title: ChIP-Seq analysis of H3K4me1 in human CD25- IL17+ Th17 stim cells; DNA_Lib 743

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 743
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8675
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.9446
****************
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: GSM772985_BI.CD4+_CD25-_IL17+_PMA-Ionomcyin_stimulated_Th17_Primary_Cells.H3K4me1.Donor_62.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 743-DNA_Lib 743-DNA_Lib 743-DNA_Lib 743.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of CD4+ CD25- IL17+ PMA-Ionomcyin stimulated Th17 Primary Cells Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me1 ChIP-Seq on CD4+ CD25- IL17+ PMA-Ionomcyin stimulated Th17 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.10771
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: 30,083,528
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 54
FINDPEAKS_SCORE: 0.3086
FINDPEAKS_PERCENTILE: 70
HOTSPOT_SCORE: 0.3248
HOTSPOT_PERCENTILE: 50
IROC_SCORE: 0.9959
IROC_PERCENTILE: 83
POISSON_SCORE: 0.4186
POISSON_PERCENTILE: 31
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM772985_BI.CD4+_CD25-_IL17+_PMA-Ionomcyin_stimulated_Th17_Primary_Cells.H3K4me1.Donor_62.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 743-DNA_Lib 743-DNA_Lib 743-DNA_Lib 743.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of CD4+ CD25- IL17+ PMA-Ionomcyin stimulated Th17 Primary Cells Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me1 ChIP-Seq read mappings from CD4+ CD25- IL17+ PMA-Ionomcyin stimulated Th17 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.11035
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: CCIPsT H3K4me1 62 43
BROWSER_TRACK_DESCRIPTION: BI CD4+ CD25- IL17+ PMA-Ionomcyin stimulated Th17 Primary Cells Histone H3K4me1 Donor 62 Library DNA_Lib 743 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 30,083,528
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 54
FINDPEAKS_SCORE: 0.3086
FINDPEAKS_PERCENTILE: 70
HOTSPOT_SCORE: 0.3248
HOTSPOT_PERCENTILE: 50
IROC_SCORE: 0.9959
IROC_PERCENTILE: 83
POISSON_SCORE: 0.4186
POISSON_PERCENTILE: 31
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: CD25- IL17+ Th17 stim is one of  CD4+  T cell subsets  that purified by microbeads, LS column and FACS ; DNA_Lib 743

value: BioSam 134

value: presumed normal

value: CD4+ T cell

value: CD25- IL17+ Th17 stim

value: Unknown

value: Primary Cell

value: Donor 62

value: Dana Farber


title: ChIP-Seq analysis of WCE in human CD25- IL17+ Th17 stim cells; DNA_Lib 740

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: 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 740
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8678
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.9446
****************
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: GSM772988_BI.CD4+_CD25-_IL17+_PMA-Ionomcyin_stimulated_Th17_Primary_Cells.Input.Donor_62.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 740-DNA_Lib 740-DNA_Lib 740-DNA_Lib 740.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of CD4+ CD25- IL17+ PMA-Ionomcyin stimulated Th17 Primary Cells ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina reads produced by ChIP-Seq Input on CD4+ CD25- IL17+ PMA-Ionomcyin stimulated Th17 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.10605
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: 32,550,112
NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 56
FINDPEAKS_SCORE: 0.0054
FINDPEAKS_PERCENTILE: 56
HOTSPOT_SCORE: 0.0255
HOTSPOT_PERCENTILE: 70
IROC_SCORE: 0.0
IROC_PERCENTILE: 33
POISSON_SCORE: 0.0681
POISSON_PERCENTILE: 62
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM772988_BI.CD4+_CD25-_IL17+_PMA-Ionomcyin_stimulated_Th17_Primary_Cells.Input.Donor_62.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 740-DNA_Lib 740-DNA_Lib 740-DNA_Lib 740.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of CD4+ CD25- IL17+ PMA-Ionomcyin stimulated Th17 Primary Cells ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina ChIP-Seq Input read mappings from CD4+ CD25- IL17+ PMA-Ionomcyin stimulated Th17 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.10869
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: CCIPsT Input 62 40
BROWSER_TRACK_DESCRIPTION: BI CD4+ CD25- IL17+ PMA-Ionomcyin stimulated Th17 Primary Cells ChIP-Seq Input Donor 62 Library DNA_Lib 740 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 32,550,112
NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 56
FINDPEAKS_SCORE: 0.0054
FINDPEAKS_PERCENTILE: 56
HOTSPOT_SCORE: 0.0255
HOTSPOT_PERCENTILE: 70
IROC_SCORE: 0.0
IROC_PERCENTILE: 33
POISSON_SCORE: 0.0681
POISSON_PERCENTILE: 62
MAXIMUM_REPLICATE_CORRELATION: NA

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

molecule: genomic DNA

organism: Homo sapiens

source_name: CD25- IL17+ Th17 stim is one of  CD4+  T cell subsets  that purified by microbeads, LS column and FACS ; DNA_Lib 740

extract_protocol: Library construction protocol: Single read - Illumina

tag: sample alias

tag: sample common name

tag: molecule

value: genomic DNA

tag: disease

tag: markers

value: standard

value: cell/nuclei lysis

value: ChIP-Seq Input

value: Input

value: Branson


title: ChIP-Seq analysis of H3K4me3 in human CD25- IL17+ Th17 stim cells; DNA_Lib 742

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 742
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8676
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.9446
****************
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: GSM772986_BI.CD4+_CD25-_IL17+_PMA-Ionomcyin_stimulated_Th17_Primary_Cells.H3K4me3.Donor_62.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 742-DNA_Lib 742-DNA_Lib 742-DNA_Lib 742.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of CD4+ CD25- IL17+ PMA-Ionomcyin stimulated Th17 Primary Cells Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me3 ChIP-Seq on CD4+ CD25- IL17+ PMA-Ionomcyin stimulated Th17 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.10810
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: 31,478,260
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 54
FINDPEAKS_SCORE: 0.1664
FINDPEAKS_PERCENTILE: 30
HOTSPOT_SCORE: 0.19
HOTSPOT_PERCENTILE: 22
IROC_SCORE: 0.9997
IROC_PERCENTILE: 76
POISSON_SCORE: 0.2246
POISSON_PERCENTILE: 17
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM772986_BI.CD4+_CD25-_IL17+_PMA-Ionomcyin_stimulated_Th17_Primary_Cells.H3K4me3.Donor_62.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 742-DNA_Lib 742-DNA_Lib 742-DNA_Lib 742.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of CD4+ CD25- IL17+ PMA-Ionomcyin stimulated Th17 Primary Cells Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me3 ChIP-Seq read mappings from CD4+ CD25- IL17+ PMA-Ionomcyin stimulated Th17 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.11074
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: CCIPsT H3K4me3 62 42
BROWSER_TRACK_DESCRIPTION: BI CD4+ CD25- IL17+ PMA-Ionomcyin stimulated Th17 Primary Cells Histone H3K4me3 Donor 62 Library DNA_Lib 742 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 31,478,260
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 54
FINDPEAKS_SCORE: 0.1664
FINDPEAKS_PERCENTILE: 30
HOTSPOT_SCORE: 0.19
HOTSPOT_PERCENTILE: 22
IROC_SCORE: 0.9997
IROC_PERCENTILE: 76
POISSON_SCORE: 0.2246
POISSON_PERCENTILE: 17
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: CD25- IL17+ Th17 stim is one of  CD4+  T cell subsets  that purified by microbeads, LS column and FACS ; DNA_Lib 742

value: Protein A-Sepharose 4B

value: 0.5 to 3 million cells

value: ~1 ug

value: 10 ul bed volume

value: Millipore

value: Histone H3K4me3


title: ChIP-Seq analysis of H3K27ac in human CD25- IL17+ Th17 stim cells; DNA_Lib 741

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 741
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8677
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.9446
****************
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: GSM772987_BI.CD4+_CD25-_IL17+_PMA-Ionomcyin_stimulated_Th17_Primary_Cells.H3K27ac.Donor_62.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 741-DNA_Lib 741-DNA_Lib 741-DNA_Lib 741.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of CD4+ CD25- IL17+ PMA-Ionomcyin stimulated Th17 Primary Cells Histone H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K27ac ChIP-Seq on CD4+ CD25- IL17+ PMA-Ionomcyin stimulated Th17 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.10610
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: 18,742,837
NUMBER_OF_H3K27ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 34
FINDPEAKS_SCORE: 0.4336
FINDPEAKS_PERCENTILE: 88
HOTSPOT_SCORE: 0.449
HOTSPOT_PERCENTILE: 88
IROC_SCORE: 0.999
IROC_PERCENTILE: 88
POISSON_SCORE: 0.4767
POISSON_PERCENTILE: 85
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM772987_BI.CD4+_CD25-_IL17+_PMA-Ionomcyin_stimulated_Th17_Primary_Cells.H3K27ac.Donor_62.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 741-DNA_Lib 741-DNA_Lib 741-DNA_Lib 741.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of CD4+ CD25- IL17+ PMA-Ionomcyin stimulated Th17 Primary Cells Histone H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K27ac ChIP-Seq read mappings from CD4+ CD25- IL17+ PMA-Ionomcyin stimulated Th17 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.10874
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: CCIPsT H3K27ac 62 41
BROWSER_TRACK_DESCRIPTION: BI CD4+ CD25- IL17+ PMA-Ionomcyin stimulated Th17 Primary Cells Histone H3K27ac Donor 62 Library DNA_Lib 741 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 18,742,837
NUMBER_OF_H3K27ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 34
FINDPEAKS_SCORE: 0.4336
FINDPEAKS_PERCENTILE: 88
HOTSPOT_SCORE: 0.449
HOTSPOT_PERCENTILE: 88
IROC_SCORE: 0.999
IROC_PERCENTILE: 88
POISSON_SCORE: 0.4767
POISSON_PERCENTILE: 85
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: CD25- IL17+ Th17 stim is one of  CD4+  T cell subsets  that purified by microbeads, LS column and FACS ; DNA_Lib 741

value: BioSam 134

value: presumed normal

value: CD4+ T cell

value: CD25- IL17+ Th17 stim

value: Abcam

value: Histone H3K27ac


title: ChIP-Seq analysis of H3K9ac in human HUES64 derived CD184+ cells; DNA_Lib 245

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 245
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8670
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: GSM772980_BI.hESC_Derived_CD184+_Endoderm_Cultured_Cells.H3K9ac.DNA_Lib_245.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 245-DNA_Lib 245-DNA_Lib 245-DNA_Lib 245-DNA_Lib 245.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of hESC Derived CD184+ Endoderm Cultured Cells Histone H3K9ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K9ac ChIP-Seq on hESC Derived CD184+ Endoderm Cultured Cells, Donor DNA_Lib 245, 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.10833
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: 5,104,456
NUMBER_OF_H3K9ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 19
FINDPEAKS_SCORE: 0.1748
FINDPEAKS_PERCENTILE: 42
HOTSPOT_SCORE: 0.2859
HOTSPOT_PERCENTILE: 74
IROC_SCORE: 0.9921
IROC_PERCENTILE: 37
POISSON_SCORE: 0.3223
POISSON_PERCENTILE: 63
MAXIMUM_REPLICATE_CORRELATION: 0.92

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

ANALYSIS FILE NAME: GSM772980_BI.hESC_Derived_CD184+_Endoderm_Cultured_Cells.H3K9ac.DNA_Lib_245.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 245-DNA_Lib 245-DNA_Lib 245-DNA_Lib 245-DNA_Lib 245.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of hESC Derived CD184+ Endoderm Cultured Cells Histone H3K9ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K9ac ChIP-Seq read mappings from hESC Derived CD184+ Endoderm Cultured Cells, Donor DNA_Lib 245, 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.11097
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 H3K9ac 45
BROWSER_TRACK_DESCRIPTION: BI hESC Derived CD184+ Endoderm Cultured Cells Histone H3K9ac Library DNA_Lib 245 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 5,104,456
NUMBER_OF_H3K9ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 19
FINDPEAKS_SCORE: 0.1748
FINDPEAKS_PERCENTILE: 42
HOTSPOT_SCORE: 0.2859
HOTSPOT_PERCENTILE: 74
IROC_SCORE: 0.9921
IROC_PERCENTILE: 37
POISSON_SCORE: 0.3223
POISSON_PERCENTILE: 63
MAXIMUM_REPLICATE_CORRELATION: 0.92

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

source_name: CD184+ endoderm differentiated in vitro from stem cells; DNA_Lib 245

value: CD184+ endoderm cultured cells

tag: lineage

tag: medium

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

value: genomic DNA

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: Histone H3K9ac


title: ChIP-Seq analysis of H3K27me3 in human angular gyrus cells; DNA_Lib 629

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 629
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8673
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: GSM772983_BI.Brain_Angular_Gyrus.H3K27me3.149.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 629-DNA_Lib 629-DNA_Lib 629.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of Brain Angular Gyrus Histone H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K27me3 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.10726
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: 23,855,341
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 49
FINDPEAKS_SCORE: 0.0205
FINDPEAKS_PERCENTILE: 47
HOTSPOT_SCORE: 0.1075
HOTSPOT_PERCENTILE: 39
IROC_SCORE: 0.6727
IROC_PERCENTILE: 22
POISSON_SCORE: 0.2631
POISSON_PERCENTILE: 43
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM772983_BI.Brain_Angular_Gyrus.H3K27me3.149.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 629-DNA_Lib 629-DNA_Lib 629.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of Brain Angular Gyrus Histone H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K27me3 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.10990
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 H3K27me3 49 29
BROWSER_TRACK_DESCRIPTION: BI Brain Angular Gyrus Histone H3K27me3 Donor 149 Library DNA_Lib 629 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 23,855,341
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 49
FINDPEAKS_SCORE: 0.0205
FINDPEAKS_PERCENTILE: 47
HOTSPOT_SCORE: 0.1075
HOTSPOT_PERCENTILE: 39
IROC_SCORE: 0.6727
IROC_PERCENTILE: 22
POISSON_SCORE: 0.2631
POISSON_PERCENTILE: 43
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: specified brain region obtained by post-mortem collection in a longitudinal study; DNA_Lib 629

value: Brain, Angular Gyrus

value: Post-Mortem

value: no AD evident at demise

value: Angular gyrus

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: Millipore

value: Histone H3K27me3

value: Branson


title: ChIP-Seq analysis of H3K9me3 in human CD25- IL17+ Th17 stim cells; DNA_Lib 744

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 744
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8674
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.9446
****************
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: GSM772984_BI.CD4+_CD25-_IL17+_PMA-Ionomcyin_stimulated_Th17_Primary_Cells.H3K9me3.Donor_62.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 744-DNA_Lib 744-DNA_Lib 744-DNA_Lib 744.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of CD4+ CD25- IL17+ PMA-Ionomcyin stimulated Th17 Primary Cells Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K9me3 ChIP-Seq on CD4+ CD25- IL17+ PMA-Ionomcyin stimulated Th17 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.10744
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: 21,639,892
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 49
FINDPEAKS_SCORE: 0.0146
FINDPEAKS_PERCENTILE: 12
HOTSPOT_SCORE: 0.0723
HOTSPOT_PERCENTILE: 22
IROC_SCORE: 0.8426
IROC_PERCENTILE: 49
POISSON_SCORE: 0.125
POISSON_PERCENTILE: 14
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM772984_BI.CD4+_CD25-_IL17+_PMA-Ionomcyin_stimulated_Th17_Primary_Cells.H3K9me3.Donor_62.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 744-DNA_Lib 744-DNA_Lib 744-DNA_Lib 744.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of CD4+ CD25- IL17+ PMA-Ionomcyin stimulated Th17 Primary Cells Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K9me3 ChIP-Seq read mappings from CD4+ CD25- IL17+ PMA-Ionomcyin stimulated Th17 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.11008
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: CCIPsT H3K9me3 62 44
BROWSER_TRACK_DESCRIPTION: BI CD4+ CD25- IL17+ PMA-Ionomcyin stimulated Th17 Primary Cells Histone H3K9me3 Donor 62 Library DNA_Lib 744 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 21,639,892
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 49
FINDPEAKS_SCORE: 0.0146
FINDPEAKS_PERCENTILE: 12
HOTSPOT_SCORE: 0.0723
HOTSPOT_PERCENTILE: 22
IROC_SCORE: 0.8426
IROC_PERCENTILE: 49
POISSON_SCORE: 0.125
POISSON_PERCENTILE: 14
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: CD25- IL17+ Th17 stim is one of  CD4+  T cell subsets  that purified by microbeads, LS column and FACS ; DNA_Lib 744

value: BioSam 134

value: presumed normal

value: genomic DNA

value: CD4+ T cell

value: CD25- IL17+ Th17 stim

value: Unknown

value: Primary Cell

value: Donor 62

value: Dana Farber

value: Abcam

value: Histone H3K9me3


title: ChIP-Seq analysis of H3K4me3 in human HUES64 derived CD184+ cells; DNA_Lib 247

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 247
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8668
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: GSM772978_BI.hESC_Derived_CD184+_Endoderm_Cultured_Cells.H3K4me3.DNA_Lib_247.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 247-DNA_Lib 247-DNA_Lib 247-DNA_Lib 247-DNA_Lib 247.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of hESC Derived CD184+ Endoderm Cultured Cells Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me3 ChIP-Seq on hESC Derived CD184+ Endoderm Cultured Cells, Donor DNA_Lib 247, 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.10728
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: 28,933,141
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 54
FINDPEAKS_SCORE: 0.3356
FINDPEAKS_PERCENTILE: 67
HOTSPOT_SCORE: 0.3842
HOTSPOT_PERCENTILE: 69
IROC_SCORE: 0.9756
IROC_PERCENTILE: 17
POISSON_SCORE: 0.49
POISSON_PERCENTILE: 78
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM772978_BI.hESC_Derived_CD184+_Endoderm_Cultured_Cells.H3K4me3.DNA_Lib_247.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 247-DNA_Lib 247-DNA_Lib 247-DNA_Lib 247-DNA_Lib 247.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of hESC Derived CD184+ Endoderm Cultured Cells Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me3 ChIP-Seq read mappings from hESC Derived CD184+ Endoderm Cultured Cells, Donor DNA_Lib 247, 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.10992
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 H3K4me3 47
BROWSER_TRACK_DESCRIPTION: BI hESC Derived CD184+ Endoderm Cultured Cells Histone H3K4me3 Library DNA_Lib 247 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 28,933,141
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 54
FINDPEAKS_SCORE: 0.3356
FINDPEAKS_PERCENTILE: 67
HOTSPOT_SCORE: 0.3842
HOTSPOT_PERCENTILE: 69
IROC_SCORE: 0.9756
IROC_PERCENTILE: 17
POISSON_SCORE: 0.49
POISSON_PERCENTILE: 78
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: CD184+ endoderm differentiated in vitro from stem cells; DNA_Lib 247

value: CD184+ endoderm cultured cells

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

value: HUES64 derived CD184+

value: in vitro culture

value: BioSAli 136

value: Cell Line

value: differentiated

value: Male

value: Harvard University

value: Protein A-Sepharose 4B

value: 0.5 to 3 million cells

value: cell/nuclei lysis

value: Histone H3K4me3


title: ChIP-Seq analysis of H3K36me3 in human CD25int CD127+ Tmem cells; DNA_Lib 732

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 732
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8671
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.9457
****************
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: GSM772981_BI.CD4+_CD25int_CD127+_Tmem_Primary_Cells.H3K36me3.Donor_62.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 732-DNA_Lib 732-DNA_Lib 732-DNA_Lib 732.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of CD4+ CD25int CD127+ Tmem Primary Cells Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K36me3 ChIP-Seq on CD4+ CD25int CD127+ Tmem 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.10795
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: 14,809,244
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 49
FINDPEAKS_SCORE: 0.0451
FINDPEAKS_PERCENTILE: 18
HOTSPOT_SCORE: 0.1659
HOTSPOT_PERCENTILE: 29
IROC_SCORE: 0.79
IROC_PERCENTILE: 8
POISSON_SCORE: 0.2704
POISSON_PERCENTILE: 12
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM772981_BI.CD4+_CD25int_CD127+_Tmem_Primary_Cells.H3K36me3.Donor_62.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 732-DNA_Lib 732-DNA_Lib 732-DNA_Lib 732.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of CD4+ CD25int CD127+ Tmem Primary Cells Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K36me3 ChIP-Seq read mappings from CD4+ CD25int CD127+ Tmem 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.11059
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: CCCTmem H3K36me3 62 32
BROWSER_TRACK_DESCRIPTION: BI CD4+ CD25int CD127+ Tmem Primary Cells Histone H3K36me3 Donor 62 Library DNA_Lib 732 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 14,809,244
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 49
FINDPEAKS_SCORE: 0.0451
FINDPEAKS_PERCENTILE: 18
HOTSPOT_SCORE: 0.1659
HOTSPOT_PERCENTILE: 29
IROC_SCORE: 0.79
IROC_PERCENTILE: 8
POISSON_SCORE: 0.2704
POISSON_PERCENTILE: 12
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: CD25int CD127+ Tmem is one of  CD4+  T cell subsets  that purified by microbeads, LS column and FACS ; DNA_Lib 732

value: BioSam 131

value: CD4+ CD25int CD127+ Tmem Primary Cells

value: presumed normal

value: genomic DNA

value: CD4+ T cell

value: CD25int CD127+ Tmem

value: Unknown

value: Primary Cell

value: Donor 62

value: ~1 ug

value: 10 ul bed volume

value: Histone H3K36me3

value: Branson


title: ChIP-Seq analysis of WCE in human HUES64 derived CD184+ cells; DNA_Lib 244

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 244
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8669
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.9460
****************
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: GSM772979_BI.hESC_Derived_CD184+_Endoderm_Cultured_Cells.Input.DNA_Lib_244.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 244-DNA_Lib 244-DNA_Lib 244-DNA_Lib 244-DNA_Lib 244.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 244, 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.10738
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: 30,922,630
NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 56
FINDPEAKS_SCORE: 0.0051
FINDPEAKS_PERCENTILE: 46
HOTSPOT_SCORE: 0.0103
HOTSPOT_PERCENTILE: 51
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.057
POISSON_PERCENTILE: 52
MAXIMUM_REPLICATE_CORRELATION: 0.96

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

ANALYSIS FILE NAME: GSM772979_BI.hESC_Derived_CD184+_Endoderm_Cultured_Cells.Input.DNA_Lib_244.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 244-DNA_Lib 244-DNA_Lib 244-DNA_Lib 244-DNA_Lib 244.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 244, 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.11002
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 44
BROWSER_TRACK_DESCRIPTION: BI hESC Derived CD184+ Endoderm Cultured Cells ChIP-Seq Input Library DNA_Lib 244 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 30,922,630
NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 56
FINDPEAKS_SCORE: 0.0051
FINDPEAKS_PERCENTILE: 46
HOTSPOT_SCORE: 0.0103
HOTSPOT_PERCENTILE: 51
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.057
POISSON_PERCENTILE: 52
MAXIMUM_REPLICATE_CORRELATION: 0.96

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

source_name: CD184+ endoderm differentiated in vitro from stem cells; DNA_Lib 244

value: CD184+ endoderm cultured cells

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

value: HUES64 derived CD184+

value: in vitro culture

value: BioSAli 137

value: Cell Line

value: differentiated

value: Male

value: Harvard University

value: standard

value: ChIP-Seq Input

value: Input


title: ChIP-Seq analysis of H3K27me3 in human HUES64 derived CD184+ cells; DNA_Lib 246

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 246
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8667
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: GSM772977_BI.hESC_Derived_CD184+_Endoderm_Cultured_Cells.H3K27me3.DNA_Lib_246.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 246-DNA_Lib 246-DNA_Lib 246-DNA_Lib 246-DNA_Lib 246.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of hESC Derived CD184+ Endoderm Cultured Cells Histone H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K27me3 ChIP-Seq on hESC Derived CD184+ Endoderm Cultured Cells, Donor DNA_Lib 246, 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.10826
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: 16,232,995
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 49
FINDPEAKS_SCORE: 0.2622
FINDPEAKS_PERCENTILE: 94
HOTSPOT_SCORE: 0.3402
HOTSPOT_PERCENTILE: 96
IROC_SCORE: 0.967
IROC_PERCENTILE: 80
POISSON_SCORE: 0.43
POISSON_PERCENTILE: 88
MAXIMUM_REPLICATE_CORRELATION: 0.99

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

ANALYSIS FILE NAME: GSM772977_BI.hESC_Derived_CD184+_Endoderm_Cultured_Cells.H3K27me3.DNA_Lib_246.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 246-DNA_Lib 246-DNA_Lib 246-DNA_Lib 246-DNA_Lib 246.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of hESC Derived CD184+ Endoderm Cultured Cells Histone H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K27me3 ChIP-Seq read mappings from hESC Derived CD184+ Endoderm Cultured Cells, Donor DNA_Lib 246, 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.11090
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 H3K27me3 46
BROWSER_TRACK_DESCRIPTION: BI hESC Derived CD184+ Endoderm Cultured Cells Histone H3K27me3 Library DNA_Lib 246 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 16,232,995
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 49
FINDPEAKS_SCORE: 0.2622
FINDPEAKS_PERCENTILE: 94
HOTSPOT_SCORE: 0.3402
HOTSPOT_PERCENTILE: 96
IROC_SCORE: 0.967
IROC_PERCENTILE: 80
POISSON_SCORE: 0.43
POISSON_PERCENTILE: 88
MAXIMUM_REPLICATE_CORRELATION: 0.99

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

source_name: CD184+ endoderm differentiated in vitro from stem cells; DNA_Lib 246

value: genomic DNA

value: presumed normal

value: BioSAli 136

value: Protein A-Sepharose 4B

value: 0.5 to 3 million cells

value: cell/nuclei lysis

value: Millipore

value: Histone H3K27me3


title: ChIP-Seq analysis of H3K27me3 in human inferior temporal lobe cells; DNA_Lib 624

description:
sample_term_id: UBERON_0001871
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 624
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8683
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.9458
****************
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: GSM772993_BI.Brain_Inferior_Temporal_Lobe.H3K27me3.149.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 624-DNA_Lib 624-DNA_Lib 624.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of Brain Inferior Temporal Lobe Histone H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K27me3 ChIP-Seq on Brain Inferior Temporal Lobe, 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.10752
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: 23,913,037
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 49
FINDPEAKS_SCORE: 0.0244
FINDPEAKS_PERCENTILE: 51
HOTSPOT_SCORE: 0.1136
HOTSPOT_PERCENTILE: 51
IROC_SCORE: 0.6968
IROC_PERCENTILE: 35
POISSON_SCORE: 0.2713
POISSON_PERCENTILE: 49
MAXIMUM_REPLICATE_CORRELATION: 0.88

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

ANALYSIS FILE NAME: GSM772993_BI.Brain_Inferior_Temporal_Lobe.H3K27me3.149.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 624-DNA_Lib 624-DNA_Lib 624.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of Brain Inferior Temporal Lobe Histone H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K27me3 ChIP-Seq read mappings from Brain Inferior Temporal Lobe, 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.11016
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: BITL H3K27me3 49 24
BROWSER_TRACK_DESCRIPTION: BI Brain Inferior Temporal Lobe Histone H3K27me3 Donor 149 Library DNA_Lib 624 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 23,913,037
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 49
FINDPEAKS_SCORE: 0.0244
FINDPEAKS_PERCENTILE: 51
HOTSPOT_SCORE: 0.1136
HOTSPOT_PERCENTILE: 51
IROC_SCORE: 0.6968
IROC_PERCENTILE: 35
POISSON_SCORE: 0.2713
POISSON_PERCENTILE: 49
MAXIMUM_REPLICATE_CORRELATION: 0.88

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

source_name: specified brain region obtained by post-mortem collection in a longitudinal study; DNA_Lib 624

value: Brain, Inferior Temporal Lobe

value: Post-Mortem

value: no AD evident at demise

value: Inferior Temporal Lobe

value: Primary Tissue

value: Brain

value: Rush University Medical Center

value: 81.0 Years

value: ~1 ug

value: 10 ul bed volume

value: Branson


title: ChIP-Seq analysis of H3K4me1 in human CD25+ CD127- Treg cells; DNA_Lib 309

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 309
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8663
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: GSM772973_BI.CD4+_CD25+_CD127-_Treg_Primary_Cells.H3K4me1.Donor_62.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 309-DNA_Lib 309-DNA_Lib 309-DNA_Lib 309.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of CD4+ CD25+ CD127- Treg Primary Cells Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me1 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.10805
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: 9,544,505
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 54
FINDPEAKS_SCORE: 0.2831
FINDPEAKS_PERCENTILE: 61
HOTSPOT_SCORE: 0.3446
HOTSPOT_PERCENTILE: 67
IROC_SCORE: 0.9907
IROC_PERCENTILE: 67
POISSON_SCORE: 0.3873
POISSON_PERCENTILE: 22
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM772973_BI.CD4+_CD25+_CD127-_Treg_Primary_Cells.H3K4me1.Donor_62.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 309-DNA_Lib 309-DNA_Lib 309-DNA_Lib 309.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of CD4+ CD25+ CD127- Treg Primary Cells Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me1 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.11069
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 H3K4me1 62 09
BROWSER_TRACK_DESCRIPTION: BI CD4+ CD25+ CD127- Treg Primary Cells Histone H3K4me1 Donor 62 Library DNA_Lib 309 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 9,544,505
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 54
FINDPEAKS_SCORE: 0.2831
FINDPEAKS_PERCENTILE: 61
HOTSPOT_SCORE: 0.3446
HOTSPOT_PERCENTILE: 67
IROC_SCORE: 0.9907
IROC_PERCENTILE: 67
POISSON_SCORE: 0.3873
POISSON_PERCENTILE: 22
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 309

value: BioSam 129

value: CD4+ CD25+ CD127- Treg Primary Cells

value: presumed normal

value: genomic DNA

value: CD4+ T cell

value: CD25+ CD127- Treg

value: Unknown

value: Primary Cell

value: Donor 62

value: Dana Farber

value: Abcam

value: Histone H3K4me1


title: ChIP-Seq analysis of H3K36me3 in human angular gyrus cells; DNA_Lib 631

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 631
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8651
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: GSM772961_BI.Brain_Angular_Gyrus.H3K36me3.149.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 631-DNA_Lib 631-DNA_Lib 631.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of Brain Angular Gyrus Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K36me3 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.10773
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: 24,762,515
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 49
FINDPEAKS_SCORE: 0.0567
FINDPEAKS_PERCENTILE: 24
HOTSPOT_SCORE: 0.1714
HOTSPOT_PERCENTILE: 35
IROC_SCORE: 0.8794
IROC_PERCENTILE: 24
POISSON_SCORE: 0.3096
POISSON_PERCENTILE: 31
MAXIMUM_REPLICATE_CORRELATION: 0.97

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

ANALYSIS FILE NAME: GSM772961_BI.Brain_Angular_Gyrus.H3K36me3.149.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 631-DNA_Lib 631-DNA_Lib 631.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of Brain Angular Gyrus Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K36me3 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.11037
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 H3K36me3 49 31
BROWSER_TRACK_DESCRIPTION: BI Brain Angular Gyrus Histone H3K36me3 Donor 149 Library DNA_Lib 631 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 24,762,515
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 49
FINDPEAKS_SCORE: 0.0567
FINDPEAKS_PERCENTILE: 24
HOTSPOT_SCORE: 0.1714
HOTSPOT_PERCENTILE: 35
IROC_SCORE: 0.8794
IROC_PERCENTILE: 24
POISSON_SCORE: 0.3096
POISSON_PERCENTILE: 31
MAXIMUM_REPLICATE_CORRELATION: 0.97

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

source_name: specified brain region obtained by post-mortem collection in a longitudinal study; DNA_Lib 631

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: Protein A-Sepharose 4B

value: 0.5 to 3 million cells

value: cell/nuclei lysis

value: Histone H3K36me3


title: ChIP-Seq analysis of WCE in human CD25int CD127+ Tmem cells; DNA_Lib 733

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 733
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8643
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.9457
****************
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: GSM772953_BI.CD4+_CD25int_CD127+_Tmem_Primary_Cells.Input.Donor_62.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 733-DNA_Lib 733-DNA_Lib 733-DNA_Lib 733.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of CD4+ CD25int CD127+ Tmem Primary Cells ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina reads produced by ChIP-Seq Input on CD4+ CD25int CD127+ Tmem 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.10626
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: 22,506,234
NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 56
FINDPEAKS_SCORE: 0.0059
FINDPEAKS_PERCENTILE: 64
HOTSPOT_SCORE: 0.0289
HOTSPOT_PERCENTILE: 72
IROC_SCORE: 0.0
IROC_PERCENTILE: 33
POISSON_SCORE: 0.0688
POISSON_PERCENTILE: 66
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM772953_BI.CD4+_CD25int_CD127+_Tmem_Primary_Cells.Input.Donor_62.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 733-DNA_Lib 733-DNA_Lib 733-DNA_Lib 733.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of CD4+ CD25int CD127+ Tmem Primary Cells ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina ChIP-Seq Input read mappings from CD4+ CD25int CD127+ Tmem 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.10890
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: CCCTmem Input 62 33
BROWSER_TRACK_DESCRIPTION: BI CD4+ CD25int CD127+ Tmem Primary Cells ChIP-Seq Input Donor 62 Library DNA_Lib 733 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 22,506,234
NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 56
FINDPEAKS_SCORE: 0.0059
FINDPEAKS_PERCENTILE: 64
HOTSPOT_SCORE: 0.0289
HOTSPOT_PERCENTILE: 72
IROC_SCORE: 0.0
IROC_PERCENTILE: 33
POISSON_SCORE: 0.0688
POISSON_PERCENTILE: 66
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: CD25int CD127+ Tmem is one of  CD4+  T cell subsets  that purified by microbeads, LS column and FACS ; DNA_Lib 733

value: BioSam 131

value: CD4+ CD25int CD127+ Tmem Primary Cells

value: presumed normal

value: genomic DNA

value: CD4+ T cell

value: CD25int CD127+ Tmem

value: Unknown

value: Primary Cell

value: standard

value: ChIP-Seq Input

value: Input

value: Branson


title: ChIP-Seq analysis of H3K4me1 in human HUES64 derived CD184+ cells; DNA_Lib 249

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 249
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8661
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: GSM772971_BI.hESC_Derived_CD184+_Endoderm_Cultured_Cells.H3K4me1.DNA_Lib_249.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 249-DNA_Lib 249-DNA_Lib 249-DNA_Lib 249-DNA_Lib 249.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of hESC Derived CD184+ Endoderm Cultured Cells Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me1 ChIP-Seq on hESC Derived CD184+ Endoderm Cultured Cells, Donor DNA_Lib 249, 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.10679
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: 24,182,467
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 54
FINDPEAKS_SCORE: 0.2842
FINDPEAKS_PERCENTILE: 67
HOTSPOT_SCORE: 0.3864
HOTSPOT_PERCENTILE: 70
IROC_SCORE: 0.9612
IROC_PERCENTILE: 39
POISSON_SCORE: 0.5654
POISSON_PERCENTILE: 85
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM772971_BI.hESC_Derived_CD184+_Endoderm_Cultured_Cells.H3K4me1.DNA_Lib_249.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 249-DNA_Lib 249-DNA_Lib 249-DNA_Lib 249-DNA_Lib 249.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of hESC Derived CD184+ Endoderm Cultured Cells Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me1 ChIP-Seq read mappings from hESC Derived CD184+ Endoderm Cultured Cells, Donor DNA_Lib 249, 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.10943
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 H3K4me1 49
BROWSER_TRACK_DESCRIPTION: BI hESC Derived CD184+ Endoderm Cultured Cells Histone H3K4me1 Library DNA_Lib 249 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 24,182,467
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 54
FINDPEAKS_SCORE: 0.2842
FINDPEAKS_PERCENTILE: 67
HOTSPOT_SCORE: 0.3864
HOTSPOT_PERCENTILE: 70
IROC_SCORE: 0.9612
IROC_PERCENTILE: 39
POISSON_SCORE: 0.5654
POISSON_PERCENTILE: 85
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: CD184+ endoderm differentiated in vitro from stem cells; DNA_Lib 249

value: CD184+ endoderm cultured cells

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

value: HUES64 derived CD184+

value: in vitro culture

value: BioSAli 136

value: Cell Line

value: differentiated

value: Male

value: Harvard University

value: ~1 ug

value: 10 ul bed volume

value: Abcam

value: Histone H3K4me1


title: ChIP-Seq analysis of H3K9me3 in human angular gyrus cells; DNA_Lib 632

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 632
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8650
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: GSM772960_BI.Brain_Angular_Gyrus.H3K9me3.149.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 632-DNA_Lib 632-DNA_Lib 632.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of Brain Angular Gyrus Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K9me3 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.10788
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: 19,148,218
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 49
FINDPEAKS_SCORE: 0.0261
FINDPEAKS_PERCENTILE: 41
HOTSPOT_SCORE: 0.1043
HOTSPOT_PERCENTILE: 47
IROC_SCORE: 0.6461
IROC_PERCENTILE: 10
POISSON_SCORE: 0.2322
POISSON_PERCENTILE: 47
MAXIMUM_REPLICATE_CORRELATION: 0.93

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

ANALYSIS FILE NAME: GSM772960_BI.Brain_Angular_Gyrus.H3K9me3.149.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 632-DNA_Lib 632-DNA_Lib 632.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of Brain Angular Gyrus Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K9me3 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.11052
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 H3K9me3 49 32
BROWSER_TRACK_DESCRIPTION: BI Brain Angular Gyrus Histone H3K9me3 Donor 149 Library DNA_Lib 632 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 19,148,218
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 49
FINDPEAKS_SCORE: 0.0261
FINDPEAKS_PERCENTILE: 41
HOTSPOT_SCORE: 0.1043
HOTSPOT_PERCENTILE: 47
IROC_SCORE: 0.6461
IROC_PERCENTILE: 10
POISSON_SCORE: 0.2322
POISSON_PERCENTILE: 47
MAXIMUM_REPLICATE_CORRELATION: 0.93

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

source_name: specified brain region obtained by post-mortem collection in a longitudinal study; DNA_Lib 632

value: Brain, Angular Gyrus

value: Post-Mortem

value: no AD evident at demise

value: genomic DNA

value: Angular gyrus

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: Histone H3K9me3


title: ChIP-Seq analysis of H3K27me3 in human CD25int CD127+ Tmem cells; DNA_Lib 731

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 731
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8645
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.9457
****************
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: GSM772955_BI.CD4+_CD25int_CD127+_Tmem_Primary_Cells.H3K27me3.Donor_62.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 731-DNA_Lib 731-DNA_Lib 731-DNA_Lib 731.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of CD4+ CD25int CD127+ Tmem Primary Cells Histone H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K27me3 ChIP-Seq on CD4+ CD25int CD127+ Tmem 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.10834
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: 12,278,600
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 49
FINDPEAKS_SCORE: 0.0168
FINDPEAKS_PERCENTILE: 35
HOTSPOT_SCORE: 0.1399
HOTSPOT_PERCENTILE: 61
IROC_SCORE: 0.6286
IROC_PERCENTILE: 16
POISSON_SCORE: 0.2205
POISSON_PERCENTILE: 35
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM772955_BI.CD4+_CD25int_CD127+_Tmem_Primary_Cells.H3K27me3.Donor_62.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 731-DNA_Lib 731-DNA_Lib 731-DNA_Lib 731.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of CD4+ CD25int CD127+ Tmem Primary Cells Histone H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K27me3 ChIP-Seq read mappings from CD4+ CD25int CD127+ Tmem 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.11098
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: CCCTmem H3K27me3 62 31
BROWSER_TRACK_DESCRIPTION: BI CD4+ CD25int CD127+ Tmem Primary Cells Histone H3K27me3 Donor 62 Library DNA_Lib 731 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 12,278,600
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 49
FINDPEAKS_SCORE: 0.0168
FINDPEAKS_PERCENTILE: 35
HOTSPOT_SCORE: 0.1399
HOTSPOT_PERCENTILE: 61
IROC_SCORE: 0.6286
IROC_PERCENTILE: 16
POISSON_SCORE: 0.2205
POISSON_PERCENTILE: 35
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: CD25int CD127+ Tmem is one of  CD4+  T cell subsets  that purified by microbeads, LS column and FACS ; DNA_Lib 731

value: BioSam 131

value: CD4+ CD25int CD127+ Tmem Primary Cells

value: presumed normal

value: CD4+ T cell

value: CD25int CD127+ Tmem

value: Unknown

value: Primary Cell

value: Donor 62

value: Dana Farber

value: ~1 ug

value: Millipore

value: Histone H3K27me3

value: Branson


title: ChIP-Seq analysis of H3K27me3 in human CD25+ CD127- Treg cells; DNA_Lib 313

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 313
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8636
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: GSM772946_BI.CD4+_CD25+_CD127-_Treg_Primary_Cells.H3K27me3.Donor_62.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 313-DNA_Lib 313-DNA_Lib 313-DNA_Lib 313.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of CD4+ CD25+ CD127- Treg Primary Cells Histone H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K27me3 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.10660
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: 23,385,881
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 49
FINDPEAKS_SCORE: 0.0206
FINDPEAKS_PERCENTILE: 49
HOTSPOT_SCORE: 0.1225
HOTSPOT_PERCENTILE: 55
IROC_SCORE: 0.7135
IROC_PERCENTILE: 39
POISSON_SCORE: 0.2958
POISSON_PERCENTILE: 57
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM772946_BI.CD4+_CD25+_CD127-_Treg_Primary_Cells.H3K27me3.Donor_62.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 313-DNA_Lib 313-DNA_Lib 313-DNA_Lib 313.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of CD4+ CD25+ CD127- Treg Primary Cells Histone H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K27me3 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.10924
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 H3K27me3 62 13
BROWSER_TRACK_DESCRIPTION: BI CD4+ CD25+ CD127- Treg Primary Cells Histone H3K27me3 Donor 62 Library DNA_Lib 313 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 23,385,881
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 49
FINDPEAKS_SCORE: 0.0206
FINDPEAKS_PERCENTILE: 49
HOTSPOT_SCORE: 0.1225
HOTSPOT_PERCENTILE: 55
IROC_SCORE: 0.7135
IROC_PERCENTILE: 39
POISSON_SCORE: 0.2958
POISSON_PERCENTILE: 57
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 313

value: BioSam 129

value: CD4+ CD25+ CD127- Treg Primary Cells

value: genomic DNA

value: CD25+ CD127- Treg

value: Protein A-Sepharose 4B

value: 10 ul bed volume


title: ChIP-Seq analysis of H3K4me3 in human angular gyrus cells; DNA_Lib 633

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 633
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8649
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: GSM772959_BI.Brain_Angular_Gyrus.H3K4me3.149.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 633-DNA_Lib 633-DNA_Lib 633.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of Brain Angular Gyrus Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me3 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.10695
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: 25,143,243
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 54
FINDPEAKS_SCORE: 0.2638
FINDPEAKS_PERCENTILE: 57
HOTSPOT_SCORE: 0.2986
HOTSPOT_PERCENTILE: 48
IROC_SCORE: 0.9999
IROC_PERCENTILE: 93
POISSON_SCORE: 0.3266
POISSON_PERCENTILE: 43
MAXIMUM_REPLICATE_CORRELATION: 0.95

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

ANALYSIS FILE NAME: GSM772959_BI.Brain_Angular_Gyrus.H3K4me3.149.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 633-DNA_Lib 633-DNA_Lib 633.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of Brain Angular Gyrus Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me3 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.10959
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 H3K4me3 49 33
BROWSER_TRACK_DESCRIPTION: BI Brain Angular Gyrus Histone H3K4me3 Donor 149 Library DNA_Lib 633 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 25,143,243
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 54
FINDPEAKS_SCORE: 0.2638
FINDPEAKS_PERCENTILE: 57
HOTSPOT_SCORE: 0.2986
HOTSPOT_PERCENTILE: 48
IROC_SCORE: 0.9999
IROC_PERCENTILE: 93
POISSON_SCORE: 0.3266
POISSON_PERCENTILE: 43
MAXIMUM_REPLICATE_CORRELATION: 0.95

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

source_name: specified brain region obtained by post-mortem collection in a longitudinal study; DNA_Lib 633

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: 0.5 to 3 million cells

value: cell/nuclei lysis

value: Histone H3K4me3


title: ChIP-Seq analysis of H3K4me3 in human CD25+ CD127- Treg cells; DNA_Lib 311

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 311
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8634
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: GSM772944_BI.CD4+_CD25+_CD127-_Treg_Primary_Cells.H3K4me3.Donor_62.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 311-DNA_Lib 311-DNA_Lib 311-DNA_Lib 311-DNA_Lib 311-DNA_Lib 311-DNA_Lib 311-DNA_Lib 311.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of CD4+ CD25+ CD127- Treg Primary Cells Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me3 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.10732
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: 5,843,205
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 54
FINDPEAKS_SCORE: 0.5112
FINDPEAKS_PERCENTILE: 91
HOTSPOT_SCORE: 0.5576
HOTSPOT_PERCENTILE: 93
IROC_SCORE: 0.9999
IROC_PERCENTILE: 93
POISSON_SCORE: 0.5456
POISSON_PERCENTILE: 87
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM772944_BI.CD4+_CD25+_CD127-_Treg_Primary_Cells.H3K4me3.Donor_62.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 311-DNA_Lib 311-DNA_Lib 311-DNA_Lib 311-DNA_Lib 311-DNA_Lib 311-DNA_Lib 311-DNA_Lib 311.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of CD4+ CD25+ CD127- Treg Primary Cells Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me3 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.10996
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 H3K4me3 62 11
BROWSER_TRACK_DESCRIPTION: BI CD4+ CD25+ CD127- Treg Primary Cells Histone H3K4me3 Donor 62 Library DNA_Lib 311 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 5,843,205
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 54
FINDPEAKS_SCORE: 0.5112
FINDPEAKS_PERCENTILE: 91
HOTSPOT_SCORE: 0.5576
HOTSPOT_PERCENTILE: 93
IROC_SCORE: 0.9999
IROC_PERCENTILE: 93
POISSON_SCORE: 0.5456
POISSON_PERCENTILE: 87
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 311

value: BioSam 129

value: CD4+ CD25+ CD127- Treg Primary Cells

value: presumed normal

value: CD4+ T cell

value: Unknown

value: Primary Cell

value: Donor 62

value: Dana Farber

value: ~1 ug

value: Millipore

value: Branson