title: ChIP-Seq analysis of WCE in human CD56+ ectoderm cells; DNA_Lib 2066

description:
sample_term_id: CL_0000221
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 2066
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.13165
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.13321
****************
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: GSM997252_BI.hESC_Derived_CD56+_Ectoderm_Cultured_Cells.Input.DNA_Lib_2066.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 2066.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of hESC Derived CD56+ Ectoderm Cultured Cells Input ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Input ChIP-Seq on the hESC Derived CD56+ Ectoderm Cultured Cells, Library DNA_Lib 2066, 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.17264
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 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 64,843,476
FINDPEAKS_SCORE: 0.0025
FINDPEAKS_PERCENTILE: 8
HOTSPOT_SCORE: 0.0017
HOTSPOT_PERCENTILE: 3
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.0117
POISSON_PERCENTILE: 2
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

ANALYSIS FILE NAME: GSM997252_BI.hESC_Derived_CD56+_Ectoderm_Cultured_Cells.Input.DNA_Lib_2066.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 2066.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of hESC Derived CD56+ Ectoderm Cultured Cells Input ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Input ChIP-Seq read mappings from the hESC Derived CD56+ Ectoderm Cultured Cells, Library DNA_Lib 2066, 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.17447
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 9
BROWSER_TRACK_NAME: hDCEcto Input 66
BROWSER_TRACK_DESCRIPTION: BI hESC Derived CD56+ Ectoderm Cultured Cells ChIP-Seq Input Library DNA_Lib 2066 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 64,843,476
FINDPEAKS_SCORE: 0.0025
FINDPEAKS_PERCENTILE: 8
HOTSPOT_SCORE: 0.0017
HOTSPOT_PERCENTILE: 3
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.0117
POISSON_PERCENTILE: 2
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

source_name: CD56+ ectodermal germ layer cells derived in vitro from embrionic stem cells by culture in the presence of inhibitors of the BMP, TGFbeta, and WNT signaling pathways.; DNA_Lib 2066

value: BioSam 706

value: ectoderm

value: Days 0-5:DMEM F12, 15% KSR, Dorsomorphin (2um), A83-01 (2um), PNU 74654 (2um)

value: presumed normal

value: CD56+ ectoderm

value: adherence

value: BioSAli 876

value: Cell Line

value: Male

value: Harvard

value: standard

value: ChIP-Seq Input

value: Input


title: ChIP-Seq analysis of H3K9me3 in human CD25- Th cells; DNA_Lib 2272

status: Public on Jul 18 2013

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 2272
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.13155
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.13313
****************
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: GSM997242_BI.CD4+_CD25-_Th_Primary_Cells.H3K9me3.Donor_332.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 2272.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of CD4+ CD25- Th Primary Cells H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K9me3 ChIP-Seq on CD4+ CD25- Th Primary Cells, Donor Donor 332, 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.17308
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 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 16,915,357
FINDPEAKS_SCORE: 0.0234
FINDPEAKS_PERCENTILE: 29
HOTSPOT_SCORE: 0.1009
HOTSPOT_PERCENTILE: 33
IROC_SCORE: 0.5421
IROC_PERCENTILE: 2
POISSON_SCORE: 0.1977
POISSON_PERCENTILE: 21
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

ANALYSIS FILE NAME: GSM997242_BI.CD4+_CD25-_Th_Primary_Cells.H3K9me3.Donor_332.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 2272.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of CD4+ CD25- Th Primary Cells H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K9me3 ChIP-Seq read mappings from CD4+ CD25- Th Primary Cells, Donor Donor 332, 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.17491
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 9
BROWSER_TRACK_NAME: CCT H3K9me3 32 72
BROWSER_TRACK_DESCRIPTION: BI CD4+ CD25- Th Primary Cells Histone H3K9me3 Donor 332 Library DNA_Lib 2272 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 16,915,357
FINDPEAKS_SCORE: 0.0234
FINDPEAKS_PERCENTILE: 29
HOTSPOT_SCORE: 0.1009
HOTSPOT_PERCENTILE: 33
IROC_SCORE: 0.5421
IROC_PERCENTILE: 2
POISSON_SCORE: 0.1977
POISSON_PERCENTILE: 21
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

molecule: genomic DNA

organism: Homo sapiens

source_name: CD25- Th  is one of  CD4+  T cell subsets  that purified by microbeads, LS column and FACS ; DNA_Lib 2272

extract_protocol: Library construction protocol: Single read - Illumina

tag: sample alias

value: BioSam 715

tag: sample common name

value: CD4+ CD25- Th Primary Cells

value: normal

tag: molecule

value: genomic DNA

tag: disease

tag: markers

value: CD4+ T cell

value: CD25- Th

value: Unknown

value: Primary Cell

value: Donor 332

value: Dana Farber

value: Protein A-Sepharose 4B

value: 0.5 to 3 million cells

value: cell/nuclei lysis

value: ~1 ug

value: 10 ul bed volume

value: Abcam

value: Histone H3K9me3

value: Branson


title: ChIP-Seq analysis of H3K4me1 in human CD25- Th cells; DNA_Lib 2273

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 2273
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.13156
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.13313
****************
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: GSM997243_BI.CD4+_CD25-_Th_Primary_Cells.H3K4me1.Donor_332.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 2273.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of CD4+ CD25- Th Primary Cells H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K4me1 ChIP-Seq on CD4+ CD25- Th Primary Cells, Donor Donor 332, 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.17259
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 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 6,178,665
FINDPEAKS_SCORE: 0.316
FINDPEAKS_PERCENTILE: 57
HOTSPOT_SCORE: 0.3964
HOTSPOT_PERCENTILE: 63
IROC_SCORE: 0.9803
IROC_PERCENTILE: 57
POISSON_SCORE: 0.5131
POISSON_PERCENTILE: 57
MAXIMUM_REPLICATE_CORRELATION: 0.96

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

ANALYSIS FILE NAME: GSM997243_BI.CD4+_CD25-_Th_Primary_Cells.H3K4me1.Donor_332.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 2273.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of CD4+ CD25- Th Primary Cells H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K4me1 ChIP-Seq read mappings from CD4+ CD25- Th Primary Cells, Donor Donor 332, 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.17442
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 9
BROWSER_TRACK_NAME: CCT H3K4me1 32 73
BROWSER_TRACK_DESCRIPTION: BI CD4+ CD25- Th Primary Cells Histone H3K4me1 Donor 332 Library DNA_Lib 2273 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 6,178,665
FINDPEAKS_SCORE: 0.316
FINDPEAKS_PERCENTILE: 57
HOTSPOT_SCORE: 0.3964
HOTSPOT_PERCENTILE: 63
IROC_SCORE: 0.9803
IROC_PERCENTILE: 57
POISSON_SCORE: 0.5131
POISSON_PERCENTILE: 57
MAXIMUM_REPLICATE_CORRELATION: 0.96

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

source_name: CD25- Th  is one of  CD4+  T cell subsets  that purified by microbeads, LS column and FACS ; DNA_Lib 2273

value: BioSam 715

value: CD4+ CD25- Th Primary Cells

value: Histone H3K4me1


title: ChIP-Seq analysis of H3K4me3 in human CD25- Th cells; DNA_Lib 2270

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 2270
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.13153
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.13313
****************
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: GSM997240_BI.CD4+_CD25-_Th_Primary_Cells.H3K4me3.Donor_332.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 2270.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of CD4+ CD25- Th Primary Cells H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K4me3 ChIP-Seq on CD4+ CD25- Th Primary Cells, Donor Donor 332, 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.17268
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 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 7,712,934
FINDPEAKS_SCORE: 0.5082
FINDPEAKS_PERCENTILE: 88
HOTSPOT_SCORE: 0.5505
HOTSPOT_PERCENTILE: 89
IROC_SCORE: 0.9987
IROC_PERCENTILE: 11
POISSON_SCORE: 0.5466
POISSON_PERCENTILE: 88
MAXIMUM_REPLICATE_CORRELATION: 0.96

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

ANALYSIS FILE NAME: GSM997240_BI.CD4+_CD25-_Th_Primary_Cells.H3K4me3.Donor_332.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 2270.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of CD4+ CD25- Th Primary Cells H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K4me3 ChIP-Seq read mappings from CD4+ CD25- Th Primary Cells, Donor Donor 332, 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.17451
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 9
BROWSER_TRACK_NAME: CCT H3K4me3 32 70
BROWSER_TRACK_DESCRIPTION: BI CD4+ CD25- Th Primary Cells Histone H3K4me3 Donor 332 Library DNA_Lib 2270 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 7,712,934
FINDPEAKS_SCORE: 0.5082
FINDPEAKS_PERCENTILE: 88
HOTSPOT_SCORE: 0.5505
HOTSPOT_PERCENTILE: 89
IROC_SCORE: 0.9987
IROC_PERCENTILE: 11
POISSON_SCORE: 0.5466
POISSON_PERCENTILE: 88
MAXIMUM_REPLICATE_CORRELATION: 0.96

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

source_name: CD25- Th  is one of  CD4+  T cell subsets  that purified by microbeads, LS column and FACS ; DNA_Lib 2270

value: normal

value: genomic DNA

value: CD4+ T cell

value: Millipore

value: Histone H3K4me3


title: ChIP-Seq analysis of H3K4me3 in human CD25- CD45RO+ mem cells; DNA_Lib 2096

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 2096
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.13149
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.13315
****************
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: GSM997236_BI.CD4+_CD25-_CD45RO+_Memory_Primary_Cells.H3K4me3.Donor_332.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 2096.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of CD4+ CD25- CD45RO+ Memory Primary Cells H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K4me3 ChIP-Seq on CD4+ CD25- CD45RO+ Memory Primary Cells, Donor Donor 332, 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.17241
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 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 1,305,503
FINDPEAKS_SCORE: 0.5112
FINDPEAKS_PERCENTILE: 89
HOTSPOT_SCORE: 0.572
HOTSPOT_PERCENTILE: 95
IROC_SCORE: NA
IROC_PERCENTILE: NA
POISSON_SCORE: 0.6312
POISSON_PERCENTILE: 100
MAXIMUM_REPLICATE_CORRELATION: 0.52

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

ANALYSIS FILE NAME: GSM997236_BI.CD4+_CD25-_CD45RO+_Memory_Primary_Cells.H3K4me3.Donor_332.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 2096.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of CD4+ CD25- CD45RO+ Memory Primary Cells H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K4me3 ChIP-Seq read mappings from CD4+ CD25- CD45RO+ Memory Primary Cells, Donor Donor 332, 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.17424
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 9
BROWSER_TRACK_NAME: CCCMM H3K4me3 32 96
BROWSER_TRACK_DESCRIPTION: BI CD4+ CD25- CD45RO+ Memory Primary Cells Histone H3K4me3 Donor 332 Library DNA_Lib 2096 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 1,305,503
FINDPEAKS_SCORE: 0.5112
FINDPEAKS_PERCENTILE: 89
HOTSPOT_SCORE: 0.572
HOTSPOT_PERCENTILE: 95
IROC_SCORE: NA
IROC_PERCENTILE: NA
POISSON_SCORE: 0.6312
POISSON_PERCENTILE: 100
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: CD25- CD45RO+ mem is one of  CD4+  T cell subsets  that purified by microbeads, LS column and FACS ; DNA_Lib 2096

value: BioSam 717

value: CD4+ CD25- CD45RO+ Memory Primary Cells

value: CD25- CD45RO+ mem

value: Unknown

value: Primary Cell

value: Donor 332

value: Dana Farber


title: ChIP-Seq analysis of H3K4me3 in human CD25- IL17- Th stim MACS cells; DNA_Lib 2258

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 2258
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.13145
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.13309
****************
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: GSM997232_BI.CD4+_CD25-_IL17-_PMA-Ionomycin_stimulated_MACS_purified_Th_Primary_Cells.H3K4me3.Donor_332.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 2258.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of CD4+ CD25- IL17- PMA-Ionomycin stimulated MACS purified Th Primary Cells H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K4me3 ChIP-Seq on CD4+ CD25- IL17- PMA-Ionomycin stimulated MACS purified Th Primary Cells, Donor Donor 332, 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.17265
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 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 11,623,602
FINDPEAKS_SCORE: 0.5013
FINDPEAKS_PERCENTILE: 80
HOTSPOT_SCORE: 0.522
HOTSPOT_PERCENTILE: 79
IROC_SCORE: 0.9988
IROC_PERCENTILE: 13
POISSON_SCORE: 0.5247
POISSON_PERCENTILE: 80
MAXIMUM_REPLICATE_CORRELATION: 0.97

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

ANALYSIS FILE NAME: GSM997232_BI.CD4+_CD25-_IL17-_PMA-Ionomycin_stimulated_MACS_purified_Th_Primary_Cells.H3K4me3.Donor_332.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 2258.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of CD4+ CD25- IL17- PMA-Ionomycin stimulated MACS purified Th Primary Cells H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K4me3 ChIP-Seq read mappings from CD4+ CD25- IL17- PMA-Ionomycin stimulated MACS purified Th Primary Cells, Donor Donor 332, 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.17448
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 9
BROWSER_TRACK_NAME: CCIPsMpT H3K4me3 32 58
BROWSER_TRACK_DESCRIPTION: BI CD4+ CD25- IL17- PMA-Ionomycin stimulated MACS purified Th Primary Cells Histone H3K4me3 Donor 332 Library DNA_Lib 2258 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 11,623,602
FINDPEAKS_SCORE: 0.5013
FINDPEAKS_PERCENTILE: 80
HOTSPOT_SCORE: 0.522
HOTSPOT_PERCENTILE: 79
IROC_SCORE: 0.9988
IROC_PERCENTILE: 13
POISSON_SCORE: 0.5247
POISSON_PERCENTILE: 80
MAXIMUM_REPLICATE_CORRELATION: 0.97

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

source_name: CD25- IL17- Th stim MACS is one of  CD4+  T cell subsets  that purified by microbeads, LS column  ; DNA_Lib 2258

value: BioSam 720

value: CD25- IL17- Th stim MACS

value: Protein A-Sepharose 4B

value: 0.5 to 3 million cells

value: cell/nuclei lysis

value: ~1 ug

value: 10 ul bed volume


title: ChIP-Seq analysis of H3K27ac in human CD25+ CD127- Treg cells; DNA_Lib 1841

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 1841
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.13146
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: GSM997233_BI.CD4+_CD25+_CD127-_Treg_Primary_Cells.H3K27ac.Donor_62.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 1841.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of CD4+ CD25+ CD127- Treg Primary Cells H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K27ac 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.17221
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 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 8,369,905
FINDPEAKS_SCORE: 0.658
FINDPEAKS_PERCENTILE: 92
HOTSPOT_SCORE: 0.6639
HOTSPOT_PERCENTILE: 93
IROC_SCORE: 0.9983
IROC_PERCENTILE: 76
POISSON_SCORE: 0.6988
POISSON_PERCENTILE: 92
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM997233_BI.CD4+_CD25+_CD127-_Treg_Primary_Cells.H3K27ac.Donor_62.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 1841.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of CD4+ CD25+ CD127- Treg Primary Cells H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K27ac 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.17404
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 9
BROWSER_TRACK_NAME: CCCTregreg H3K27ac 62 41
BROWSER_TRACK_DESCRIPTION: BI CD4+ CD25+ CD127- Treg Primary Cells Histone H3K27ac Donor 62 Library DNA_Lib 1841 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 8,369,905
FINDPEAKS_SCORE: 0.658
FINDPEAKS_PERCENTILE: 92
HOTSPOT_SCORE: 0.6639
HOTSPOT_PERCENTILE: 93
IROC_SCORE: 0.9983
IROC_PERCENTILE: 76
POISSON_SCORE: 0.6988
POISSON_PERCENTILE: 92
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 1841

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: Donor 62

value: Active Motif

value: Histone H3K27ac

value: Branson


title: ChIP-Seq analysis of H3K27ac in human CD25- Th cells; DNA_Lib 2275

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 2275
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.13152
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.13313
****************
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: GSM997239_BI.CD4+_CD25-_Th_Primary_Cells.H3K27ac.Donor_332.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 2275.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of CD4+ CD25- Th Primary Cells H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K27ac ChIP-Seq on CD4+ CD25- Th Primary Cells, Donor Donor 332, 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.17230
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 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 16,781,790
FINDPEAKS_SCORE: 0.1741
FINDPEAKS_PERCENTILE: 19
HOTSPOT_SCORE: 0.221
HOTSPOT_PERCENTILE: 18
IROC_SCORE: 0.9972
IROC_PERCENTILE: 66
POISSON_SCORE: 0.2572
POISSON_PERCENTILE: 9
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM997239_BI.CD4+_CD25-_Th_Primary_Cells.H3K27ac.Donor_332.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 2275.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of CD4+ CD25- Th Primary Cells H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K27ac ChIP-Seq read mappings from CD4+ CD25- Th Primary Cells, Donor Donor 332, 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.17413
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 9
BROWSER_TRACK_NAME: CCT H3K27ac 32 75
BROWSER_TRACK_DESCRIPTION: BI CD4+ CD25- Th Primary Cells Histone H3K27ac Donor 332 Library DNA_Lib 2275 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 16,781,790
FINDPEAKS_SCORE: 0.1741
FINDPEAKS_PERCENTILE: 19
HOTSPOT_SCORE: 0.221
HOTSPOT_PERCENTILE: 18
IROC_SCORE: 0.9972
IROC_PERCENTILE: 66
POISSON_SCORE: 0.2572
POISSON_PERCENTILE: 9
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: CD25- Th  is one of  CD4+  T cell subsets  that purified by microbeads, LS column and FACS ; DNA_Lib 2275

value: BioSam 715

value: CD4+ CD25- Th Primary Cells

value: normal

value: CD25- Th

value: Unknown

value: Primary Cell

value: Donor 332

value: Dana Farber


title: ChIP-Seq analysis of H3K36me3 in human CD25+ CD127- Treg cells; DNA_Lib 2090

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 2090
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.13143
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.13312
****************
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: GSM997230_BI.CD4+_CD25+_CD127-_Treg_Primary_Cells.H3K36me3.Donor_332.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 2090.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of CD4+ CD25+ CD127- Treg Primary Cells H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K36me3 ChIP-Seq on CD4+ CD25+ CD127- Treg Primary Cells, Donor Donor 332, 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.17274
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 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 6,505,675
FINDPEAKS_SCORE: 0.3722
FINDPEAKS_PERCENTILE: 75
HOTSPOT_SCORE: 0.4085
HOTSPOT_PERCENTILE: 91
IROC_SCORE: 0.977
IROC_PERCENTILE: 49
POISSON_SCORE: 0.5665
POISSON_PERCENTILE: 75
MAXIMUM_REPLICATE_CORRELATION: 0.96

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

ANALYSIS FILE NAME: GSM997230_BI.CD4+_CD25+_CD127-_Treg_Primary_Cells.H3K36me3.Donor_332.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 2090.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of CD4+ CD25+ CD127- Treg Primary Cells H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K36me3 ChIP-Seq read mappings from CD4+ CD25+ CD127- Treg Primary Cells, Donor Donor 332, 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.17457
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 9
BROWSER_TRACK_NAME: CCCTregreg H3K36me3 32 90
BROWSER_TRACK_DESCRIPTION: BI CD4+ CD25+ CD127- Treg Primary Cells Histone H3K36me3 Donor 332 Library DNA_Lib 2090 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 6,505,675
FINDPEAKS_SCORE: 0.3722
FINDPEAKS_PERCENTILE: 75
HOTSPOT_SCORE: 0.4085
HOTSPOT_PERCENTILE: 91
IROC_SCORE: 0.977
IROC_PERCENTILE: 49
POISSON_SCORE: 0.5665
POISSON_PERCENTILE: 75
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 2090

value: BioSam 713

value: CD4+ CD25+ CD127- Treg Primary Cells

value: Protein A-Sepharose 4B

value: 0.5 to 3 million cells

value: cell/nuclei lysis

value: ~1 ug

value: 10 ul bed volume

value: Abcam

value: Histone H3K36me3


title: ChIP-Seq analysis of H3K27me3 in human CD25- Th cells; DNA_Lib 2274

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 2274
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.13144
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.13313
****************
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: GSM997231_BI.CD4+_CD25-_Th_Primary_Cells.H3K27me3.Donor_332.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 2274.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of CD4+ CD25- Th Primary Cells H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K27me3 ChIP-Seq on CD4+ CD25- Th Primary Cells, Donor Donor 332, 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.17312
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 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 13,319,513
FINDPEAKS_SCORE: 0.0619
FINDPEAKS_PERCENTILE: 46
HOTSPOT_SCORE: 0.2052
HOTSPOT_PERCENTILE: 64
IROC_SCORE: 0.8129
IROC_PERCENTILE: 31
POISSON_SCORE: 0.3354
POISSON_PERCENTILE: 48
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

ANALYSIS FILE NAME: GSM997231_BI.CD4+_CD25-_Th_Primary_Cells.H3K27me3.Donor_332.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 2274.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of CD4+ CD25- Th Primary Cells H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K27me3 ChIP-Seq read mappings from CD4+ CD25- Th Primary Cells, Donor Donor 332, 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.17495
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 9
BROWSER_TRACK_NAME: CCT H3K27me3 32 74
BROWSER_TRACK_DESCRIPTION: BI CD4+ CD25- Th Primary Cells Histone H3K27me3 Donor 332 Library DNA_Lib 2274 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 13,319,513
FINDPEAKS_SCORE: 0.0619
FINDPEAKS_PERCENTILE: 46
HOTSPOT_SCORE: 0.2052
HOTSPOT_PERCENTILE: 64
IROC_SCORE: 0.8129
IROC_PERCENTILE: 31
POISSON_SCORE: 0.3354
POISSON_PERCENTILE: 48
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

source_name: CD25- Th  is one of  CD4+  T cell subsets  that purified by microbeads, LS column and FACS ; DNA_Lib 2274

value: BioSam 715

value: genomic DNA

value: CD4+ T cell

value: Millipore

value: Histone H3K27me3

value: Branson


title: ChIP-Seq analysis of H3K9me3 in human CD25- CD45RA+ naive cells; DNA_Lib 2210

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 2210
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.13141
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.13318
****************
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: GSM997228_BI.CD4+_CD25-_CD45RA+_Naive_Primary_Cells.H3K9me3.Donor_332.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 2210.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of CD4+ CD25- CD45RA+ Naive Primary Cells H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K9me3 ChIP-Seq on CD4+ CD25- CD45RA+ Naive Primary Cells, Donor Donor 332, 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.17296
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 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 35,528,554
FINDPEAKS_SCORE: 0.019
FINDPEAKS_PERCENTILE: 15
HOTSPOT_SCORE: 0.0565
HOTSPOT_PERCENTILE: 10
IROC_SCORE: 0.8463
IROC_PERCENTILE: 58
POISSON_SCORE: 0.1816
POISSON_PERCENTILE: 15
MAXIMUM_REPLICATE_CORRELATION: 0.97

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

ANALYSIS FILE NAME: GSM997228_BI.CD4+_CD25-_CD45RA+_Naive_Primary_Cells.H3K9me3.Donor_332.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 2210.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of CD4+ CD25- CD45RA+ Naive Primary Cells H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K9me3 ChIP-Seq read mappings from CD4+ CD25- CD45RA+ Naive Primary Cells, Donor Donor 332, 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.17479
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 9
BROWSER_TRACK_NAME: CCCNN H3K9me3 32 10
BROWSER_TRACK_DESCRIPTION: BI CD4+ CD25- CD45RA+ Naive Primary Cells Histone H3K9me3 Donor 332 Library DNA_Lib 2210 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 35,528,554
FINDPEAKS_SCORE: 0.019
FINDPEAKS_PERCENTILE: 15
HOTSPOT_SCORE: 0.0565
HOTSPOT_PERCENTILE: 10
IROC_SCORE: 0.8463
IROC_PERCENTILE: 58
POISSON_SCORE: 0.1816
POISSON_PERCENTILE: 15
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: CD25- CD45RA+ naive is one of  CD4+  T cell subsets  that purified by microbeads, LS column and FACS ; DNA_Lib 2210

value: BioSam 718

value: CD4+ CD25- CD45RA+ Naive Primary Cells

value: normal

value: CD25- CD45RA+ naive

value: Unknown

value: Primary Cell

value: Donor 332

value: Histone H3K9me3


title: ChIP-Seq analysis of H3K4me1 in human CD25- IL17+ Th17 stim cells; DNA_Lib 2217

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 2217
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.13137
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.13317
****************
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: GSM997224_BI.CD4+_CD25-_IL17+_PMA-Ionomcyin_stimulated_Th17_Primary_Cells.H3K4me1.Donor_332.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 2217.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of CD4+ CD25- IL17+ PMA-Ionomcyin stimulated Th17 Primary Cells H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K4me1 ChIP-Seq on CD4+ CD25- IL17+ PMA-Ionomcyin stimulated Th17 Primary Cells, Donor Donor 332, 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.17278
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 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 23,393,600
FINDPEAKS_SCORE: 0.3268
FINDPEAKS_PERCENTILE: 61
HOTSPOT_SCORE: 0.3355
HOTSPOT_PERCENTILE: 50
IROC_SCORE: 0.9951
IROC_PERCENTILE: 81
POISSON_SCORE: 0.4344
POISSON_PERCENTILE: 37
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

ANALYSIS FILE NAME: GSM997224_BI.CD4+_CD25-_IL17+_PMA-Ionomcyin_stimulated_Th17_Primary_Cells.H3K4me1.Donor_332.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 2217.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of CD4+ CD25- IL17+ PMA-Ionomcyin stimulated Th17 Primary Cells H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K4me1 ChIP-Seq read mappings from CD4+ CD25- IL17+ PMA-Ionomcyin stimulated Th17 Primary Cells, Donor Donor 332, 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.17461
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 9
BROWSER_TRACK_NAME: CCIPsT H3K4me1 32 17
BROWSER_TRACK_DESCRIPTION: BI CD4+ CD25- IL17+ PMA-Ionomcyin stimulated Th17 Primary Cells Histone H3K4me1 Donor 332 Library DNA_Lib 2217 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 23,393,600
FINDPEAKS_SCORE: 0.3268
FINDPEAKS_PERCENTILE: 61
HOTSPOT_SCORE: 0.3355
HOTSPOT_PERCENTILE: 50
IROC_SCORE: 0.9951
IROC_PERCENTILE: 81
POISSON_SCORE: 0.4344
POISSON_PERCENTILE: 37
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

source_name: CD25- IL17+ Th17 stim is one of  CD4+  T cell subsets  that purified by microbeads, LS column and FACS ; DNA_Lib 2217

value: BioSam 719

value: CD25- IL17+ Th17 stim

value: Dana Farber

value: Protein A-Sepharose 4B

value: 0.5 to 3 million cells

value: cell/nuclei lysis

value: ~1 ug

value: 10 ul bed volume

value: Histone H3K4me1


title: ChIP-Seq analysis of H3K4me1 in human CD25- CD45RO+ mem cells; DNA_Lib 2095

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 2095
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.13148
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.13315
****************
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: GSM997235_BI.CD4+_CD25-_CD45RO+_Memory_Primary_Cells.H3K4me1.Donor_332.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 2095.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of CD4+ CD25- CD45RO+ Memory Primary Cells H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K4me1 ChIP-Seq on CD4+ CD25- CD45RO+ Memory Primary Cells, Donor Donor 332, 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.17226
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 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 8,081,182
FINDPEAKS_SCORE: 0.471
FINDPEAKS_PERCENTILE: 89
HOTSPOT_SCORE: 0.5003
HOTSPOT_PERCENTILE: 89
IROC_SCORE: 0.9972
IROC_PERCENTILE: 89
POISSON_SCORE: 0.5709
POISSON_PERCENTILE: 81
MAXIMUM_REPLICATE_CORRELATION: 0.96

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

ANALYSIS FILE NAME: GSM997235_BI.CD4+_CD25-_CD45RO+_Memory_Primary_Cells.H3K4me1.Donor_332.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 2095.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of CD4+ CD25- CD45RO+ Memory Primary Cells H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K4me1 ChIP-Seq read mappings from CD4+ CD25- CD45RO+ Memory Primary Cells, Donor Donor 332, 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.17409
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 9
BROWSER_TRACK_NAME: CCCMM H3K4me1 32 95
BROWSER_TRACK_DESCRIPTION: BI CD4+ CD25- CD45RO+ Memory Primary Cells Histone H3K4me1 Donor 332 Library DNA_Lib 2095 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 8,081,182
FINDPEAKS_SCORE: 0.471
FINDPEAKS_PERCENTILE: 89
HOTSPOT_SCORE: 0.5003
HOTSPOT_PERCENTILE: 89
IROC_SCORE: 0.9972
IROC_PERCENTILE: 89
POISSON_SCORE: 0.5709
POISSON_PERCENTILE: 81
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: CD25- CD45RO+ mem is one of  CD4+  T cell subsets  that purified by microbeads, LS column and FACS ; DNA_Lib 2095

value: BioSam 717

value: CD4+ CD25- CD45RO+ Memory Primary Cells

value: genomic DNA

value: CD4+ T cell

value: CD25- CD45RO+ mem

value: Abcam

value: Branson


title: ChIP-Seq analysis of H3K36me3 in human CD25- CD45RO+ mem cells; DNA_Lib 2097

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 2097
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.13150
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.13315
****************
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: GSM997237_BI.CD4+_CD25-_CD45RO+_Memory_Primary_Cells.H3K36me3.Donor_332.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 2097.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of CD4+ CD25- CD45RO+ Memory Primary Cells H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K36me3 ChIP-Seq on CD4+ CD25- CD45RO+ Memory Primary Cells, Donor Donor 332, 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.17318
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 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 3,193,218
FINDPEAKS_SCORE: 0.1152
FINDPEAKS_PERCENTILE: 13
HOTSPOT_SCORE: 0.3181
HOTSPOT_PERCENTILE: 56
IROC_SCORE: 0.8494
IROC_PERCENTILE: 7
POISSON_SCORE: 0.5222
POISSON_PERCENTILE: 62
MAXIMUM_REPLICATE_CORRELATION: 0.91

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

ANALYSIS FILE NAME: GSM997237_BI.CD4+_CD25-_CD45RO+_Memory_Primary_Cells.H3K36me3.Donor_332.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 2097.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of CD4+ CD25- CD45RO+ Memory Primary Cells H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K36me3 ChIP-Seq read mappings from CD4+ CD25- CD45RO+ Memory Primary Cells, Donor Donor 332, 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.17501
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 9
BROWSER_TRACK_NAME: CCCMM H3K36me3 32 97
BROWSER_TRACK_DESCRIPTION: BI CD4+ CD25- CD45RO+ Memory Primary Cells Histone H3K36me3 Donor 332 Library DNA_Lib 2097 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 3,193,218
FINDPEAKS_SCORE: 0.1152
FINDPEAKS_PERCENTILE: 13
HOTSPOT_SCORE: 0.3181
HOTSPOT_PERCENTILE: 56
IROC_SCORE: 0.8494
IROC_PERCENTILE: 7
POISSON_SCORE: 0.5222
POISSON_PERCENTILE: 62
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: CD25- CD45RO+ mem is one of  CD4+  T cell subsets  that purified by microbeads, LS column and FACS ; DNA_Lib 2097

value: normal

value: Unknown

value: Primary Cell

value: Donor 332

value: Histone H3K36me3


title: ChIP-Seq analysis of H3K27me3 in human CD25- CD45RA+ naive cells; DNA_Lib 2212

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 2212
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.13140
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.13318
****************
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: GSM997227_BI.CD4+_CD25-_CD45RA+_Naive_Primary_Cells.H3K27me3.Donor_332.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 2212.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of CD4+ CD25- CD45RA+ Naive Primary Cells H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K27me3 ChIP-Seq on CD4+ CD25- CD45RA+ Naive Primary Cells, Donor Donor 332, 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.17321
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 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 11,939,278
FINDPEAKS_SCORE: 0.0482
FINDPEAKS_PERCENTILE: 43
HOTSPOT_SCORE: 0.1917
HOTSPOT_PERCENTILE: 55
IROC_SCORE: 0.78
IROC_PERCENTILE: 26
POISSON_SCORE: 0.3229
POISSON_PERCENTILE: 45
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

ANALYSIS FILE NAME: GSM997227_BI.CD4+_CD25-_CD45RA+_Naive_Primary_Cells.H3K27me3.Donor_332.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 2212.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of CD4+ CD25- CD45RA+ Naive Primary Cells H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K27me3 ChIP-Seq read mappings from CD4+ CD25- CD45RA+ Naive Primary Cells, Donor Donor 332, 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.17504
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 9
BROWSER_TRACK_NAME: CCCNN H3K27me3 32 12
BROWSER_TRACK_DESCRIPTION: BI CD4+ CD25- CD45RA+ Naive Primary Cells Histone H3K27me3 Donor 332 Library DNA_Lib 2212 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 11,939,278
FINDPEAKS_SCORE: 0.0482
FINDPEAKS_PERCENTILE: 43
HOTSPOT_SCORE: 0.1917
HOTSPOT_PERCENTILE: 55
IROC_SCORE: 0.78
IROC_PERCENTILE: 26
POISSON_SCORE: 0.3229
POISSON_PERCENTILE: 45
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: CD25- CD45RA+ naive is one of  CD4+  T cell subsets  that purified by microbeads, LS column and FACS ; DNA_Lib 2212

value: BioSam 718

value: CD4+ CD25- CD45RA+ Naive Primary Cells

value: CD25- CD45RA+ naive

value: Dana Farber

value: Protein A-Sepharose 4B

value: 0.5 to 3 million cells

value: Millipore

value: Histone H3K27me3


title: ChIP-Seq analysis of H3K36me3 in human CD25- IL17+ Th17 stim cells; DNA_Lib 2215

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 2215
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.13139
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.13317
****************
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: GSM997226_BI.CD4+_CD25-_IL17+_PMA-Ionomcyin_stimulated_Th17_Primary_Cells.H3K36me3.Donor_332.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 2215.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of CD4+ CD25- IL17+ PMA-Ionomcyin stimulated Th17 Primary Cells H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K36me3 ChIP-Seq on CD4+ CD25- IL17+ PMA-Ionomcyin stimulated Th17 Primary Cells, Donor Donor 332, 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.17262
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 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 34,908,150
FINDPEAKS_SCORE: 0.2584
FINDPEAKS_PERCENTILE: 44
HOTSPOT_SCORE: 0.2597
HOTSPOT_PERCENTILE: 29
IROC_SCORE: 0.9847
IROC_PERCENTILE: 64
POISSON_SCORE: 0.4741
POISSON_PERCENTILE: 47
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

ANALYSIS FILE NAME: GSM997226_BI.CD4+_CD25-_IL17+_PMA-Ionomcyin_stimulated_Th17_Primary_Cells.H3K36me3.Donor_332.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 2215.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of CD4+ CD25- IL17+ PMA-Ionomcyin stimulated Th17 Primary Cells H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K36me3 ChIP-Seq read mappings from CD4+ CD25- IL17+ PMA-Ionomcyin stimulated Th17 Primary Cells, Donor Donor 332, 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.17445
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 9
BROWSER_TRACK_NAME: CCIPsT H3K36me3 32 15
BROWSER_TRACK_DESCRIPTION: BI CD4+ CD25- IL17+ PMA-Ionomcyin stimulated Th17 Primary Cells Histone H3K36me3 Donor 332 Library DNA_Lib 2215 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 34,908,150
FINDPEAKS_SCORE: 0.2584
FINDPEAKS_PERCENTILE: 44
HOTSPOT_SCORE: 0.2597
HOTSPOT_PERCENTILE: 29
IROC_SCORE: 0.9847
IROC_PERCENTILE: 64
POISSON_SCORE: 0.4741
POISSON_PERCENTILE: 47
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

source_name: CD25- IL17+ Th17 stim is one of  CD4+  T cell subsets  that purified by microbeads, LS column and FACS ; DNA_Lib 2215

value: BioSam 719

value: genomic DNA

value: CD4+ T cell

value: CD25- IL17+ Th17 stim

value: cell/nuclei lysis

value: ~1 ug

value: 10 ul bed volume


title: ChIP-Seq analysis of H3K4me3 in human CD25- IL17+ Th17 stim cells; DNA_Lib 2214

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 2214
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.13138
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.13317
****************
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: GSM997225_BI.CD4+_CD25-_IL17+_PMA-Ionomcyin_stimulated_Th17_Primary_Cells.H3K4me3.Donor_332.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 2214.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of CD4+ CD25- IL17+ PMA-Ionomcyin stimulated Th17 Primary Cells H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K4me3 ChIP-Seq on CD4+ CD25- IL17+ PMA-Ionomcyin stimulated Th17 Primary Cells, Donor Donor 332, 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.17281
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 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 5,727,738
FINDPEAKS_SCORE: 0.5052
FINDPEAKS_PERCENTILE: 86
HOTSPOT_SCORE: 0.5399
HOTSPOT_PERCENTILE: 86
IROC_SCORE: 0.9997
IROC_PERCENTILE: 25
POISSON_SCORE: 0.5524
POISSON_PERCENTILE: 93
MAXIMUM_REPLICATE_CORRELATION: 0.95

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

ANALYSIS FILE NAME: GSM997225_BI.CD4+_CD25-_IL17+_PMA-Ionomcyin_stimulated_Th17_Primary_Cells.H3K4me3.Donor_332.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 2214.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of CD4+ CD25- IL17+ PMA-Ionomcyin stimulated Th17 Primary Cells H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K4me3 ChIP-Seq read mappings from CD4+ CD25- IL17+ PMA-Ionomcyin stimulated Th17 Primary Cells, Donor Donor 332, 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.17464
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 9
BROWSER_TRACK_NAME: CCIPsT H3K4me3 32 14
BROWSER_TRACK_DESCRIPTION: BI CD4+ CD25- IL17+ PMA-Ionomcyin stimulated Th17 Primary Cells Histone H3K4me3 Donor 332 Library DNA_Lib 2214 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 5,727,738
FINDPEAKS_SCORE: 0.5052
FINDPEAKS_PERCENTILE: 86
HOTSPOT_SCORE: 0.5399
HOTSPOT_PERCENTILE: 86
IROC_SCORE: 0.9997
IROC_PERCENTILE: 25
POISSON_SCORE: 0.5524
POISSON_PERCENTILE: 93
MAXIMUM_REPLICATE_CORRELATION: 0.95

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

source_name: CD25- IL17+ Th17 stim is one of  CD4+  T cell subsets  that purified by microbeads, LS column and FACS ; DNA_Lib 2214

value: normal

value: Unknown

value: Primary Cell

value: Donor 332

value: Histone H3K4me3

value: Branson


title: ChIP-Seq analysis of H3K9me3 in human CD25- IL17+ Th17 stim cells; DNA_Lib 2216

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 2216
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.13136
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.13317
****************
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: GSM997223_BI.CD4+_CD25-_IL17+_PMA-Ionomcyin_stimulated_Th17_Primary_Cells.H3K9me3.Donor_332.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 2216.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of CD4+ CD25- IL17+ PMA-Ionomcyin stimulated Th17 Primary Cells H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K9me3 ChIP-Seq on CD4+ CD25- IL17+ PMA-Ionomcyin stimulated Th17 Primary Cells, Donor Donor 332, 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.17203
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 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 29,784,842
FINDPEAKS_SCORE: 0.02
FINDPEAKS_PERCENTILE: 23
HOTSPOT_SCORE: 0.0656
HOTSPOT_PERCENTILE: 17
IROC_SCORE: 0.7781
IROC_PERCENTILE: 42
POISSON_SCORE: 0.2034
POISSON_PERCENTILE: 25
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

ANALYSIS FILE NAME: GSM997223_BI.CD4+_CD25-_IL17+_PMA-Ionomcyin_stimulated_Th17_Primary_Cells.H3K9me3.Donor_332.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 2216.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of CD4+ CD25- IL17+ PMA-Ionomcyin stimulated Th17 Primary Cells H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K9me3 ChIP-Seq read mappings from CD4+ CD25- IL17+ PMA-Ionomcyin stimulated Th17 Primary Cells, Donor Donor 332, 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.17386
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 9
BROWSER_TRACK_NAME: CCIPsT H3K9me3 32 16
BROWSER_TRACK_DESCRIPTION: BI CD4+ CD25- IL17+ PMA-Ionomcyin stimulated Th17 Primary Cells Histone H3K9me3 Donor 332 Library DNA_Lib 2216 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 29,784,842
FINDPEAKS_SCORE: 0.02
FINDPEAKS_PERCENTILE: 23
HOTSPOT_SCORE: 0.0656
HOTSPOT_PERCENTILE: 17
IROC_SCORE: 0.7781
IROC_PERCENTILE: 42
POISSON_SCORE: 0.2034
POISSON_PERCENTILE: 25
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

source_name: CD25- IL17+ Th17 stim is one of  CD4+  T cell subsets  that purified by microbeads, LS column and FACS ; DNA_Lib 2216

value: Dana Farber

value: Protein A-Sepharose 4B

value: Abcam

value: Histone H3K9me3


title: ChIP-Seq analysis of H3K27me3 in human CD25- IL17+ Th17 stim cells; DNA_Lib 2218

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 2218
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.13135
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.13317
****************
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: GSM997222_BI.CD4+_CD25-_IL17+_PMA-Ionomcyin_stimulated_Th17_Primary_Cells.H3K27me3.Donor_332.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 2218.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of CD4+ CD25- IL17+ PMA-Ionomcyin stimulated Th17 Primary Cells H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K27me3 ChIP-Seq on CD4+ CD25- IL17+ PMA-Ionomcyin stimulated Th17 Primary Cells, Donor Donor 332, 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.17223
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 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 22,565,162
FINDPEAKS_SCORE: 0.0371
FINDPEAKS_PERCENTILE: 32
HOTSPOT_SCORE: 0.1367
HOTSPOT_PERCENTILE: 36
IROC_SCORE: 0.7658
IROC_PERCENTILE: 22
POISSON_SCORE: 0.3369
POISSON_PERCENTILE: 50
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

ANALYSIS FILE NAME: GSM997222_BI.CD4+_CD25-_IL17+_PMA-Ionomcyin_stimulated_Th17_Primary_Cells.H3K27me3.Donor_332.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 2218.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of CD4+ CD25- IL17+ PMA-Ionomcyin stimulated Th17 Primary Cells H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K27me3 ChIP-Seq read mappings from CD4+ CD25- IL17+ PMA-Ionomcyin stimulated Th17 Primary Cells, Donor Donor 332, 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.17406
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 9
BROWSER_TRACK_NAME: CCIPsT H3K27me3 32 18
BROWSER_TRACK_DESCRIPTION: BI CD4+ CD25- IL17+ PMA-Ionomcyin stimulated Th17 Primary Cells Histone H3K27me3 Donor 332 Library DNA_Lib 2218 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 22,565,162
FINDPEAKS_SCORE: 0.0371
FINDPEAKS_PERCENTILE: 32
HOTSPOT_SCORE: 0.1367
HOTSPOT_PERCENTILE: 36
IROC_SCORE: 0.7658
IROC_PERCENTILE: 22
POISSON_SCORE: 0.3369
POISSON_PERCENTILE: 50
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

source_name: CD25- IL17+ Th17 stim is one of  CD4+  T cell subsets  that purified by microbeads, LS column and FACS ; DNA_Lib 2218

value: BioSam 719

value: 0.5 to 3 million cells

value: Millipore

value: Histone H3K27me3


title: ChIP-Seq analysis of H3K27me3 in human CD25- CD45RO+ mem cells; DNA_Lib 2098

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 2098
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.13151
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.13315
****************
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: GSM997238_BI.CD4+_CD25-_CD45RO+_Memory_Primary_Cells.H3K27me3.Donor_332.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 2098.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of CD4+ CD25- CD45RO+ Memory Primary Cells H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K27me3 ChIP-Seq on CD4+ CD25- CD45RO+ Memory Primary Cells, Donor Donor 332, 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.17209
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 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 9,945,447
FINDPEAKS_SCORE: 0.1083
FINDPEAKS_PERCENTILE: 66
HOTSPOT_SCORE: 0.2499
HOTSPOT_PERCENTILE: 70
IROC_SCORE: 0.8713
IROC_PERCENTILE: 43
POISSON_SCORE: 0.4089
POISSON_PERCENTILE: 68
MAXIMUM_REPLICATE_CORRELATION: 0.97

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

ANALYSIS FILE NAME: GSM997238_BI.CD4+_CD25-_CD45RO+_Memory_Primary_Cells.H3K27me3.Donor_332.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 2098.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of CD4+ CD25- CD45RO+ Memory Primary Cells H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K27me3 ChIP-Seq read mappings from CD4+ CD25- CD45RO+ Memory Primary Cells, Donor Donor 332, 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.17392
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 9
BROWSER_TRACK_NAME: CCCMM H3K27me3 32 98
BROWSER_TRACK_DESCRIPTION: BI CD4+ CD25- CD45RO+ Memory Primary Cells Histone H3K27me3 Donor 332 Library DNA_Lib 2098 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 9,945,447
FINDPEAKS_SCORE: 0.1083
FINDPEAKS_PERCENTILE: 66
HOTSPOT_SCORE: 0.2499
HOTSPOT_PERCENTILE: 70
IROC_SCORE: 0.8713
IROC_PERCENTILE: 43
POISSON_SCORE: 0.4089
POISSON_PERCENTILE: 68
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: CD25- CD45RO+ mem is one of  CD4+  T cell subsets  that purified by microbeads, LS column and FACS ; DNA_Lib 2098

value: BioSam 717

value: CD4+ CD25- CD45RO+ Memory Primary Cells

value: genomic DNA

value: CD4+ T cell

value: CD25- CD45RO+ mem

value: cell/nuclei lysis


title: ChIP-Seq analysis of WCE in human CD25+ CD127- Treg cells; DNA_Lib 2094

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 2094
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.13147
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.13312
****************
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: GSM997234_BI.CD4+_CD25+_CD127-_Treg_Primary_Cells.Input.Donor_332.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 2094.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of CD4+ CD25+ CD127- Treg Primary Cells Input ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Input ChIP-Seq on CD4+ CD25+ CD127- Treg Primary Cells, Donor Donor 332, 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.17216
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 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 36,012,367
FINDPEAKS_SCORE: 0.0074
FINDPEAKS_PERCENTILE: 79
HOTSPOT_SCORE: 0.0053
HOTSPOT_PERCENTILE: 29
IROC_SCORE: 0.0
IROC_PERCENTILE: 26
POISSON_SCORE: 0.0228
POISSON_PERCENTILE: 10
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

ANALYSIS FILE NAME: GSM997234_BI.CD4+_CD25+_CD127-_Treg_Primary_Cells.Input.Donor_332.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 2094.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of CD4+ CD25+ CD127- Treg Primary Cells Input ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Input ChIP-Seq read mappings from CD4+ CD25+ CD127- Treg Primary Cells, Donor Donor 332, 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.17399
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 9
BROWSER_TRACK_NAME: CCCTregreg Input 32 94
BROWSER_TRACK_DESCRIPTION: BI CD4+ CD25+ CD127- Treg Primary Cells ChIP-Seq Input Donor 332 Library DNA_Lib 2094 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 36,012,367
FINDPEAKS_SCORE: 0.0074
FINDPEAKS_PERCENTILE: 79
HOTSPOT_SCORE: 0.0053
HOTSPOT_PERCENTILE: 29
IROC_SCORE: 0.0
IROC_PERCENTILE: 26
POISSON_SCORE: 0.0228
POISSON_PERCENTILE: 10
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 2094

value: BioSam 713

value: CD4+ CD25+ CD127- Treg Primary Cells

value: normal

value: CD25+ CD127- Treg

value: Unknown

value: Primary Cell

value: Donor 332

value: standard

value: ChIP-Seq Input

value: Input


title: ChIP-Seq analysis of H3K4me1 in human CD25- CD45RA+ naive cells; DNA_Lib 2211

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 2211
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.13142
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.13318
****************
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: GSM997229_BI.CD4+_CD25-_CD45RA+_Naive_Primary_Cells.H3K4me1.Donor_332.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 2211.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of CD4+ CD25- CD45RA+ Naive Primary Cells H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K4me1 ChIP-Seq on CD4+ CD25- CD45RA+ Naive Primary Cells, Donor Donor 332, 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.17252
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 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 9,296,840
FINDPEAKS_SCORE: 0.3341
FINDPEAKS_PERCENTILE: 63
HOTSPOT_SCORE: 0.3816
HOTSPOT_PERCENTILE: 59
IROC_SCORE: 0.9906
IROC_PERCENTILE: 74
POISSON_SCORE: 0.4787
POISSON_PERCENTILE: 56
MAXIMUM_REPLICATE_CORRELATION: 0.97

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

ANALYSIS FILE NAME: GSM997229_BI.CD4+_CD25-_CD45RA+_Naive_Primary_Cells.H3K4me1.Donor_332.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 2211.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of CD4+ CD25- CD45RA+ Naive Primary Cells H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K4me1 ChIP-Seq read mappings from CD4+ CD25- CD45RA+ Naive Primary Cells, Donor Donor 332, 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.17435
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 9
BROWSER_TRACK_NAME: CCCNN H3K4me1 32 11
BROWSER_TRACK_DESCRIPTION: BI CD4+ CD25- CD45RA+ Naive Primary Cells Histone H3K4me1 Donor 332 Library DNA_Lib 2211 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 9,296,840
FINDPEAKS_SCORE: 0.3341
FINDPEAKS_PERCENTILE: 63
HOTSPOT_SCORE: 0.3816
HOTSPOT_PERCENTILE: 59
IROC_SCORE: 0.9906
IROC_PERCENTILE: 74
POISSON_SCORE: 0.4787
POISSON_PERCENTILE: 56
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: CD25- CD45RA+ naive is one of  CD4+  T cell subsets  that purified by microbeads, LS column and FACS ; DNA_Lib 2211

value: BioSam 718

value: CD4+ CD25- CD45RA+ Naive Primary Cells

value: CD25- CD45RA+ naive

value: Dana Farber

value: Protein A-Sepharose 4B

value: 0.5 to 3 million cells

value: ~1 ug

value: 10 ul bed volume

value: Abcam

value: Histone H3K4me1

value: Branson