMR90
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.1632

source_name: IMR90 Cell Line; DS13219-exon

value: ATCC

value: Cell Line

value: Fetal lung fibroblast

value: Eagle's Minimum Essential Medium, Catalog No. 30-2003.

tag: Sex

value: Female


title: ChIP-Seq analysis of H3K36me3 in human WA-7 cells; 30H88AAXX090617-3-S

description:
sample_term_id: NTR_0000837
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Solexa-12610
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.2131
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.2130
****************
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: GSM537640_BI.ES-WA7.H3K36me3.Solexa-12610.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: 30H88AAXX090617-3-S.hg19.level.1
ANALYSIS TITLE: Mapping of ES-WA7 Cell Line Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K36me3 ChIP-Seq on the ES-WA7 Cell Line, Library Solexa-12610 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.4805
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: 0.0432
FINDPEAKS_PERCENTILE: 9
HOTSPOT_SCORE: 0.1545
HOTSPOT_PERCENTILE: 13
IROC_SCORE: 0.7713
IROC_PERCENTILE: 7
POISSON_SCORE: 0.2486
POISSON_PERCENTILE: 4

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

ANALYSIS FILE NAME: GSM537640_BI.ES-WA7.H3K36me3.Solexa-12610.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: 30H88AAXX090617-3-S.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of ES-WA7 Cell Line Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K36me3 ChIP-Seq read mappings from the ES-WA7 Cell Line, Library Solexa-12610 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.5079
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: ESWA7 H3K36me3 10
BROWSER_TRACK_DESCRIPTION: BI ES-WA7 Cell Line Histone H3K36me3 Library Solexa-12610 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED: 54
FINDPEAKS_SCORE: 0.0432
FINDPEAKS_PERCENTILE: 9
HOTSPOT_SCORE: 0.1545
HOTSPOT_PERCENTILE: 13
IROC_SCORE: 0.7713
IROC_PERCENTILE: 7
POISSON_SCORE: 0.2486
POISSON_PERCENTILE: 4

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

source_name: WA7 stem cells; 30H88AAXX090617-3-S

value: Harvard University

value: embrionic stem cell

value: undifferentiated

value: KSR

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 H3K27me3 in human CD34 cells, 30CAVAAXX081115-1-S

description:
sample_term_id: CL_0001059
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.1568
Library name: Solexa-8323
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.1569
****************
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: GSM486704_BI.CD34_Primary_Cells.H3K27me3.CD34_39661.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: 30CAVAAXX081115-1-S.hg19.level.1
ANALYSIS TITLE: Mapping of CD34 Primary Cells Histone H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K27me3 ChIP-Seq on CD34 Primary Cells, Donor CD34_39661 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.4563
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_H3K27me3_EXPERIMENTS_SCORED: 52
FINDPEAKS_SCORE: 0.2578
FINDPEAKS_PERCENTILE: 73
HOTSPOT_SCORE: 0.3095
HOTSPOT_PERCENTILE: 83
IROC_SCORE: 0.963
IROC_PERCENTILE: 77
POISSON_SCORE: 0.5114
POISSON_PERCENTILE: 71

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

ANALYSIS FILE NAME: GSM486704_BI.CD34_Primary_Cells.H3K27me3.CD34_39661.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: 30CAVAAXX081115-1-S.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of CD34 Primary Cells Histone H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K27me3 ChIP-Seq read mappings from CD34 Primary Cells, Donor CD34_39661 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.4837
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: CD34 H3K27me3 61
BROWSER_TRACK_DESCRIPTION: BI CD34 Primary Cells Histone H3K27me3 Donor CD34_39661 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED: 52
FINDPEAKS_SCORE: 0.2578
FINDPEAKS_PERCENTILE: 73
HOTSPOT_SCORE: 0.3095
HOTSPOT_PERCENTILE: 83
IROC_SCORE: 0.963
IROC_PERCENTILE: 77
POISSON_SCORE: 0.5114
POISSON_PERCENTILE: 71

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

source_name: ChIP-Seq analysis ofH3K27me3 in human CD34 cells

value: genomic DNA

value: FHCRC

value: Primary Cell

value: CD34 Primary Cells

value: Unknown

value: Histone H3K27me3


title: ChIP-Seq analysis of H3K27me3 in human CD3 cells; 30EBYAAXX090127-2-S

description:
sample_term_id: CL_0000084
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Solexa-9762
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.1950
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.1949
****************
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: GSM537631_BI.CD3_Primary_Cells.H3K27me3.CD3_39804.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: 30EBYAAXX090127-2-S.hg19.level.1
ANALYSIS TITLE: Mapping of CD3 Primary Cells Histone H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K27me3 ChIP-Seq on CD3 Primary Cells, Donor CD3_39804 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.4655
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_H3K27me3_EXPERIMENTS_SCORED: 52
FINDPEAKS_SCORE: 0.1825
FINDPEAKS_PERCENTILE: 58
HOTSPOT_SCORE: 0.2211
HOTSPOT_PERCENTILE: 50
IROC_SCORE: 0.8939
IROC_PERCENTILE: 40
POISSON_SCORE: 0.4432
POISSON_PERCENTILE: 50

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

ANALYSIS FILE NAME: GSM537631_BI.CD3_Primary_Cells.H3K27me3.CD3_39804.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: 30EBYAAXX090127-2-S.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of CD3 Primary Cells Histone H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K27me3 ChIP-Seq read mappings from CD3 Primary Cells, Donor CD3_39804 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.4929
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: CD3 H3K27me3 04
BROWSER_TRACK_DESCRIPTION: BI CD3 Primary Cells Histone H3K27me3 Donor CD3_39804 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED: 52
FINDPEAKS_SCORE: 0.1825
FINDPEAKS_PERCENTILE: 58
HOTSPOT_SCORE: 0.2211
HOTSPOT_PERCENTILE: 50
IROC_SCORE: 0.8939
IROC_PERCENTILE: 40
POISSON_SCORE: 0.4432
POISSON_PERCENTILE: 50

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

source_name: flow sorted CD3+ cells from cord blood; 30EBYAAXX090127-2-S

value: CD3 Primary Cells

value: Upstate


title: Exon arrays of Roadmap cell types; Fetal Lung primary tissue, day 103; DS13985-exon

description:
sample_term_id: UBERON_0002048
assay_term_id: OBI_0001463
nucleic_acid_term_id:
Exon profiling of NREMC cell types, these coincide with chromatin accessibility sequencing assays.
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.3489
sample alias: fLung.H-23090d103
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.3123

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

value: Primary Tissue

value: fetal lung

value: UW

value: fetal

value: day 103

value: Male