title: ChIP-Seq analysis of H3K27me3 in human colon smooth muscle cells; DNA_Lib 1849

description:
sample_term_id: UBERON_0012489
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 1849
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.13172
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.9758
****************
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: GSM997259_BI.Colon_Smooth_Muscle.H3K27me3.156.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 1849.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Colon Smooth Muscle H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K27me3 ChIP-Seq on Colon Smooth Muscle, Donor 156, 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.17267
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: 29,759,496
FINDPEAKS_SCORE: 0.0294
FINDPEAKS_PERCENTILE: 21
HOTSPOT_SCORE: 0.0728
HOTSPOT_PERCENTILE: 9
IROC_SCORE: 0.9428
IROC_PERCENTILE: 70
POISSON_SCORE: 0.1673
POISSON_PERCENTILE: 4
MAXIMUM_REPLICATE_CORRELATION: 0.97

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

ANALYSIS FILE NAME: GSM997259_BI.Colon_Smooth_Muscle.H3K27me3.156.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 1849.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Colon Smooth Muscle H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K27me3 ChIP-Seq read mappings from Colon Smooth Muscle, Donor 156, 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.17450
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: CSM H3K27me3 56 49
BROWSER_TRACK_DESCRIPTION: BI Colon Smooth Muscle Histone H3K27me3 Donor 156 Library DNA_Lib 1849 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 29,759,496
FINDPEAKS_SCORE: 0.0294
FINDPEAKS_PERCENTILE: 21
HOTSPOT_SCORE: 0.0728
HOTSPOT_PERCENTILE: 9
IROC_SCORE: 0.9428
IROC_PERCENTILE: 70
POISSON_SCORE: 0.1673
POISSON_PERCENTILE: 4
MAXIMUM_REPLICATE_CORRELATION: 0.97

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

source_name: Smooth muscle from wall of colon obtained during surgery and confirmed by pathology examination to be healthy tissue; DNA_Lib 1849

value: Colon Smooth Muscle

value: Surgery

value: NL smooth muscle, colon rmvd as part of abdmnl Sarc.

value: Smooth Muscle

value: Caucasian

value: Female

value: Primary Tissue

value: Colon

value: MGH

value: 56.0 Years

value: 0.5 to 3 million cells

value: cell/nuclei lysis

value: ~1 ug

value: 10 ul bed volume

value: Histone H3K27me3

value: Branson


title: ChIP-Seq analysis of WCE in human CD25- CD45RO+ mem cells; DNA_Lib 2101

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_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 2101
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.13170
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
****************

library_source: genomic

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

ANALYSIS FILE NAME: GSM997257_BI.CD4+_CD25-_CD45RO+_Memory_Primary_Cells.Input.Donor_332.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 2101.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of CD4+ CD25- CD45RO+ Memory Primary Cells Input ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Input 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.17269
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: 27,773,621
FINDPEAKS_SCORE: 0.0091
FINDPEAKS_PERCENTILE: 86
HOTSPOT_SCORE: 0.0091
HOTSPOT_PERCENTILE: 44
IROC_SCORE: 0.9855
IROC_PERCENTILE: 74
POISSON_SCORE: 0.0369
POISSON_PERCENTILE: 33
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

ANALYSIS FILE NAME: GSM997257_BI.CD4+_CD25-_CD45RO+_Memory_Primary_Cells.Input.Donor_332.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 2101.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of CD4+ CD25- CD45RO+ Memory Primary Cells Input ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Input 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.17452
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 Input 32 01
BROWSER_TRACK_DESCRIPTION: BI CD4+ CD25- CD45RO+ Memory Primary Cells ChIP-Seq Input Donor 332 Library DNA_Lib 2101 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 27,773,621
FINDPEAKS_SCORE: 0.0091
FINDPEAKS_PERCENTILE: 86
HOTSPOT_SCORE: 0.0091
HOTSPOT_PERCENTILE: 44
IROC_SCORE: 0.9855
IROC_PERCENTILE: 74
POISSON_SCORE: 0.0369
POISSON_PERCENTILE: 33
MAXIMUM_REPLICATE_CORRELATION: NA

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

molecule: genomic DNA

organism: Homo sapiens

source_name: CD25- CD45RO+ mem is one of  CD4+  T cell subsets  that purified by microbeads, LS column and FACS ; DNA_Lib 2101

extract_protocol: Library construction protocol: Single read - Illumina

tag: sample alias

value: BioSam 717

tag: sample common name

value: CD4+ CD25- CD45RO+ Memory Primary Cells

value: normal

tag: molecule

value: genomic DNA

tag: disease

tag: markers

value: CD4+ T cell

value: CD25- CD45RO+ mem

value: Unknown

value: Primary Cell

value: Donor 332

value: Dana Farber

value: standard

value: ChIP-Seq Input

value: Input


title: ChIP-Seq analysis of H3K36me3 in human CD25- CD45RA+ naive cells; DNA_Lib 2209

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 2209
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.13168
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: GSM997255_BI.CD4+_CD25-_CD45RA+_Naive_Primary_Cells.H3K36me3.Donor_332.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 2209.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of CD4+ CD25- CD45RA+ Naive Primary Cells H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K36me3 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.17276
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: 29,030,702
FINDPEAKS_SCORE: 0.2879
FINDPEAKS_PERCENTILE: 53
HOTSPOT_SCORE: 0.2749
HOTSPOT_PERCENTILE: 40
IROC_SCORE: 0.9846
IROC_PERCENTILE: 62
POISSON_SCORE: 0.4984
POISSON_PERCENTILE: 53
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

ANALYSIS FILE NAME: GSM997255_BI.CD4+_CD25-_CD45RA+_Naive_Primary_Cells.H3K36me3.Donor_332.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 2209.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of CD4+ CD25- CD45RA+ Naive Primary Cells H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K36me3 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.17459
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 H3K36me3 32 09
BROWSER_TRACK_DESCRIPTION: BI CD4+ CD25- CD45RA+ Naive Primary Cells Histone H3K36me3 Donor 332 Library DNA_Lib 2209 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 29,030,702
FINDPEAKS_SCORE: 0.2879
FINDPEAKS_PERCENTILE: 53
HOTSPOT_SCORE: 0.2749
HOTSPOT_PERCENTILE: 40
IROC_SCORE: 0.9846
IROC_PERCENTILE: 62
POISSON_SCORE: 0.4984
POISSON_PERCENTILE: 53
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 2209

value: BioSam 718

value: CD4+ CD25- CD45RA+ Naive Primary Cells

value: CD25- CD45RA+ naive

value: Protein A-Sepharose 4B

value: 0.5 to 3 million cells

value: cell/nuclei lysis

value: ~1 ug

value: Abcam

value: Histone H3K36me3


title: ChIP-Seq analysis of H3K27ac in human CD25- IL17- Th stim MACS cells; DNA_Lib 2263

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 2263
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.13179
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: GSM997266_BI.CD4+_CD25-_IL17-_PMA-Ionomycin_stimulated_MACS_purified_Th_Primary_Cells.H3K27ac.Donor_332.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 2263.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of CD4+ CD25- IL17- PMA-Ionomycin stimulated MACS purified Th Primary Cells H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K27ac 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.17227
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: 11,184,775
FINDPEAKS_SCORE: 0.5146
FINDPEAKS_PERCENTILE: 78
HOTSPOT_SCORE: 0.5291
HOTSPOT_PERCENTILE: 76
IROC_SCORE: 0.9951
IROC_PERCENTILE: 52
POISSON_SCORE: 0.5837
POISSON_PERCENTILE: 78
MAXIMUM_REPLICATE_CORRELATION: 0.97

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

ANALYSIS FILE NAME: GSM997266_BI.CD4+_CD25-_IL17-_PMA-Ionomycin_stimulated_MACS_purified_Th_Primary_Cells.H3K27ac.Donor_332.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 2263.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of CD4+ CD25- IL17- PMA-Ionomycin stimulated MACS purified Th Primary Cells H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K27ac 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.17410
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 H3K27ac 32 63
BROWSER_TRACK_DESCRIPTION: BI CD4+ CD25- IL17- PMA-Ionomycin stimulated MACS purified Th Primary Cells Histone H3K27ac Donor 332 Library DNA_Lib 2263 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 11,184,775
FINDPEAKS_SCORE: 0.5146
FINDPEAKS_PERCENTILE: 78
HOTSPOT_SCORE: 0.5291
HOTSPOT_PERCENTILE: 76
IROC_SCORE: 0.9951
IROC_PERCENTILE: 52
POISSON_SCORE: 0.5837
POISSON_PERCENTILE: 78
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 2263

value: BioSam 720

value: normal

value: genomic DNA

value: CD4+ T cell

value: CD25- IL17- Th stim MACS

value: 10 ul bed volume

value: Active Motif

value: Histone H3K27ac

value: Branson


title: ChIP-Seq analysis of H3K4me1 in human CD25- IL17- Th stim MACS cells; DNA_Lib 2261

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 2261
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.13181
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: GSM997268_BI.CD4+_CD25-_IL17-_PMA-Ionomycin_stimulated_MACS_purified_Th_Primary_Cells.H3K4me1.Donor_332.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 2261.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of CD4+ CD25- IL17- PMA-Ionomycin stimulated MACS purified Th Primary Cells H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K4me1 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.17215
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: 21,224,988
FINDPEAKS_SCORE: 0.4185
FINDPEAKS_PERCENTILE: 80
HOTSPOT_SCORE: 0.4129
HOTSPOT_PERCENTILE: 69
IROC_SCORE: 0.9969
IROC_PERCENTILE: 87
POISSON_SCORE: 0.5349
POISSON_PERCENTILE: 72
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

ANALYSIS FILE NAME: GSM997268_BI.CD4+_CD25-_IL17-_PMA-Ionomycin_stimulated_MACS_purified_Th_Primary_Cells.H3K4me1.Donor_332.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 2261.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of CD4+ CD25- IL17- PMA-Ionomycin stimulated MACS purified Th Primary Cells H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K4me1 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.17398
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 H3K4me1 32 61
BROWSER_TRACK_DESCRIPTION: BI CD4+ CD25- IL17- PMA-Ionomycin stimulated MACS purified Th Primary Cells Histone H3K4me1 Donor 332 Library DNA_Lib 2261 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 21,224,988
FINDPEAKS_SCORE: 0.4185
FINDPEAKS_PERCENTILE: 80
HOTSPOT_SCORE: 0.4129
HOTSPOT_PERCENTILE: 69
IROC_SCORE: 0.9969
IROC_PERCENTILE: 87
POISSON_SCORE: 0.5349
POISSON_PERCENTILE: 72
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

source_name: CD25- IL17- Th stim MACS is one of  CD4+  T cell subsets  that purified by microbeads, LS column  ; DNA_Lib 2261

value: Unknown

value: Primary Cell

value: Donor 332

value: Dana Farber

value: Histone H3K4me1


title: ChIP-Seq analysis of H3K9me3 in human CD25- CD45RO+ mem cells; DNA_Lib 2099

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 2099
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.13188
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: GSM997275_BI.CD4+_CD25-_CD45RO+_Memory_Primary_Cells.H3K9me3.Donor_332.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 2099.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of CD4+ CD25- CD45RO+ Memory Primary Cells H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K9me3 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.17271
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: 7,367,033
FINDPEAKS_SCORE: 0.0431
FINDPEAKS_PERCENTILE: 52
HOTSPOT_SCORE: 0.1852
HOTSPOT_PERCENTILE: 69
IROC_SCORE: 0.6915
IROC_PERCENTILE: 29
POISSON_SCORE: 0.3446
POISSON_PERCENTILE: 69
MAXIMUM_REPLICATE_CORRELATION: 0.97

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

ANALYSIS FILE NAME: GSM997275_BI.CD4+_CD25-_CD45RO+_Memory_Primary_Cells.H3K9me3.Donor_332.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 2099.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of CD4+ CD25- CD45RO+ Memory Primary Cells H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K9me3 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.17454
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 H3K9me3 32 99
BROWSER_TRACK_DESCRIPTION: BI CD4+ CD25- CD45RO+ Memory Primary Cells Histone H3K9me3 Donor 332 Library DNA_Lib 2099 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 7,367,033
FINDPEAKS_SCORE: 0.0431
FINDPEAKS_PERCENTILE: 52
HOTSPOT_SCORE: 0.1852
HOTSPOT_PERCENTILE: 69
IROC_SCORE: 0.6915
IROC_PERCENTILE: 29
POISSON_SCORE: 0.3446
POISSON_PERCENTILE: 69
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 2099

value: BioSam 717

value: CD4+ CD25- CD45RO+ Memory Primary Cells

value: CD25- CD45RO+ mem

value: Protein A-Sepharose 4B

value: 0.5 to 3 million cells

value: cell/nuclei lysis

value: ~1 ug

value: Histone H3K9me3


title: ChIP-Seq analysis of H3K4me3 in human CD25int CD127+ Tmem cells; DNA_Lib 2264

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 2264
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.13178
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.13316
****************
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: GSM997265_BI.CD4+_CD25int_CD127+_Tmem_Primary_Cells.H3K4me3.Donor_332.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 2264.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of CD4+ CD25int CD127+ Tmem Primary Cells H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K4me3 ChIP-Seq on CD4+ CD25int CD127+ Tmem 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.17243
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: 9,423,871
FINDPEAKS_SCORE: 0.359
FINDPEAKS_PERCENTILE: 36
HOTSPOT_SCORE: 0.4148
HOTSPOT_PERCENTILE: 50
IROC_SCORE: 0.9991
IROC_PERCENTILE: 16
POISSON_SCORE: 0.4231
POISSON_PERCENTILE: 55
MAXIMUM_REPLICATE_CORRELATION: 0.97

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

ANALYSIS FILE NAME: GSM997265_BI.CD4+_CD25int_CD127+_Tmem_Primary_Cells.H3K4me3.Donor_332.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 2264.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of CD4+ CD25int CD127+ Tmem Primary Cells H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K4me3 ChIP-Seq read mappings from CD4+ CD25int CD127+ Tmem 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.17426
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: CCCTmemmem H3K4me3 32 64
BROWSER_TRACK_DESCRIPTION: BI CD4+ CD25int CD127+ Tmem Primary Cells Histone H3K4me3 Donor 332 Library DNA_Lib 2264 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 9,423,871
FINDPEAKS_SCORE: 0.359
FINDPEAKS_PERCENTILE: 36
HOTSPOT_SCORE: 0.4148
HOTSPOT_PERCENTILE: 50
IROC_SCORE: 0.9991
IROC_PERCENTILE: 16
POISSON_SCORE: 0.4231
POISSON_PERCENTILE: 55
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: CD25int CD127+ Tmem is one of  CD4+  T cell subsets  that purified by microbeads, LS column and FACS ; DNA_Lib 2264

value: BioSam 716

value: CD4+ CD25int CD127+ Tmem Primary Cells

value: normal

value: genomic DNA

value: CD4+ T cell

value: CD25int CD127+ Tmem

value: 10 ul bed volume

value: Millipore

value: Histone H3K4me3


title: ChIP-Seq analysis of H3K9me3 in human CD25int CD127+ Tmem cells; DNA_Lib 2266

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 2266
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.13176
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.13316
****************
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: GSM997263_BI.CD4+_CD25int_CD127+_Tmem_Primary_Cells.H3K9me3.Donor_332.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 2266.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of CD4+ CD25int CD127+ Tmem Primary Cells H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K9me3 ChIP-Seq on CD4+ CD25int CD127+ Tmem 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.17232
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: 13,893,421
FINDPEAKS_SCORE: 0.0333
FINDPEAKS_PERCENTILE: 44
HOTSPOT_SCORE: 0.1443
HOTSPOT_PERCENTILE: 52
IROC_SCORE: 0.6381
IROC_PERCENTILE: 13
POISSON_SCORE: 0.2732
POISSON_PERCENTILE: 40
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

ANALYSIS FILE NAME: GSM997263_BI.CD4+_CD25int_CD127+_Tmem_Primary_Cells.H3K9me3.Donor_332.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 2266.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of CD4+ CD25int CD127+ Tmem Primary Cells H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K9me3 ChIP-Seq read mappings from CD4+ CD25int CD127+ Tmem 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.17415
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: CCCTmemmem H3K9me3 32 66
BROWSER_TRACK_DESCRIPTION: BI CD4+ CD25int CD127+ Tmem Primary Cells Histone H3K9me3 Donor 332 Library DNA_Lib 2266 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 13,893,421
FINDPEAKS_SCORE: 0.0333
FINDPEAKS_PERCENTILE: 44
HOTSPOT_SCORE: 0.1443
HOTSPOT_PERCENTILE: 52
IROC_SCORE: 0.6381
IROC_PERCENTILE: 13
POISSON_SCORE: 0.2732
POISSON_PERCENTILE: 40
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: CD25int CD127+ Tmem is one of  CD4+  T cell subsets  that purified by microbeads, LS column and FACS ; DNA_Lib 2266

value: Unknown

value: Primary Cell

value: Donor 332

value: Dana Farber

value: Abcam

value: Branson


title: ChIP-Seq analysis of H3K27ac in human CD25int CD127+ Tmem cells; DNA_Lib 2269

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 2269
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.13173
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.13316
****************
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: GSM997260_BI.CD4+_CD25int_CD127+_Tmem_Primary_Cells.H3K27ac.Donor_332.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 2269.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of CD4+ CD25int CD127+ Tmem Primary Cells H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K27ac ChIP-Seq on CD4+ CD25int CD127+ Tmem 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.17204
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: 7,577,525
FINDPEAKS_SCORE: 0.2647
FINDPEAKS_PERCENTILE: 33
HOTSPOT_SCORE: 0.3534
HOTSPOT_PERCENTILE: 40
IROC_SCORE: 0.994
IROC_PERCENTILE: 47
POISSON_SCORE: 0.4067
POISSON_PERCENTILE: 35
MAXIMUM_REPLICATE_CORRELATION: 0.97

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

ANALYSIS FILE NAME: GSM997260_BI.CD4+_CD25int_CD127+_Tmem_Primary_Cells.H3K27ac.Donor_332.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 2269.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of CD4+ CD25int CD127+ Tmem Primary Cells H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K27ac ChIP-Seq read mappings from CD4+ CD25int CD127+ Tmem 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.17387
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: CCCTmemmem H3K27ac 32 69
BROWSER_TRACK_DESCRIPTION: BI CD4+ CD25int CD127+ Tmem Primary Cells Histone H3K27ac Donor 332 Library DNA_Lib 2269 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 7,577,525
FINDPEAKS_SCORE: 0.2647
FINDPEAKS_PERCENTILE: 33
HOTSPOT_SCORE: 0.3534
HOTSPOT_PERCENTILE: 40
IROC_SCORE: 0.994
IROC_PERCENTILE: 47
POISSON_SCORE: 0.4067
POISSON_PERCENTILE: 35
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: CD25int CD127+ Tmem is one of  CD4+  T cell subsets  that purified by microbeads, LS column and FACS ; DNA_Lib 2269

value: Protein A-Sepharose 4B

value: 0.5 to 3 million cells

value: cell/nuclei lysis

value: ~1 ug

value: Active Motif

value: Histone H3K27ac


title: ChIP-Seq analysis of H3K36me3 in human CD25int CD127+ Tmem cells; DNA_Lib 2265

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 2265
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.13177
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.13316
****************
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: GSM997264_BI.CD4+_CD25int_CD127+_Tmem_Primary_Cells.H3K36me3.Donor_332.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 2265.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of CD4+ CD25int CD127+ Tmem Primary Cells H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K36me3 ChIP-Seq on CD4+ CD25int CD127+ Tmem 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.17218
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: 17,049,873
FINDPEAKS_SCORE: 0.2757
FINDPEAKS_PERCENTILE: 49
HOTSPOT_SCORE: 0.2917
HOTSPOT_PERCENTILE: 47
IROC_SCORE: 0.9752
IROC_PERCENTILE: 45
POISSON_SCORE: 0.467
POISSON_PERCENTILE: 44
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

ANALYSIS FILE NAME: GSM997264_BI.CD4+_CD25int_CD127+_Tmem_Primary_Cells.H3K36me3.Donor_332.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 2265.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of CD4+ CD25int CD127+ Tmem Primary Cells H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K36me3 ChIP-Seq read mappings from CD4+ CD25int CD127+ Tmem 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.17401
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: CCCTmemmem H3K36me3 32 65
BROWSER_TRACK_DESCRIPTION: BI CD4+ CD25int CD127+ Tmem Primary Cells Histone H3K36me3 Donor 332 Library DNA_Lib 2265 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 17,049,873
FINDPEAKS_SCORE: 0.2757
FINDPEAKS_PERCENTILE: 49
HOTSPOT_SCORE: 0.2917
HOTSPOT_PERCENTILE: 47
IROC_SCORE: 0.9752
IROC_PERCENTILE: 45
POISSON_SCORE: 0.467
POISSON_PERCENTILE: 44
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: CD25int CD127+ Tmem is one of  CD4+  T cell subsets  that purified by microbeads, LS column and FACS ; DNA_Lib 2265

value: BioSam 716

value: CD4+ CD25int CD127+ Tmem Primary Cells

value: normal

value: genomic DNA

value: CD4+ T cell

value: Histone H3K36me3


title: ChIP-Seq analysis of H3K27me3 in human CD25int CD127+ Tmem cells; DNA_Lib 2268

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 2268
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.13174
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.13316
****************
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: GSM997261_BI.CD4+_CD25int_CD127+_Tmem_Primary_Cells.H3K27me3.Donor_332.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 2268.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of CD4+ CD25int CD127+ Tmem Primary Cells H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K27me3 ChIP-Seq on CD4+ CD25int CD127+ Tmem 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.17294
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: 7,975,805
FINDPEAKS_SCORE: 0.0781
FINDPEAKS_PERCENTILE: 54
HOTSPOT_SCORE: 0.2548
HOTSPOT_PERCENTILE: 71
IROC_SCORE: 0.8285
IROC_PERCENTILE: 35
POISSON_SCORE: 0.3537
POISSON_PERCENTILE: 55
MAXIMUM_REPLICATE_CORRELATION: 0.97

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

ANALYSIS FILE NAME: GSM997261_BI.CD4+_CD25int_CD127+_Tmem_Primary_Cells.H3K27me3.Donor_332.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 2268.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of CD4+ CD25int CD127+ Tmem Primary Cells H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K27me3 ChIP-Seq read mappings from CD4+ CD25int CD127+ Tmem 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.17477
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: CCCTmemmem H3K27me3 32 68
BROWSER_TRACK_DESCRIPTION: BI CD4+ CD25int CD127+ Tmem Primary Cells Histone H3K27me3 Donor 332 Library DNA_Lib 2268 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 7,975,805
FINDPEAKS_SCORE: 0.0781
FINDPEAKS_PERCENTILE: 54
HOTSPOT_SCORE: 0.2548
HOTSPOT_PERCENTILE: 71
IROC_SCORE: 0.8285
IROC_PERCENTILE: 35
POISSON_SCORE: 0.3537
POISSON_PERCENTILE: 55
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: CD25int CD127+ Tmem is one of  CD4+  T cell subsets  that purified by microbeads, LS column and FACS ; DNA_Lib 2268

value: CD25int CD127+ Tmem

value: Unknown

value: Primary Cell

value: 10 ul bed volume

value: Millipore

value: Histone H3K27me3


title: ChIP-Seq analysis of H3K4me1 in human CD25int CD127+ Tmem cells; DNA_Lib 2267

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 2267
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.13175
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.13316
****************
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: GSM997262_BI.CD4+_CD25int_CD127+_Tmem_Primary_Cells.H3K4me1.Donor_332.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 2267.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of CD4+ CD25int CD127+ Tmem Primary Cells H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K4me1 ChIP-Seq on CD4+ CD25int CD127+ Tmem 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.17319
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: 6,799,973
FINDPEAKS_SCORE: 0.3909
FINDPEAKS_PERCENTILE: 74
HOTSPOT_SCORE: 0.4394
HOTSPOT_PERCENTILE: 74
IROC_SCORE: 0.993
IROC_PERCENTILE: 76
POISSON_SCORE: 0.5238
POISSON_PERCENTILE: 69
MAXIMUM_REPLICATE_CORRELATION: 0.96

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

ANALYSIS FILE NAME: GSM997262_BI.CD4+_CD25int_CD127+_Tmem_Primary_Cells.H3K4me1.Donor_332.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 2267.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of CD4+ CD25int CD127+ Tmem Primary Cells H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K4me1 ChIP-Seq read mappings from CD4+ CD25int CD127+ Tmem 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.17502
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: CCCTmemmem H3K4me1 32 67
BROWSER_TRACK_DESCRIPTION: BI CD4+ CD25int CD127+ Tmem Primary Cells Histone H3K4me1 Donor 332 Library DNA_Lib 2267 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 6,799,973
FINDPEAKS_SCORE: 0.3909
FINDPEAKS_PERCENTILE: 74
HOTSPOT_SCORE: 0.4394
HOTSPOT_PERCENTILE: 74
IROC_SCORE: 0.993
IROC_PERCENTILE: 76
POISSON_SCORE: 0.5238
POISSON_PERCENTILE: 69
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: CD25int CD127+ Tmem is one of  CD4+  T cell subsets  that purified by microbeads, LS column and FACS ; DNA_Lib 2267

value: Donor 332

value: Dana Farber

value: Protein A-Sepharose 4B

value: 0.5 to 3 million cells

value: Abcam

value: Histone H3K4me1

value: Branson


title: ChIP-Seq analysis of WCE in human CD25- Th cells; DNA_Lib 2278

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 2278
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.14608
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: GSM1112781_BI.CD4+_CD25-_Th_Primary_Cells.Input.Donor_332.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 2278.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of CD4+ CD25- Th Primary Cells Input ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Input 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.17233
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: 31,491,577
FINDPEAKS_SCORE: 0.006
FINDPEAKS_PERCENTILE: 59
HOTSPOT_SCORE: 0.005
HOTSPOT_PERCENTILE: 27
IROC_SCORE: 0.0
IROC_PERCENTILE: 26
POISSON_SCORE: 0.0295
POISSON_PERCENTILE: 27
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

ANALYSIS FILE NAME: GSM1112781_BI.CD4+_CD25-_Th_Primary_Cells.Input.Donor_332.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 2278.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of CD4+ CD25- Th Primary Cells Input ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Input 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.17416
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 Input 32 78
BROWSER_TRACK_DESCRIPTION: BI CD4+ CD25- Th Primary Cells ChIP-Seq Input Donor 332 Library DNA_Lib 2278 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 31,491,577
FINDPEAKS_SCORE: 0.006
FINDPEAKS_PERCENTILE: 59
HOTSPOT_SCORE: 0.005
HOTSPOT_PERCENTILE: 27
IROC_SCORE: 0.0
IROC_PERCENTILE: 26
POISSON_SCORE: 0.0295
POISSON_PERCENTILE: 27
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 2278

value: CD4+ CD25- Th Primary Cells

tag: sra sample accession

value: normal

value: CD25- Th

value: standard

value: cell/nuclei lysis

value: ChIP-Seq Input

value: Input


title: ChIP-Seq analysis of H3K9me3 in human colon smooth muscle cells; DNA_Lib 1850

description:
sample_term_id: UBERON_0012489
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 1850
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.13190
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.9758
****************
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: GSM997277_BI.Colon_Smooth_Muscle.H3K9me3.156.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 1850.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Colon Smooth Muscle H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K9me3 ChIP-Seq on Colon Smooth Muscle, Donor 156, 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.17320
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: 13,034,346
FINDPEAKS_SCORE: 0.0245
FINDPEAKS_PERCENTILE: 33
HOTSPOT_SCORE: 0.1196
HOTSPOT_PERCENTILE: 42
IROC_SCORE: 0.5925
IROC_PERCENTILE: 6
POISSON_SCORE: 0.2047
POISSON_PERCENTILE: 27
MAXIMUM_REPLICATE_CORRELATION: 0.97

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

ANALYSIS FILE NAME: GSM997277_BI.Colon_Smooth_Muscle.H3K9me3.156.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 1850.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Colon Smooth Muscle H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K9me3 ChIP-Seq read mappings from Colon Smooth Muscle, Donor 156, 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.17503
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: CSM H3K9me3 56 50
BROWSER_TRACK_DESCRIPTION: BI Colon Smooth Muscle Histone H3K9me3 Donor 156 Library DNA_Lib 1850 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 13,034,346
FINDPEAKS_SCORE: 0.0245
FINDPEAKS_PERCENTILE: 33
HOTSPOT_SCORE: 0.1196
HOTSPOT_PERCENTILE: 42
IROC_SCORE: 0.5925
IROC_PERCENTILE: 6
POISSON_SCORE: 0.2047
POISSON_PERCENTILE: 27
MAXIMUM_REPLICATE_CORRELATION: 0.97

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

source_name: Smooth muscle from wall of colon obtained during surgery and confirmed by pathology examination to be healthy tissue; DNA_Lib 1850

value: Colon Smooth Muscle

value: Surgery

value: NL smooth muscle, colon rmvd as part of abdmnl Sarc.

value: genomic DNA

value: Smooth Muscle

value: Caucasian

value: Female

value: Primary Tissue

value: Colon

value: MGH

value: 56.0 Years

value: ~1 ug

value: 10 ul bed volume

value: Histone H3K9me3


title: ChIP-Seq analysis of H3K27ac in human HUES 6 cells; DNA_Lib 835

description:
sample_term_id: NTR_0000841
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 835
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.14601
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.5642
****************
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: GSM1112774_BI.HUES6.H3K27ac.DNA_Lib_835.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 835.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of HUES6 Cell Line H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K27ac ChIP-Seq on the HUES6 Cell Line, Library DNA_Lib 835, 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.17306
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: 22,214,831
FINDPEAKS_SCORE: 0.0519
FINDPEAKS_PERCENTILE: 2
HOTSPOT_SCORE: 0.1283
HOTSPOT_PERCENTILE: 11
IROC_SCORE: 0.9358
IROC_PERCENTILE: 6
POISSON_SCORE: 0.2157
POISSON_PERCENTILE: 5
MAXIMUM_REPLICATE_CORRELATION: 0.97

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

ANALYSIS FILE NAME: GSM1112774_BI.HUES6.H3K27ac.DNA_Lib_835.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 835.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of HUES6 Cell Line H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K27ac ChIP-Seq read mappings from the HUES6 Cell Line, Library DNA_Lib 835, 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.17489
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: HUES6 H3K27ac 35
BROWSER_TRACK_DESCRIPTION: BI HUES6 Cell Line Histone H3K27ac Library DNA_Lib 835 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 22,214,831
FINDPEAKS_SCORE: 0.0519
FINDPEAKS_PERCENTILE: 2
HOTSPOT_SCORE: 0.1283
HOTSPOT_PERCENTILE: 11
IROC_SCORE: 0.9358
IROC_PERCENTILE: 6
POISSON_SCORE: 0.2157
POISSON_PERCENTILE: 5
MAXIMUM_REPLICATE_CORRELATION: 0.97

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

source_name: Harvard University Embryonic Stem Cells; DNA_Lib 835

value: HUES6 Cell Line

tag: lineage

value: embrionic stem cell

tag: medium

value: KSR

tag: passage

tag: line

value: HUES 6

tag: batch

value: ES cell HUES_6-1

value: Cell Line

value: undifferentiated

tag: Sex

value: Unknown

value: Harvard University

value: Protein A-Sepharose 4B

value: 0.5 to 3 million cells

value: cell/nuclei lysis

value: Abcam

value: Histone H3K27ac

value: Branson


title: ChIP-Seq analysis of H3K27me3 in human CD25- IL17- Th stim MACS cells; DNA_Lib 2262

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 2262
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.13180
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: GSM997267_BI.CD4+_CD25-_IL17-_PMA-Ionomycin_stimulated_MACS_purified_Th_Primary_Cells.H3K27me3.Donor_332.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 2262.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of CD4+ CD25- IL17- PMA-Ionomycin stimulated MACS purified Th Primary Cells H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K27me3 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.17249
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: 17,673,270
FINDPEAKS_SCORE: 0.0631
FINDPEAKS_PERCENTILE: 48
HOTSPOT_SCORE: 0.1845
HOTSPOT_PERCENTILE: 50
IROC_SCORE: 0.8276
IROC_PERCENTILE: 33
POISSON_SCORE: 0.365
POISSON_PERCENTILE: 57
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

ANALYSIS FILE NAME: GSM997267_BI.CD4+_CD25-_IL17-_PMA-Ionomycin_stimulated_MACS_purified_Th_Primary_Cells.H3K27me3.Donor_332.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 2262.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of CD4+ CD25- IL17- PMA-Ionomycin stimulated MACS purified Th Primary Cells H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K27me3 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.17432
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 H3K27me3 32 62
BROWSER_TRACK_DESCRIPTION: BI CD4+ CD25- IL17- PMA-Ionomycin stimulated MACS purified Th Primary Cells Histone H3K27me3 Donor 332 Library DNA_Lib 2262 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 17,673,270
FINDPEAKS_SCORE: 0.0631
FINDPEAKS_PERCENTILE: 48
HOTSPOT_SCORE: 0.1845
HOTSPOT_PERCENTILE: 50
IROC_SCORE: 0.8276
IROC_PERCENTILE: 33
POISSON_SCORE: 0.365
POISSON_PERCENTILE: 57
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

source_name: CD25- IL17- Th stim MACS is one of  CD4+  T cell subsets  that purified by microbeads, LS column  ; DNA_Lib 2262

value: BioSam 720

value: normal

value: genomic DNA

value: CD4+ T cell

value: CD25- IL17- Th stim MACS

value: Primary Cell

value: Donor 332

value: Dana Farber

value: ~1 ug

value: 10 ul bed volume

value: Millipore

value: Histone H3K27me3


title: ChIP-Seq analysis of H3K36me3 in human colon smooth muscle cells; DNA_Lib 1851

description:
sample_term_id: UBERON_0012489
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 1851
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.13189
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.9758
****************
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: GSM997276_BI.Colon_Smooth_Muscle.H3K36me3.156.DNA_Lib_1851.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 1851.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Colon Smooth Muscle H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K36me3 ChIP-Seq on Colon Smooth Muscle, Donor 156, 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.17277
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: 14,855,750
FINDPEAKS_SCORE: NA
FINDPEAKS_PERCENTILE: NA
HOTSPOT_SCORE: NA
HOTSPOT_PERCENTILE: NA
IROC_SCORE: NA
IROC_PERCENTILE: NA
POISSON_SCORE: NA
POISSON_PERCENTILE: NA
MAXIMUM_REPLICATE_CORRELATION: 0.97

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

ANALYSIS FILE NAME: GSM997276_BI.Colon_Smooth_Muscle.H3K36me3.156.DNA_Lib_1851.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 1851.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Colon Smooth Muscle H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K36me3 ChIP-Seq read mappings from Colon Smooth Muscle, Donor 156, 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.17460
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: CSM H3K36me3 56 51
BROWSER_TRACK_DESCRIPTION: BI Colon Smooth Muscle Histone H3K36me3 Donor 156 Library DNA_Lib 1851 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 14,855,750
FINDPEAKS_SCORE: NA
FINDPEAKS_PERCENTILE: NA
HOTSPOT_SCORE: NA
HOTSPOT_PERCENTILE: NA
IROC_SCORE: NA
IROC_PERCENTILE: NA
POISSON_SCORE: NA
POISSON_PERCENTILE: NA
MAXIMUM_REPLICATE_CORRELATION: 0.97

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

source_name: Smooth muscle from wall of colon obtained during surgery and confirmed by pathology examination to be healthy tissue; DNA_Lib 1851

value: Colon Smooth Muscle

value: Surgery

value: NL smooth muscle, colon rmvd as part of abdmnl Sarc.

value: Smooth Muscle

value: Caucasian

value: Female

value: Primary Tissue

value: Colon

value: MGH

value: 56.0 Years

value: Protein A-Sepharose 4B

value: 0.5 to 3 million cells

value: Histone H3K36me3


title: ChIP-Seq analysis of H3K9me3 in human CD25- IL17- Th stim MACS cells; DNA_Lib 2260

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 2260
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.13182
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: GSM997269_BI.CD4+_CD25-_IL17-_PMA-Ionomycin_stimulated_MACS_purified_Th_Primary_Cells.H3K9me3.Donor_332.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 2260.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of CD4+ CD25- IL17- PMA-Ionomycin stimulated MACS purified Th Primary Cells H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K9me3 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.17261
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: 19,874,989
FINDPEAKS_SCORE: 0.0284
FINDPEAKS_PERCENTILE: 35
HOTSPOT_SCORE: 0.1008
HOTSPOT_PERCENTILE: 31
IROC_SCORE: 0.6463
IROC_PERCENTILE: 21
POISSON_SCORE: 0.2383
POISSON_PERCENTILE: 33
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

ANALYSIS FILE NAME: GSM997269_BI.CD4+_CD25-_IL17-_PMA-Ionomycin_stimulated_MACS_purified_Th_Primary_Cells.H3K9me3.Donor_332.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 2260.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of CD4+ CD25- IL17- PMA-Ionomycin stimulated MACS purified Th Primary Cells H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K9me3 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.17444
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 H3K9me3 32 60
BROWSER_TRACK_DESCRIPTION: BI CD4+ CD25- IL17- PMA-Ionomycin stimulated MACS purified Th Primary Cells Histone H3K9me3 Donor 332 Library DNA_Lib 2260 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 19,874,989
FINDPEAKS_SCORE: 0.0284
FINDPEAKS_PERCENTILE: 35
HOTSPOT_SCORE: 0.1008
HOTSPOT_PERCENTILE: 31
IROC_SCORE: 0.6463
IROC_PERCENTILE: 21
POISSON_SCORE: 0.2383
POISSON_PERCENTILE: 33
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

source_name: CD25- IL17- Th stim MACS is one of  CD4+  T cell subsets  that purified by microbeads, LS column  ; DNA_Lib 2260

value: BioSam 720

value: normal

value: genomic DNA

value: CD4+ T cell

value: CD25- IL17- Th stim MACS

value: Unknown

value: Primary Cell

value: Donor 332

value: Dana Farber

value: cell/nuclei lysis

value: ~1 ug

value: Abcam

value: Histone H3K9me3

value: Branson


title: ChIP-Seq analysis of H3K27me3 in human CD25+ CD127- Treg cells; DNA_Lib 2091

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 2091
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.13184
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: GSM997271_BI.CD4+_CD25+_CD127-_Treg_Primary_Cells.H3K27me3.Donor_332.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 2091.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of CD4+ CD25+ CD127- Treg Primary Cells H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K27me3 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.17301
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: 12,712,956
FINDPEAKS_SCORE: 0.1278
FINDPEAKS_PERCENTILE: 75
HOTSPOT_SCORE: 0.2707
HOTSPOT_PERCENTILE: 73
IROC_SCORE: 0.8978
IROC_PERCENTILE: 54
POISSON_SCORE: 0.4169
POISSON_PERCENTILE: 75
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

ANALYSIS FILE NAME: GSM997271_BI.CD4+_CD25+_CD127-_Treg_Primary_Cells.H3K27me3.Donor_332.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 2091.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of CD4+ CD25+ CD127- Treg Primary Cells H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K27me3 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.17484
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 H3K27me3 32 91
BROWSER_TRACK_DESCRIPTION: BI CD4+ CD25+ CD127- Treg Primary Cells Histone H3K27me3 Donor 332 Library DNA_Lib 2091 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 12,712,956
FINDPEAKS_SCORE: 0.1278
FINDPEAKS_PERCENTILE: 75
HOTSPOT_SCORE: 0.2707
HOTSPOT_PERCENTILE: 73
IROC_SCORE: 0.8978
IROC_PERCENTILE: 54
POISSON_SCORE: 0.4169
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 2091

value: BioSam 713

value: CD4+ CD25+ CD127- Treg Primary Cells

value: CD25+ CD127- Treg

value: Protein A-Sepharose 4B

value: 10 ul bed volume

value: Millipore

value: Histone H3K27me3


title: ChIP-Seq analysis of H3K4me1 in human CD25+ CD127- Treg cells; DNA_Lib 2088

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 2088
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.13158
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: GSM997245_BI.CD4+_CD25+_CD127-_Treg_Primary_Cells.H3K4me1.Donor_332.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 2088.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of CD4+ CD25+ CD127- Treg Primary Cells H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K4me1 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.17200
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: 7,748,379
FINDPEAKS_SCORE: 0.4109
FINDPEAKS_PERCENTILE: 78
HOTSPOT_SCORE: 0.4559
HOTSPOT_PERCENTILE: 76
IROC_SCORE: 0.9958
IROC_PERCENTILE: 83
POISSON_SCORE: 0.5386
POISSON_PERCENTILE: 74
MAXIMUM_REPLICATE_CORRELATION: 0.97

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

ANALYSIS FILE NAME: GSM997245_BI.CD4+_CD25+_CD127-_Treg_Primary_Cells.H3K4me1.Donor_332.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 2088.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of CD4+ CD25+ CD127- Treg Primary Cells H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K4me1 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.17383
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 H3K4me1 32 88
BROWSER_TRACK_DESCRIPTION: BI CD4+ CD25+ CD127- Treg Primary Cells Histone H3K4me1 Donor 332 Library DNA_Lib 2088 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 7,748,379
FINDPEAKS_SCORE: 0.4109
FINDPEAKS_PERCENTILE: 78
HOTSPOT_SCORE: 0.4559
HOTSPOT_PERCENTILE: 76
IROC_SCORE: 0.9958
IROC_PERCENTILE: 83
POISSON_SCORE: 0.5386
POISSON_PERCENTILE: 74
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 2088

value: normal

value: genomic DNA

value: CD4+ T cell

value: 0.5 to 3 million cells

value: Histone H3K4me1


title: ChIP-Seq analysis of H3K9me3 in human CD25+ CD127- Treg cells; DNA_Lib 2092

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 2092
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.13157
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: GSM997244_BI.CD4+_CD25+_CD127-_Treg_Primary_Cells.H3K9me3.Donor_332.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 2092.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of CD4+ CD25+ CD127- Treg Primary Cells H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K9me3 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.17246
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: 17,091,044
FINDPEAKS_SCORE: 0.0399
FINDPEAKS_PERCENTILE: 48
HOTSPOT_SCORE: 0.1303
HOTSPOT_PERCENTILE: 48
IROC_SCORE: 0.6448
IROC_PERCENTILE: 19
POISSON_SCORE: 0.2839
POISSON_PERCENTILE: 44
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

ANALYSIS FILE NAME: GSM997244_BI.CD4+_CD25+_CD127-_Treg_Primary_Cells.H3K9me3.Donor_332.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 2092.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of CD4+ CD25+ CD127- Treg Primary Cells H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K9me3 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.17429
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 H3K9me3 32 92
BROWSER_TRACK_DESCRIPTION: BI CD4+ CD25+ CD127- Treg Primary Cells Histone H3K9me3 Donor 332 Library DNA_Lib 2092 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 17,091,044
FINDPEAKS_SCORE: 0.0399
FINDPEAKS_PERCENTILE: 48
HOTSPOT_SCORE: 0.1303
HOTSPOT_PERCENTILE: 48
IROC_SCORE: 0.6448
IROC_PERCENTILE: 19
POISSON_SCORE: 0.2839
POISSON_PERCENTILE: 44
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 2092

value: Unknown

value: Primary Cell

value: Donor 332

value: Dana Farber

value: cell/nuclei lysis


title: ChIP-Seq analysis of H3K4me3 in human CD25+ CD127- Treg cells; DNA_Lib 2089

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 2089
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.13159
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: GSM997246_BI.CD4+_CD25+_CD127-_Treg_Primary_Cells.H3K4me3.Donor_332.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 2089.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of CD4+ CD25+ CD127- Treg Primary Cells H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K4me3 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.17212
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: 9,278,400
FINDPEAKS_SCORE: 0.5924
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.5937
HOTSPOT_PERCENTILE: 98
IROC_SCORE: 0.9989
IROC_PERCENTILE: 15
POISSON_SCORE: 0.6112
POISSON_PERCENTILE: 98
MAXIMUM_REPLICATE_CORRELATION: 0.96

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

ANALYSIS FILE NAME: GSM997246_BI.CD4+_CD25+_CD127-_Treg_Primary_Cells.H3K4me3.Donor_332.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 2089.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of CD4+ CD25+ CD127- Treg Primary Cells H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K4me3 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.17395
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 H3K4me3 32 89
BROWSER_TRACK_DESCRIPTION: BI CD4+ CD25+ CD127- Treg Primary Cells Histone H3K4me3 Donor 332 Library DNA_Lib 2089 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 9,278,400
FINDPEAKS_SCORE: 0.5924
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.5937
HOTSPOT_PERCENTILE: 98
IROC_SCORE: 0.9989
IROC_PERCENTILE: 15
POISSON_SCORE: 0.6112
POISSON_PERCENTILE: 98
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 2089

value: BioSam 713

value: ~1 ug

value: Histone H3K4me3

value: Branson