title: ChIP-Seq analysis of H3K36me3 in human CD25+ CD127- Treg cells; DNA_Lib 312

description:
sample_term_id: CL_0000792
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 312
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8635
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.9459
****************
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: GSM772945_BI.CD4+_CD25+_CD127-_Treg_Primary_Cells.H3K36me3.Donor_62.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 312-DNA_Lib 312-DNA_Lib 312-DNA_Lib 312.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of CD4+ CD25+ CD127- Treg Primary Cells Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K36me3 ChIP-Seq on CD4+ CD25+ CD127- Treg Primary Cells, Donor Donor 62, 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.10602
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 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 22,933,944
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 49
FINDPEAKS_SCORE: 0.2987
FINDPEAKS_PERCENTILE: 73
HOTSPOT_SCORE: 0.2835
HOTSPOT_PERCENTILE: 67
IROC_SCORE: 0.9855
IROC_PERCENTILE: 69
POISSON_SCORE: 0.4795
POISSON_PERCENTILE: 76
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM772945_BI.CD4+_CD25+_CD127-_Treg_Primary_Cells.H3K36me3.Donor_62.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 312-DNA_Lib 312-DNA_Lib 312-DNA_Lib 312.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of CD4+ CD25+ CD127- Treg Primary Cells Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K36me3 ChIP-Seq read mappings from CD4+ CD25+ CD127- Treg Primary Cells, Donor Donor 62, 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.10866
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 5
BROWSER_TRACK_NAME: CCCTreg H3K36me3 62 12
BROWSER_TRACK_DESCRIPTION: BI CD4+ CD25+ CD127- Treg Primary Cells Histone H3K36me3 Donor 62 Library DNA_Lib 312 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 22,933,944
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 49
FINDPEAKS_SCORE: 0.2987
FINDPEAKS_PERCENTILE: 73
HOTSPOT_SCORE: 0.2835
HOTSPOT_PERCENTILE: 67
IROC_SCORE: 0.9855
IROC_PERCENTILE: 69
POISSON_SCORE: 0.4795
POISSON_PERCENTILE: 76
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: CD25+ CD127- Treg is one of  CD4+  T cell subsets  that purified by microbeads, LS column and FACS ; DNA_Lib 312

value: genomic DNA

value: CD25+ CD127- Treg

value: Protein A-Sepharose 4B

value: 10 ul bed volume

value: Abcam

value: Histone H3K36me3


title: ChIP-Seq analysis of H3K27me3 in human substantia nigra cells; DNA_Lib 559

status: Public on Dec 28 2011

type: SRA

city: Cambridge

first: BROAD

last: INSTITUTE

state: MA

country: USA

institute: Broad Institute

description:
sample_term_id: UBERON_0002038
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 559
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8627
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.9444
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

library_source: genomic

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

ANALYSIS FILE NAME: GSM772937_BI.Brain_Substantia_Nigra.H3K27me3.149.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 559-DNA_Lib 559-DNA_Lib 559.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of Brain Substantia Nigra Histone H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K27me3 ChIP-Seq on Brain Substantia Nigra, Donor 149, 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.10627
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 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 19,777,120
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 49
FINDPEAKS_SCORE: 0.0189
FINDPEAKS_PERCENTILE: 39
HOTSPOT_SCORE: 0.1104
HOTSPOT_PERCENTILE: 43
IROC_SCORE: 0.686
IROC_PERCENTILE: 33
POISSON_SCORE: 0.2658
POISSON_PERCENTILE: 45
MAXIMUM_REPLICATE_CORRELATION: 0.86

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

ANALYSIS FILE NAME: GSM772937_BI.Brain_Substantia_Nigra.H3K27me3.149.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 559-DNA_Lib 559-DNA_Lib 559.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of Brain Substantia Nigra Histone H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K27me3 ChIP-Seq read mappings from Brain Substantia Nigra, Donor 149, 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.10891
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 5
BROWSER_TRACK_NAME: BSN H3K27me3 49 59
BROWSER_TRACK_DESCRIPTION: BI Brain Substantia Nigra Histone H3K27me3 Donor 149 Library DNA_Lib 559 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 19,777,120
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 49
FINDPEAKS_SCORE: 0.0189
FINDPEAKS_PERCENTILE: 39
HOTSPOT_SCORE: 0.1104
HOTSPOT_PERCENTILE: 43
IROC_SCORE: 0.686
IROC_PERCENTILE: 33
POISSON_SCORE: 0.2658
POISSON_PERCENTILE: 45
MAXIMUM_REPLICATE_CORRELATION: 0.86

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

molecule: genomic DNA

organism: Homo sapiens

source_name: specified brain region obtained by post-mortem collection in a longitudinal study; DNA_Lib 559

extract_protocol: Library construction protocol: Single read - Illumina

tag: sample alias

tag: sample common name

value: Brain, Substantia Nigra

value: Post-Mortem

value: no AD evident at demise

tag: molecule

tag: disease

value: Substantia Nigra

value: Male

value: Primary Tissue

value: Brain

value: Rush University Medical Center

value: 81.0 Years

value: 0.5 to 3 million cells

value: cell/nuclei lysis

value: ~1 ug

value: Millipore

value: Histone H3K27me3

value: Branson


title: ChIP-Seq analysis of H3K9me3 in human Mobilized CD34 cells; DNA_Lib 254

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: DNA_Lib 254
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8628
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.2397
****************
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: GSM772938_BI.Mobilized_CD34_Primary_Cells.H3K9me3.RO_01536.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 254-DNA_Lib 254-DNA_Lib 254-DNA_Lib 254-DNA_Lib 254.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of Mobilized CD34 Primary Cells Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K9me3 ChIP-Seq on Mobilized CD34 Primary Cells, Donor RO 01536, 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.10754
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 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 11,948,706
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 49
FINDPEAKS_SCORE: 0.2982
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.3614
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.9556
IROC_PERCENTILE: 96
POISSON_SCORE: 0.4866
POISSON_PERCENTILE: 100
MAXIMUM_REPLICATE_CORRELATION: 0.92

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

ANALYSIS FILE NAME: GSM772938_BI.Mobilized_CD34_Primary_Cells.H3K9me3.RO_01536.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 254-DNA_Lib 254-DNA_Lib 254-DNA_Lib 254-DNA_Lib 254.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of Mobilized CD34 Primary Cells Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K9me3 ChIP-Seq read mappings from Mobilized CD34 Primary Cells, Donor RO 01536, 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.11018
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 5
BROWSER_TRACK_NAME: MCD34 H3K9me3 36 54
BROWSER_TRACK_DESCRIPTION: BI Mobilized CD34 Primary Cells Histone H3K9me3 Donor RO 01536 Library DNA_Lib 254 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 11,948,706
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 49
FINDPEAKS_SCORE: 0.2982
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.3614
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.9556
IROC_PERCENTILE: 96
POISSON_SCORE: 0.4866
POISSON_PERCENTILE: 100
MAXIMUM_REPLICATE_CORRELATION: 0.92

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

source_name: flow sorted CD34+ cells from cord blood; DNA_Lib 254

value: CD34 Primary Cells

value: genomic DNA

value: FHCRC HEIMFELD

value: Primary Cell

tag: markers

value: 27 years

value: Female

value: Hispanic

value: Protein A-Sepharose 4B

value: 10 ul bed volume

value: Abcam

value: Histone H3K9me3


title: ChIP-Seq analysis of H3K9me3 in human CD25+ CD127- Treg cells; DNA_Lib 310

description:
sample_term_id: CL_0000792
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 310
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8633
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.9459
****************
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: GSM772943_BI.CD4+_CD25+_CD127-_Treg_Primary_Cells.H3K9me3.Donor_62.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 310-DNA_Lib 310-DNA_Lib 310-DNA_Lib 310.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of CD4+ CD25+ CD127- Treg Primary Cells Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K9me3 ChIP-Seq on CD4+ CD25+ CD127- Treg Primary Cells, Donor Donor 62, 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.10648
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 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 21,412,637
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 49
FINDPEAKS_SCORE: 0.0595
FINDPEAKS_PERCENTILE: 61
HOTSPOT_SCORE: 0.1264
HOTSPOT_PERCENTILE: 61
IROC_SCORE: 0.7236
IROC_PERCENTILE: 20
POISSON_SCORE: 0.317
POISSON_PERCENTILE: 61
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM772943_BI.CD4+_CD25+_CD127-_Treg_Primary_Cells.H3K9me3.Donor_62.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 310-DNA_Lib 310-DNA_Lib 310-DNA_Lib 310.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of CD4+ CD25+ CD127- Treg Primary Cells Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K9me3 ChIP-Seq read mappings from CD4+ CD25+ CD127- Treg Primary Cells, Donor Donor 62, 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.10912
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 5
BROWSER_TRACK_NAME: CCCTreg H3K9me3 62 10
BROWSER_TRACK_DESCRIPTION: BI CD4+ CD25+ CD127- Treg Primary Cells Histone H3K9me3 Donor 62 Library DNA_Lib 310 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 21,412,637
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 49
FINDPEAKS_SCORE: 0.0595
FINDPEAKS_PERCENTILE: 61
HOTSPOT_SCORE: 0.1264
HOTSPOT_PERCENTILE: 61
IROC_SCORE: 0.7236
IROC_PERCENTILE: 20
POISSON_SCORE: 0.317
POISSON_PERCENTILE: 61
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: CD25+ CD127- Treg is one of  CD4+  T cell subsets  that purified by microbeads, LS column and FACS ; DNA_Lib 310

value: BioSam 129

value: CD4+ CD25+ CD127- Treg Primary Cells

value: presumed normal

value: CD4+ T cell

value: CD25+ CD127- Treg

value: Unknown

value: Donor 62

value: Dana Farber

value: 0.5 to 3 million cells


title: ChIP-Seq analysis of H3K9me3 in human CD25- CD45RO+ mem cells; DNA_Lib 721

description:
sample_term_id: CL_0000897
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 721
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8617
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.9449
****************
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: GSM772927_BI.CD4+_CD25-_CD45RO+_Memory_Primary_Cells.H3K9me3.Donor_62.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 721-DNA_Lib 721-DNA_Lib 721.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of CD4+ CD25- CD45RO+ Memory Primary Cells Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K9me3 ChIP-Seq on CD4+ CD25- CD45RO+ Memory Primary Cells, Donor Donor 62, 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.10669
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 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 20,059,569
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 49
FINDPEAKS_SCORE: 0.0246
FINDPEAKS_PERCENTILE: 37
HOTSPOT_SCORE: 0.0862
HOTSPOT_PERCENTILE: 35
IROC_SCORE: 0.8191
IROC_PERCENTILE: 43
POISSON_SCORE: 0.1824
POISSON_PERCENTILE: 29
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM772927_BI.CD4+_CD25-_CD45RO+_Memory_Primary_Cells.H3K9me3.Donor_62.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 721-DNA_Lib 721-DNA_Lib 721.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of CD4+ CD25- CD45RO+ Memory Primary Cells Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K9me3 ChIP-Seq read mappings from CD4+ CD25- CD45RO+ Memory Primary Cells, Donor Donor 62, 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.10933
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 5
BROWSER_TRACK_NAME: CCCM H3K9me3 62 21
BROWSER_TRACK_DESCRIPTION: BI CD4+ CD25- CD45RO+ Memory Primary Cells Histone H3K9me3 Donor 62 Library DNA_Lib 721 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 20,059,569
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 49
FINDPEAKS_SCORE: 0.0246
FINDPEAKS_PERCENTILE: 37
HOTSPOT_SCORE: 0.0862
HOTSPOT_PERCENTILE: 35
IROC_SCORE: 0.8191
IROC_PERCENTILE: 43
POISSON_SCORE: 0.1824
POISSON_PERCENTILE: 29
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: CD25- CD45RO+ mem is one of  CD4+  T cell subsets  that purified by microbeads, LS column and FACS ; DNA_Lib 721

value: BioSam 132

value: CD4+ CD25- CD45RO+ Memory Primary Cells

value: genomic DNA

value: CD25- CD45RO+ mem

value: Primary Cell

value: cell/nuclei lysis

value: ~1 ug

value: Branson


title: ChIP-Seq analysis of H3K36me3 in human CD25- CD45RA+ naive cells; DNA_Lib 725

description:
sample_term_id: CL_0000492
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 725
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8613
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.9443
****************
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: GSM772923_BI.CD4+_CD25-_CD45RA+_Naive_Primary_Cells.H3K36me3.Donor_62.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 725-DNA_Lib 725-DNA_Lib 725-DNA_Lib 725.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of CD4+ CD25- CD45RA+ Naive Primary Cells Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K36me3 ChIP-Seq on CD4+ CD25- CD45RA+ Naive Primary Cells, Donor Donor 62, 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.10590
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 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 13,741,822
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 49
FINDPEAKS_SCORE: 0.0756
FINDPEAKS_PERCENTILE: 39
HOTSPOT_SCORE: 0.1938
HOTSPOT_PERCENTILE: 41
IROC_SCORE: 0.8543
IROC_PERCENTILE: 16
POISSON_SCORE: 0.2839
POISSON_PERCENTILE: 18
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM772923_BI.CD4+_CD25-_CD45RA+_Naive_Primary_Cells.H3K36me3.Donor_62.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 725-DNA_Lib 725-DNA_Lib 725-DNA_Lib 725.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of CD4+ CD25- CD45RA+ Naive Primary Cells Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K36me3 ChIP-Seq read mappings from CD4+ CD25- CD45RA+ Naive Primary Cells, Donor Donor 62, 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.10854
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 5
BROWSER_TRACK_NAME: CCCN H3K36me3 62 25
BROWSER_TRACK_DESCRIPTION: BI CD4+ CD25- CD45RA+ Naive Primary Cells Histone H3K36me3 Donor 62 Library DNA_Lib 725 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 13,741,822
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 49
FINDPEAKS_SCORE: 0.0756
FINDPEAKS_PERCENTILE: 39
HOTSPOT_SCORE: 0.1938
HOTSPOT_PERCENTILE: 41
IROC_SCORE: 0.8543
IROC_PERCENTILE: 16
POISSON_SCORE: 0.2839
POISSON_PERCENTILE: 18
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: CD25- CD45RA+ naive is one of  CD4+  T cell subsets  that purified by microbeads, LS column and FACS ; DNA_Lib 725

value: BioSam 133

value: CD4+ CD25- CD45RA+ Naive Primary Cells

value: CD25- CD45RA+ naive

value: Protein A-Sepharose 4B

value: 10 ul bed volume

value: Abcam

value: Histone H3K36me3


title: ChIP-Seq analysis of H3K9me3 in human CD25- CD45RA+ naive cells; DNA_Lib 728

description:
sample_term_id: CL_0000492
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 728
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8611
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.9443
****************
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: GSM772921_BI.CD4+_CD25-_CD45RA+_Naive_Primary_Cells.H3K9me3.Donor_62.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 728-DNA_Lib 728-DNA_Lib 728-DNA_Lib 728.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of CD4+ CD25- CD45RA+ Naive Primary Cells Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K9me3 ChIP-Seq on CD4+ CD25- CD45RA+ Naive Primary Cells, Donor Donor 62, 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.10739
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 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 10,696,515
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 49
FINDPEAKS_SCORE: 0.0345
FINDPEAKS_PERCENTILE: 53
HOTSPOT_SCORE: 0.1237
HOTSPOT_PERCENTILE: 57
IROC_SCORE: 0.5816
IROC_PERCENTILE: 6
POISSON_SCORE: 0.2078
POISSON_PERCENTILE: 39
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM772921_BI.CD4+_CD25-_CD45RA+_Naive_Primary_Cells.H3K9me3.Donor_62.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 728-DNA_Lib 728-DNA_Lib 728-DNA_Lib 728.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of CD4+ CD25- CD45RA+ Naive Primary Cells Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K9me3 ChIP-Seq read mappings from CD4+ CD25- CD45RA+ Naive Primary Cells, Donor Donor 62, 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.11003
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 5
BROWSER_TRACK_NAME: CCCN H3K9me3 62 28
BROWSER_TRACK_DESCRIPTION: BI CD4+ CD25- CD45RA+ Naive Primary Cells Histone H3K9me3 Donor 62 Library DNA_Lib 728 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 10,696,515
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 49
FINDPEAKS_SCORE: 0.0345
FINDPEAKS_PERCENTILE: 53
HOTSPOT_SCORE: 0.1237
HOTSPOT_PERCENTILE: 57
IROC_SCORE: 0.5816
IROC_PERCENTILE: 6
POISSON_SCORE: 0.2078
POISSON_PERCENTILE: 39
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: CD25- CD45RA+ naive is one of  CD4+  T cell subsets  that purified by microbeads, LS column and FACS ; DNA_Lib 728

value: presumed normal

value: CD4+ T cell

value: Unknown

value: Donor 62

value: Dana Farber

value: Histone H3K9me3


title: ChIP-Seq analysis of WCE in human CD25+ CD127- Treg cells; DNA_Lib 265

description:
sample_term_id: CL_0000792
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 265
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8604
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.9459
****************
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: GSM772914_BI.CD4+_CD25+_CD127-_Treg_Primary_Cells.Input.Donor_62.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 265-DNA_Lib 265-DNA_Lib 265-DNA_Lib 265.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of CD4+ CD25+ CD127- Treg Primary Cells ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina reads produced by ChIP-Seq Input on CD4+ CD25+ CD127- Treg Primary Cells, Donor Donor 62, 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.10596
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 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 40,578,679
NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 56
FINDPEAKS_SCORE: 0.0056
FINDPEAKS_PERCENTILE: 59
HOTSPOT_SCORE: 0.0035
HOTSPOT_PERCENTILE: 16
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.0255
POISSON_PERCENTILE: 13
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM772914_BI.CD4+_CD25+_CD127-_Treg_Primary_Cells.Input.Donor_62.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 265-DNA_Lib 265-DNA_Lib 265-DNA_Lib 265.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of CD4+ CD25+ CD127- Treg Primary Cells ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina ChIP-Seq Input read mappings from CD4+ CD25+ CD127- Treg Primary Cells, Donor Donor 62, 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.10860
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 5
BROWSER_TRACK_NAME: CCCTreg Input 62 65
BROWSER_TRACK_DESCRIPTION: BI CD4+ CD25+ CD127- Treg Primary Cells ChIP-Seq Input Donor 62 Library DNA_Lib 265 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 40,578,679
NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 56
FINDPEAKS_SCORE: 0.0056
FINDPEAKS_PERCENTILE: 59
HOTSPOT_SCORE: 0.0035
HOTSPOT_PERCENTILE: 16
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.0255
POISSON_PERCENTILE: 13
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: CD25+ CD127- Treg is one of  CD4+  T cell subsets  that purified by microbeads, LS column and FACS ; DNA_Lib 265

value: BioSam 129

value: CD4+ CD25+ CD127- Treg Primary Cells

value: genomic DNA

value: CD25+ CD127- Treg

value: Primary Cell

value: standard

value: ChIP-Seq Input

value: Input


title: ChIP-Seq analysis of H3K4me1 in human angular gyrus cells; DNA_Lib 630

description:
sample_term_id: UBERON_0002686
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 630
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8652
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.9456
****************
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: GSM772962_BI.Brain_Angular_Gyrus.H3K4me1.149.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 630-DNA_Lib 630-DNA_Lib 630.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of Brain Angular Gyrus Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me1 ChIP-Seq on Brain Angular Gyrus, Donor 149, 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.10697
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 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 29,655,347
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 54
FINDPEAKS_SCORE: 0.1284
FINDPEAKS_PERCENTILE: 19
HOTSPOT_SCORE: 0.2356
HOTSPOT_PERCENTILE: 19
IROC_SCORE: 0.9264
IROC_PERCENTILE: 24
POISSON_SCORE: 0.4189
POISSON_PERCENTILE: 33
MAXIMUM_REPLICATE_CORRELATION: 0.96

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

ANALYSIS FILE NAME: GSM772962_BI.Brain_Angular_Gyrus.H3K4me1.149.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 630-DNA_Lib 630-DNA_Lib 630.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of Brain Angular Gyrus Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me1 ChIP-Seq read mappings from Brain Angular Gyrus, Donor 149, 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.10961
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 5
BROWSER_TRACK_NAME: BAG H3K4me1 49 30
BROWSER_TRACK_DESCRIPTION: BI Brain Angular Gyrus Histone H3K4me1 Donor 149 Library DNA_Lib 630 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 29,655,347
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 54
FINDPEAKS_SCORE: 0.1284
FINDPEAKS_PERCENTILE: 19
HOTSPOT_SCORE: 0.2356
HOTSPOT_PERCENTILE: 19
IROC_SCORE: 0.9264
IROC_PERCENTILE: 24
POISSON_SCORE: 0.4189
POISSON_PERCENTILE: 33
MAXIMUM_REPLICATE_CORRELATION: 0.96

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

source_name: specified brain region obtained by post-mortem collection in a longitudinal study; DNA_Lib 630

value: Brain, Angular Gyrus

value: Post-Mortem

value: no AD evident at demise

value: Angular gyrus

value: Male

value: Primary Tissue

value: Brain

value: Rush University Medical Center

value: 81.0 Years

value: Protein A-Sepharose 4B

value: 0.5 to 3 million cells

value: cell/nuclei lysis

value: ~1 ug

value: 10 ul bed volume

value: Histone H3K4me1

value: Branson


title: ChIP-Seq analysis of WCE in human CD25- Th cells; DNA_Lib 266

description:
sample_term_id: CL_0000492
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 266
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8605
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.9442
****************
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: GSM772915_BI.CD4+_CD25-_Th_Primary_Cells.Input.Donor_62.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 266-DNA_Lib 266-DNA_Lib 266-DNA_Lib 266.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of CD4+ CD25- Th Primary Cells ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina reads produced by ChIP-Seq Input on CD4+ CD25- Th Primary Cells, Donor Donor 62, 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.10655
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 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 34,542,739
NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 56
FINDPEAKS_SCORE: 0.006
FINDPEAKS_PERCENTILE: 67
HOTSPOT_SCORE: 0.0048
HOTSPOT_PERCENTILE: 28
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.0321
POISSON_PERCENTILE: 18
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM772915_BI.CD4+_CD25-_Th_Primary_Cells.Input.Donor_62.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 266-DNA_Lib 266-DNA_Lib 266-DNA_Lib 266.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of CD4+ CD25- Th Primary Cells ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina ChIP-Seq Input read mappings from CD4+ CD25- Th Primary Cells, Donor Donor 62, 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.10919
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 5
BROWSER_TRACK_NAME: CCT Input 62 66
BROWSER_TRACK_DESCRIPTION: BI CD4+ CD25- Th Primary Cells ChIP-Seq Input Donor 62 Library DNA_Lib 266 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 34,542,739
NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 56
FINDPEAKS_SCORE: 0.006
FINDPEAKS_PERCENTILE: 67
HOTSPOT_SCORE: 0.0048
HOTSPOT_PERCENTILE: 28
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.0321
POISSON_PERCENTILE: 18
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: CD25- Th  is one of  CD4+  T cell subsets  that purified by microbeads, LS column and FACS ; DNA_Lib 266

value: BioSam 130

value: CD4+ CD25- Th Primary Cells

value: presumed normal

value: genomic DNA

value: CD4+ T cell

value: CD25- Th

value: Unknown

value: Primary Cell

value: Donor 62

value: Dana Farber

value: standard

value: ChIP-Seq Input

value: Input


title: ChIP-Seq analysis of H3K27me3 in human CD25- CD45RA+ naive cells; DNA_Lib 724

description:
sample_term_id: CL_0000492
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 724
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8601
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.9443
****************
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: GSM772911_BI.CD4+_CD25-_CD45RA+_Naive_Primary_Cells.H3K27me3.Donor_62.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 724-DNA_Lib 724-DNA_Lib 724-DNA_Lib 724.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of CD4+ CD25- CD45RA+ Naive Primary Cells Histone H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K27me3 ChIP-Seq on CD4+ CD25- CD45RA+ Naive Primary Cells, Donor Donor 62, 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.10796
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 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 12,061,395
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 49
FINDPEAKS_SCORE: 0.0377
FINDPEAKS_PERCENTILE: 57
HOTSPOT_SCORE: 0.1676
HOTSPOT_PERCENTILE: 69
IROC_SCORE: 0.7366
IROC_PERCENTILE: 45
POISSON_SCORE: 0.2679
POISSON_PERCENTILE: 47
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM772911_BI.CD4+_CD25-_CD45RA+_Naive_Primary_Cells.H3K27me3.Donor_62.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 724-DNA_Lib 724-DNA_Lib 724-DNA_Lib 724.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of CD4+ CD25- CD45RA+ Naive Primary Cells Histone H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K27me3 ChIP-Seq read mappings from CD4+ CD25- CD45RA+ Naive Primary Cells, Donor Donor 62, 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.11060
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 5
BROWSER_TRACK_NAME: CCCN H3K27me3 62 24
BROWSER_TRACK_DESCRIPTION: BI CD4+ CD25- CD45RA+ Naive Primary Cells Histone H3K27me3 Donor 62 Library DNA_Lib 724 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 12,061,395
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 49
FINDPEAKS_SCORE: 0.0377
FINDPEAKS_PERCENTILE: 57
HOTSPOT_SCORE: 0.1676
HOTSPOT_PERCENTILE: 69
IROC_SCORE: 0.7366
IROC_PERCENTILE: 45
POISSON_SCORE: 0.2679
POISSON_PERCENTILE: 47
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: CD25- CD45RA+ naive is one of  CD4+  T cell subsets  that purified by microbeads, LS column and FACS ; DNA_Lib 724

value: BioSam 133

value: CD4+ CD25- CD45RA+ Naive Primary Cells

value: CD25- CD45RA+ naive

value: Protein A-Sepharose 4B

value: 0.5 to 3 million cells

value: cell/nuclei lysis

value: ~1 ug

value: Millipore

value: Histone H3K27me3


title: ChIP-Seq analysis of WCE in human HUES64 derived CD184+ cells; DNA_Lib 264

description:
sample_term_id: CL_0000223
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 264
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8603
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.9461
****************
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: GSM772913_BI.hESC_Derived_CD184+_Endoderm_Cultured_Cells.Input.DNA_Lib_264.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 264-DNA_Lib 264-DNA_Lib 264-DNA_Lib 264.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of hESC Derived CD184+ Endoderm Cultured Cells ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina reads produced by ChIP-Seq Input on hESC Derived CD184+ Endoderm Cultured Cells, Donor DNA_Lib 264, 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.10762
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 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 29,970,166
NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 56
FINDPEAKS_SCORE: 0.0055
FINDPEAKS_PERCENTILE: 57
HOTSPOT_SCORE: 0.0082
HOTSPOT_PERCENTILE: 36
IROC_SCORE: 0.0
IROC_PERCENTILE: 33
POISSON_SCORE: 0.0474
POISSON_PERCENTILE: 41
MAXIMUM_REPLICATE_CORRELATION: 0.96

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

ANALYSIS FILE NAME: GSM772913_BI.hESC_Derived_CD184+_Endoderm_Cultured_Cells.Input.DNA_Lib_264.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 264-DNA_Lib 264-DNA_Lib 264-DNA_Lib 264.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of hESC Derived CD184+ Endoderm Cultured Cells ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina ChIP-Seq Input read mappings from hESC Derived CD184+ Endoderm Cultured Cells, Donor DNA_Lib 264, 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.11026
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 5
BROWSER_TRACK_NAME: hDCE Input 64
BROWSER_TRACK_DESCRIPTION: BI hESC Derived CD184+ Endoderm Cultured Cells ChIP-Seq Input Library DNA_Lib 264 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 29,970,166
NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 56
FINDPEAKS_SCORE: 0.0055
FINDPEAKS_PERCENTILE: 57
HOTSPOT_SCORE: 0.0082
HOTSPOT_PERCENTILE: 36
IROC_SCORE: 0.0
IROC_PERCENTILE: 33
POISSON_SCORE: 0.0474
POISSON_PERCENTILE: 41
MAXIMUM_REPLICATE_CORRELATION: 0.96

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

source_name: CD184+ endoderm differentiated in vitro from stem cells; DNA_Lib 264

value: CD184+ endoderm cultured cells

tag: lineage

tag: medium

value: RPMI 100ng/mL Activin A 50ng/mL Wnt3a

value: genomic DNA

value: presumed normal

tag: passage

tag: line

value: HUES64 derived CD184+

value: in vitro culture

tag: batch

value: BioSAli 136

value: Cell Line

value: differentiated

tag: Sex

value: Male

value: Harvard University

value: Branson


title: ChIP-Seq analysis of H3K36me3 in human HUES64 derived CD184+ cells; DNA_Lib 263

description:
sample_term_id: CL_0000223
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 263
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8602
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.9461
****************
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: GSM772912_BI.hESC_Derived_CD184+_Endoderm_Cultured_Cells.H3K36me3.DNA_Lib_263.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 263-DNA_Lib 263-DNA_Lib 263-DNA_Lib 263.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of hESC Derived CD184+ Endoderm Cultured Cells Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K36me3 ChIP-Seq on hESC Derived CD184+ Endoderm Cultured Cells, Donor DNA_Lib 263, 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.10621
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 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 28,933,418
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 49
FINDPEAKS_SCORE: 0.3927
FINDPEAKS_PERCENTILE: 86
HOTSPOT_SCORE: 0.3304
HOTSPOT_PERCENTILE: 80
IROC_SCORE: 0.9888
IROC_PERCENTILE: 71
POISSON_SCORE: 0.6052
POISSON_PERCENTILE: 92
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM772912_BI.hESC_Derived_CD184+_Endoderm_Cultured_Cells.H3K36me3.DNA_Lib_263.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 263-DNA_Lib 263-DNA_Lib 263-DNA_Lib 263.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of hESC Derived CD184+ Endoderm Cultured Cells Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K36me3 ChIP-Seq read mappings from hESC Derived CD184+ Endoderm Cultured Cells, Donor DNA_Lib 263, 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.10885
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 5
BROWSER_TRACK_NAME: hDCE H3K36me3 63
BROWSER_TRACK_DESCRIPTION: BI hESC Derived CD184+ Endoderm Cultured Cells Histone H3K36me3 Library DNA_Lib 263 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 28,933,418
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 49
FINDPEAKS_SCORE: 0.3927
FINDPEAKS_PERCENTILE: 86
HOTSPOT_SCORE: 0.3304
HOTSPOT_PERCENTILE: 80
IROC_SCORE: 0.9888
IROC_PERCENTILE: 71
POISSON_SCORE: 0.6052
POISSON_PERCENTILE: 92
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: CD184+ endoderm differentiated in vitro from stem cells; DNA_Lib 263

value: Protein A-Sepharose 4B

value: 0.5 to 3 million cells

value: 10 ul bed volume

value: Abcam

value: Histone H3K36me3


title: ChIP-Seq analysis of WCE in human CD25- CD45RA+ naive cells; DNA_Lib 729

description:
sample_term_id: CL_0000492
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 729
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8610
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.9443
****************
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: GSM772920_BI.CD4+_CD25-_CD45RA+_Naive_Primary_Cells.Input.Donor_62.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 729-DNA_Lib 729-DNA_Lib 729-DNA_Lib 729.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of CD4+ CD25- CD45RA+ Naive Primary Cells ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina reads produced by ChIP-Seq Input on CD4+ CD25- CD45RA+ Naive Primary Cells, Donor Donor 62, 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.10599
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 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 14,830,470
NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 56
FINDPEAKS_SCORE: 0.0111
FINDPEAKS_PERCENTILE: 98
HOTSPOT_SCORE: 0.1152
HOTSPOT_PERCENTILE: 98
IROC_SCORE: 0.5934
IROC_PERCENTILE: 37
POISSON_SCORE: 0.1656
POISSON_PERCENTILE: 98
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM772920_BI.CD4+_CD25-_CD45RA+_Naive_Primary_Cells.Input.Donor_62.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 729-DNA_Lib 729-DNA_Lib 729-DNA_Lib 729.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of CD4+ CD25- CD45RA+ Naive Primary Cells ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina ChIP-Seq Input read mappings from CD4+ CD25- CD45RA+ Naive Primary Cells, Donor Donor 62, 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.10863
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 5
BROWSER_TRACK_NAME: CCCN Input 62 29
BROWSER_TRACK_DESCRIPTION: BI CD4+ CD25- CD45RA+ Naive Primary Cells ChIP-Seq Input Donor 62 Library DNA_Lib 729 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 14,830,470
NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 56
FINDPEAKS_SCORE: 0.0111
FINDPEAKS_PERCENTILE: 98
HOTSPOT_SCORE: 0.1152
HOTSPOT_PERCENTILE: 98
IROC_SCORE: 0.5934
IROC_PERCENTILE: 37
POISSON_SCORE: 0.1656
POISSON_PERCENTILE: 98
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: CD25- CD45RA+ naive is one of  CD4+  T cell subsets  that purified by microbeads, LS column and FACS ; DNA_Lib 729

value: BioSam 133

value: CD4+ CD25- CD45RA+ Naive Primary Cells

value: CD4+ T cell

value: CD25- CD45RA+ naive

value: Unknown

value: Primary Cell

value: Donor 62

value: Dana Farber

value: standard

value: cell/nuclei lysis

value: ChIP-Seq Input

value: Input


title: ChIP-Seq analysis of H3K4me1 in human CD15 cells; Lib EpiLabSPL Row 1796

description:
sample_term_id: CL_0000775
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib EpiLabSPL Row 1796
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8453
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.2562
****************
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: GSM773038_BI.CD15_Primary_Cells.H3K4me1.23.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib EpiLabSPL Row 1796.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of CD15 Primary Cells Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me1 ChIP-Seq on CD15 Primary Cells, Donor 23.0, 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.10819
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 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 30,199,571
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 54
FINDPEAKS_SCORE: 0.5325
FINDPEAKS_PERCENTILE: 94
HOTSPOT_SCORE: 0.5141
HOTSPOT_PERCENTILE: 91
IROC_SCORE: 0.9999
IROC_PERCENTILE: 100
POISSON_SCORE: 0.5761
POISSON_PERCENTILE: 87
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM773038_BI.CD15_Primary_Cells.H3K4me1.23.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib EpiLabSPL Row 1796.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of CD15 Primary Cells Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me1 ChIP-Seq read mappings from CD15 Primary Cells, Donor 23.0, 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.11083
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 5
BROWSER_TRACK_NAME: CD15 H3K4me1 23.0 96
BROWSER_TRACK_DESCRIPTION: BI CD15 Primary Cells Histone H3K4me1 Donor 23.0 Library Lib EpiLabSPL Row 1796 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 30,199,571
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 54
FINDPEAKS_SCORE: 0.5325
FINDPEAKS_PERCENTILE: 94
HOTSPOT_SCORE: 0.5141
HOTSPOT_PERCENTILE: 91
IROC_SCORE: 0.9999
IROC_PERCENTILE: 100
POISSON_SCORE: 0.5761
POISSON_PERCENTILE: 87
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: flow sorted CD15+ cells from cord blood; Lib EpiLabSPL Row 1796

value: CD15 Primary Cells

value: genomic DNA

value: FHCRC

value: Male

value: Protein A-Sepharose 4B

value: 10 million cells

value: SDS lysis

value: 70 ul bed volume

value: Histone H3K4me1

value: Bioruptor


title: ChIP-Seq analysis of H3K9me3 in human CD15 cells; Lib EpiLabSPL Row 1798

description:
sample_term_id: CL_0000775
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib EpiLabSPL Row 1798
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8450
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.2562
****************
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: GSM773035_BI.CD15_Primary_Cells.H3K9me3.23.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib EpiLabSPL Row 1798.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of CD15 Primary Cells Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K9me3 ChIP-Seq on CD15 Primary Cells, Donor 23.0, 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.10716
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 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 24,425,293
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 49
FINDPEAKS_SCORE: 0.1098
FINDPEAKS_PERCENTILE: 86
HOTSPOT_SCORE: 0.1764
HOTSPOT_PERCENTILE: 84
IROC_SCORE: 0.8404
IROC_PERCENTILE: 47
POISSON_SCORE: 0.4075
POISSON_PERCENTILE: 86
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM773035_BI.CD15_Primary_Cells.H3K9me3.23.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib EpiLabSPL Row 1798.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of CD15 Primary Cells Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K9me3 ChIP-Seq read mappings from CD15 Primary Cells, Donor 23.0, 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.10980
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 5
BROWSER_TRACK_NAME: CD15 H3K9me3 23.0 98
BROWSER_TRACK_DESCRIPTION: BI CD15 Primary Cells Histone H3K9me3 Donor 23.0 Library Lib EpiLabSPL Row 1798 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 24,425,293
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 49
FINDPEAKS_SCORE: 0.1098
FINDPEAKS_PERCENTILE: 86
HOTSPOT_SCORE: 0.1764
HOTSPOT_PERCENTILE: 84
IROC_SCORE: 0.8404
IROC_PERCENTILE: 47
POISSON_SCORE: 0.4075
POISSON_PERCENTILE: 86
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: flow sorted CD15+ cells from cord blood; Lib EpiLabSPL Row 1798

value: Primary Cell

value: Abcam

value: Histone H3K9me3


title: ChIP-Seq analysis of H3K27me3 in human CD25- CD45RO+ mem cells; DNA_Lib 717

description:
sample_term_id: CL_0000897
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 717
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8596
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.9449
****************
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: GSM772906_BI.CD4+_CD25-_CD45RO+_Memory_Primary_Cells.H3K27me3.Donor_62.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 717-DNA_Lib 717-DNA_Lib 717.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of CD4+ CD25- CD45RO+ Memory Primary Cells Histone H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K27me3 ChIP-Seq on CD4+ CD25- CD45RO+ Memory Primary Cells, Donor Donor 62, 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.10830
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 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 21,957,381
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 49
FINDPEAKS_SCORE: 0.0085
FINDPEAKS_PERCENTILE: 16
HOTSPOT_SCORE: 0.0987
HOTSPOT_PERCENTILE: 22
IROC_SCORE: 0.6028
IROC_PERCENTILE: 14
POISSON_SCORE: 0.21
POISSON_PERCENTILE: 29
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM772906_BI.CD4+_CD25-_CD45RO+_Memory_Primary_Cells.H3K27me3.Donor_62.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 717-DNA_Lib 717-DNA_Lib 717.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of CD4+ CD25- CD45RO+ Memory Primary Cells Histone H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K27me3 ChIP-Seq read mappings from CD4+ CD25- CD45RO+ Memory Primary Cells, Donor Donor 62, 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.11094
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 5
BROWSER_TRACK_NAME: CCCM H3K27me3 62 17
BROWSER_TRACK_DESCRIPTION: BI CD4+ CD25- CD45RO+ Memory Primary Cells Histone H3K27me3 Donor 62 Library DNA_Lib 717 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 21,957,381
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 49
FINDPEAKS_SCORE: 0.0085
FINDPEAKS_PERCENTILE: 16
HOTSPOT_SCORE: 0.0987
HOTSPOT_PERCENTILE: 22
IROC_SCORE: 0.6028
IROC_PERCENTILE: 14
POISSON_SCORE: 0.21
POISSON_PERCENTILE: 29
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: CD25- CD45RO+ mem is one of  CD4+  T cell subsets  that purified by microbeads, LS column and FACS ; DNA_Lib 717

value: BioSam 132

value: CD4+ CD25- CD45RO+ Memory Primary Cells

value: presumed normal

value: CD4+ T cell

value: CD25- CD45RO+ mem

value: Unknown

value: Donor 62

value: Dana Farber

value: 0.5 to 3 million cells

value: ~1 ug

value: 10 ul bed volume

value: Millipore

value: Histone H3K27me3

value: Branson


title: ChIP-Seq analysis of H3K4me1 in human CD25- CD45RO+ mem cells; DNA_Lib 720

description:
sample_term_id: CL_0000897
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 720
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8618
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.9449
****************
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: GSM772928_BI.CD4+_CD25-_CD45RO+_Memory_Primary_Cells.H3K4me1.Donor_62.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 720-DNA_Lib 720-DNA_Lib 720.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of CD4+ CD25- CD45RO+ Memory Primary Cells Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me1 ChIP-Seq on CD4+ CD25- CD45RO+ Memory Primary Cells, Donor Donor 62, 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.10707
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 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 11,455,899
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 54
FINDPEAKS_SCORE: 0.374
FINDPEAKS_PERCENTILE: 80
HOTSPOT_SCORE: 0.4179
HOTSPOT_PERCENTILE: 80
IROC_SCORE: 0.9964
IROC_PERCENTILE: 89
POISSON_SCORE: 0.4805
POISSON_PERCENTILE: 61
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM772928_BI.CD4+_CD25-_CD45RO+_Memory_Primary_Cells.H3K4me1.Donor_62.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 720-DNA_Lib 720-DNA_Lib 720.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of CD4+ CD25- CD45RO+ Memory Primary Cells Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me1 ChIP-Seq read mappings from CD4+ CD25- CD45RO+ Memory Primary Cells, Donor Donor 62, 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.10971
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 5
BROWSER_TRACK_NAME: CCCM H3K4me1 62 20
BROWSER_TRACK_DESCRIPTION: BI CD4+ CD25- CD45RO+ Memory Primary Cells Histone H3K4me1 Donor 62 Library DNA_Lib 720 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 11,455,899
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 54
FINDPEAKS_SCORE: 0.374
FINDPEAKS_PERCENTILE: 80
HOTSPOT_SCORE: 0.4179
HOTSPOT_PERCENTILE: 80
IROC_SCORE: 0.9964
IROC_PERCENTILE: 89
POISSON_SCORE: 0.4805
POISSON_PERCENTILE: 61
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: CD25- CD45RO+ mem is one of  CD4+  T cell subsets  that purified by microbeads, LS column and FACS ; DNA_Lib 720

value: genomic DNA

value: Primary Cell

value: Protein A-Sepharose 4B

value: cell/nuclei lysis

value: Histone H3K4me1


title: ChIP-Seq analysis of H3K27me3 in human hiPS-18a cells; DNA_Lib 348

description:
sample_term_id: NTR_0001165
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 348
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8625
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.9471
****************
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: GSM772935_BI.iPS-18a.H3K27me3.DNA_Lib_348.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 348-DNA_Lib 348-DNA_Lib 348-DNA_Lib 348.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of iPS-18a Cell Line Histone H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K27me3 ChIP-Seq on the iPS-18a Cell Line, Library DNA_Lib 348, 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.10651
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 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 29,271,816
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 49
FINDPEAKS_SCORE: 0.3547
FINDPEAKS_PERCENTILE: 98
HOTSPOT_SCORE: 0.3692
HOTSPOT_PERCENTILE: 98
IROC_SCORE: 0.9979
IROC_PERCENTILE: 92
POISSON_SCORE: 0.4225
POISSON_PERCENTILE: 86
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM772935_BI.iPS-18a.H3K27me3.DNA_Lib_348.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 348-DNA_Lib 348-DNA_Lib 348-DNA_Lib 348.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of iPS-18a Cell Line Histone H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K27me3 ChIP-Seq read mappings from the iPS-18a Cell Line, Library DNA_Lib 348, 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.10915
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 5
BROWSER_TRACK_NAME: iPS18a H3K27me3 48
BROWSER_TRACK_DESCRIPTION: BI iPS-18a Cell Line Histone H3K27me3 Library DNA_Lib 348 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 29,271,816
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 49
FINDPEAKS_SCORE: 0.3547
FINDPEAKS_PERCENTILE: 98
HOTSPOT_SCORE: 0.3692
HOTSPOT_PERCENTILE: 98
IROC_SCORE: 0.9979
IROC_PERCENTILE: 92
POISSON_SCORE: 0.4225
POISSON_PERCENTILE: 86
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: induced pleuripotent 18a stem cell line; DNA_Lib 348

value: induced pluripotent stem cells

value: BioSam 173

value: iPS-18a Cell Line

value: induced pluripotent cells

value: 10% KOSR (Invitrogen)

value: presumed normal

value: BioSAli 176

value: Cell Line

value: undifferentiated

value: Harvard


title: ChIP-Seq analysis of WCE in human CD25- IL17- Th stim MACS cells; DNA_Lib 715

description:
sample_term_id: CL_0000492
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 715
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8594
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.9445
****************
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: GSM772904_BI.CD4+_CD25-_IL17-_PMA-Ionomycin_stimulated_MACS_purified_Th_Primary_Cells.Input.Donor_62.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 715-DNA_Lib 715-DNA_Lib 715.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of CD4+ CD25- IL17- PMA-Ionomycin stimulated MACS purified Th Primary Cells ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina reads produced by ChIP-Seq Input on CD4+ CD25- IL17- PMA-Ionomycin stimulated MACS purified Th Primary Cells, Donor Donor 62, 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.10588
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 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 33,290,923
NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 56
FINDPEAKS_SCORE: 0.0063
FINDPEAKS_PERCENTILE: 72
HOTSPOT_SCORE: 0.0101
HOTSPOT_PERCENTILE: 49
IROC_SCORE: 0.0
IROC_PERCENTILE: 33
POISSON_SCORE: 0.0575
POISSON_PERCENTILE: 54
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM772904_BI.CD4+_CD25-_IL17-_PMA-Ionomycin_stimulated_MACS_purified_Th_Primary_Cells.Input.Donor_62.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 715-DNA_Lib 715-DNA_Lib 715.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of CD4+ CD25- IL17- PMA-Ionomycin stimulated MACS purified Th Primary Cells ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina ChIP-Seq Input read mappings from CD4+ CD25- IL17- PMA-Ionomycin stimulated MACS purified Th Primary Cells, Donor Donor 62, 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.10852
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 5
BROWSER_TRACK_NAME: CCIPsMpT Input 62 15
BROWSER_TRACK_DESCRIPTION: BI CD4+ CD25- IL17- PMA-Ionomycin stimulated MACS purified Th Primary Cells ChIP-Seq Input Donor 62 Library DNA_Lib 715 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 33,290,923
NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 56
FINDPEAKS_SCORE: 0.0063
FINDPEAKS_PERCENTILE: 72
HOTSPOT_SCORE: 0.0101
HOTSPOT_PERCENTILE: 49
IROC_SCORE: 0.0
IROC_PERCENTILE: 33
POISSON_SCORE: 0.0575
POISSON_PERCENTILE: 54
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: CD25- IL17- Th stim MACS is one of  CD4+  T cell subsets  that purified by microbeads, LS column  ; DNA_Lib 715

value: BioSam 135

value: CD4+ T cell

value: CD25- IL17- Th stim MACS

value: Unknown

value: Donor 62

value: Dana Farber

value: standard

value: ChIP-Seq Input

value: Input


title: ChIP-Seq analysis of H3K9me3 in human CD25- IL17- Th stim MACS cells; DNA_Lib 714

description:
sample_term_id: CL_0000492
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 714
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8593
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.9445
****************
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: GSM772903_BI.CD4+_CD25-_IL17-_PMA-Ionomycin_stimulated_MACS_purified_Th_Primary_Cells.H3K9me3.Donor_62.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 714-DNA_Lib 714-DNA_Lib 714.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of CD4+ CD25- IL17- PMA-Ionomycin stimulated MACS purified Th Primary Cells Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K9me3 ChIP-Seq on CD4+ CD25- IL17- PMA-Ionomycin stimulated MACS purified Th Primary Cells, Donor Donor 62, 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.10674
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 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 36,266,834
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 49
FINDPEAKS_SCORE: 0.0277
FINDPEAKS_PERCENTILE: 47
HOTSPOT_SCORE: 0.0662
HOTSPOT_PERCENTILE: 18
IROC_SCORE: 0.9091
IROC_PERCENTILE: 80
POISSON_SCORE: 0.1994
POISSON_PERCENTILE: 35
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM772903_BI.CD4+_CD25-_IL17-_PMA-Ionomycin_stimulated_MACS_purified_Th_Primary_Cells.H3K9me3.Donor_62.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 714-DNA_Lib 714-DNA_Lib 714.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of CD4+ CD25- IL17- PMA-Ionomycin stimulated MACS purified Th Primary Cells Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K9me3 ChIP-Seq read mappings from CD4+ CD25- IL17- PMA-Ionomycin stimulated MACS purified Th Primary Cells, Donor Donor 62, 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.10938
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 5
BROWSER_TRACK_NAME: CCIPsMpT H3K9me3 62 14
BROWSER_TRACK_DESCRIPTION: BI CD4+ CD25- IL17- PMA-Ionomycin stimulated MACS purified Th Primary Cells Histone H3K9me3 Donor 62 Library DNA_Lib 714 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 36,266,834
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 49
FINDPEAKS_SCORE: 0.0277
FINDPEAKS_PERCENTILE: 47
HOTSPOT_SCORE: 0.0662
HOTSPOT_PERCENTILE: 18
IROC_SCORE: 0.9091
IROC_PERCENTILE: 80
POISSON_SCORE: 0.1994
POISSON_PERCENTILE: 35
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: CD25- IL17- Th stim MACS is one of  CD4+  T cell subsets  that purified by microbeads, LS column  ; DNA_Lib 714

value: genomic DNA

value: Primary Cell

value: Protein A-Sepharose 4B

value: 0.5 to 3 million cells

value: cell/nuclei lysis

value: ~1 ug

value: 10 ul bed volume

value: Abcam

value: Histone H3K9me3

value: Branson