title: ChIP-Seq analysis of WCE in human hSKM cells; Lib:MC:20100222:15--ChIP:MC:20100216:15:hSKM:WCE

description:
sample_term_id: CL_0000594
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib:MC:20100222:15--ChIP:MC:20100216:15:hSKM:WCE
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.3167
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.3209
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************
BED and WIG files were replaced on April 29, 2014

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

ANALYSIS FILE NAME: GSM621743_BI.Muscle_Satellite_Cultured_Cells.Input.hSKM-1.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:MC:20100222:15--ChIP:MC:20100216:15:hSKM:WCE.hg19.level.1
ANALYSIS TITLE: Mapping of Muscle Satellite Cultured Cells ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina reads produced by ChIP-Seq Input on Muscle Satellite Cultured Cells, Donor hSKM-1 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.4686
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 2

QUALITY SCORES:
NUMBER_OF_Input_EXPERIMENTS_SCORED: 67
FINDPEAKS_SCORE: 0.0058
FINDPEAKS_PERCENTILE: 15
HOTSPOT_SCORE: 0.0256
HOTSPOT_PERCENTILE: 38
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.2353
POISSON_PERCENTILE: 48

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

ANALYSIS FILE NAME: GSM621743_BI.Muscle_Satellite_Cultured_Cells.Input.hSKM-1.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:MC:20100222:15--ChIP:MC:20100216:15:hSKM:WCE.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Muscle Satellite Cultured Cells ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina ChIP-Seq Input read mappings from Muscle Satellite Cultured Cells, Donor hSKM-1 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.4960
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: MS Input 1
BROWSER_TRACK_DESCRIPTION: BI Muscle Satellite Cultured Cells ChIP-Seq Input Donor hSKM-1 EA Release 2

QUALITY SCORES:
NUMBER_OF_Input_EXPERIMENTS_SCORED: 67
FINDPEAKS_SCORE: 0.0058
FINDPEAKS_PERCENTILE: 15
HOTSPOT_SCORE: 0.0256
HOTSPOT_PERCENTILE: 38
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.2353
POISSON_PERCENTILE: 48

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

source_name: "Expanded from muscle spindle cells (Muoio et al; Diabetes 51, 901 (2002))"; Lib:MC:20100222:15--ChIP:MC:20100216:15:hSKM:WCE

value: mesoderm

value: DMEM

value: hSKM

value: in vivo

value: Cell Line

value: differentiated

value: Unknown

value: Duke University

value: standard

value: ChIP-Seq Input

value: Input


title: ChIP-Seq analysis of H3K9ac in Skeletal muscle cells; Lib:XZ:20100628:12--ChIP:XZ:20100621:12:Skeletal muscle:H3K9Ac

status: Public on Nov 12 2010

type: SRA

city: Cambridge

first: BROAD

last: INSTITUTE

state: MA

country: USA

institute: Broad Institute

description:
sample_term_id: UBERON_0001134
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib:XZ:20100628:12--ChIP:XZ:20100621:12:Skeletal muscle:H3K9Ac
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.3266
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.3356
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************
BED and WIG files were replaced on April 29, 2014

library_source: genomic

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

ANALYSIS FILE NAME: GSM621682_BI.Skeletal_Muscle.H3K9ac.62.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100628:12--ChIP:XZ:20100621:12:Skeletal muscle:H3K9Ac.hg19.level.1
ANALYSIS TITLE: Mapping of Skeletal Muscle Histone H3K9ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K9ac ChIP-Seq on Skeletal Muscle, Donor 62 were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.4773
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 2

QUALITY SCORES:
NUMBER_OF_H3K9ac_EXPERIMENTS_SCORED: 35
FINDPEAKS_SCORE: 0.4064
FINDPEAKS_PERCENTILE: 77
HOTSPOT_SCORE: 0.4828
HOTSPOT_PERCENTILE: 80
IROC_SCORE: 0.9722
IROC_PERCENTILE: 40
POISSON_SCORE: 0.7945
POISSON_PERCENTILE: 94

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

ANALYSIS FILE NAME: GSM621682_BI.Skeletal_Muscle.H3K9ac.62.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100628:12--ChIP:XZ:20100621:12:Skeletal muscle:H3K9Ac.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Skeletal Muscle Histone H3K9ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K9ac ChIP-Seq read mappings from Skeletal Muscle, Donor 62 were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.5047
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: SM H3K9ac 62
BROWSER_TRACK_DESCRIPTION: BI Skeletal Muscle Histone H3K9ac Donor 62 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K9ac_EXPERIMENTS_SCORED: 35
FINDPEAKS_SCORE: 0.4064
FINDPEAKS_PERCENTILE: 77
HOTSPOT_SCORE: 0.4828
HOTSPOT_PERCENTILE: 80
IROC_SCORE: 0.9722
IROC_PERCENTILE: 40
POISSON_SCORE: 0.7945
POISSON_PERCENTILE: 94

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

molecule: genomic DNA

organism: Homo sapiens

source_name: Primary skeletal muscle tissue; Lib:XZ:20100628:12--ChIP:XZ:20100621:12:Skeletal muscle:H3K9Ac

extract_protocol: Library construction protocol: not specified

value: surgery

value: "NL muscle,... PVD - BKA"

tag: molecule

value: genomic DNA

tag: disease

value: Skeletal muscle

value: white

value: Female

value: Primary Tissue

value: unknown

value: MGH Pathology

value: 72 years

value: Protein A-Sepharose 4B

value: 10 million cells

value: SDS lysis

value: 70 ul bed volume

value: Abcam

value: Histone H3K9ac

value: Bioruptor


title: ChIP-Seq analysis of H3K36me3 in Skeletal muscle cells; Lib:XZ:20100628:10--ChIP:XZ:20100621:10:Skeletal muscle:H3K36Me3

description:
sample_term_id: UBERON_0001134
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib:XZ:20100628:10--ChIP:XZ:20100621:10:Skeletal muscle:H3K36Me3
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.3268
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.3356
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************
BED and WIG files were replaced on April 29, 2014

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

ANALYSIS FILE NAME: GSM621684_BI.Skeletal_Muscle.H3K36me3.62.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100628:10--ChIP:XZ:20100621:10:Skeletal muscle:H3K36Me3.hg19.level.1
ANALYSIS TITLE: Mapping of Skeletal Muscle Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K36me3 ChIP-Seq on Skeletal Muscle, Donor 62 were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.4705
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 2

QUALITY SCORES:
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED: 54
FINDPEAKS_SCORE: 0.1677
FINDPEAKS_PERCENTILE: 31
HOTSPOT_SCORE: 0.2021
HOTSPOT_PERCENTILE: 30
IROC_SCORE: 0.9842
IROC_PERCENTILE: 78
POISSON_SCORE: 0.4826
POISSON_PERCENTILE: 46

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

ANALYSIS FILE NAME: GSM621684_BI.Skeletal_Muscle.H3K36me3.62.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100628:10--ChIP:XZ:20100621:10:Skeletal muscle:H3K36Me3.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Skeletal Muscle Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K36me3 ChIP-Seq read mappings from Skeletal Muscle, Donor 62 were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.4979
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: SM H3K36me3 62
BROWSER_TRACK_DESCRIPTION: BI Skeletal Muscle Histone H3K36me3 Donor 62 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED: 54
FINDPEAKS_SCORE: 0.1677
FINDPEAKS_PERCENTILE: 31
HOTSPOT_SCORE: 0.2021
HOTSPOT_PERCENTILE: 30
IROC_SCORE: 0.9842
IROC_PERCENTILE: 78
POISSON_SCORE: 0.4826
POISSON_PERCENTILE: 46

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

source_name: Primary skeletal muscle tissue; Lib:XZ:20100628:10--ChIP:XZ:20100621:10:Skeletal muscle:H3K36Me3

value: surgery

value: Histone H3K36me3


title: ChIP-Seq analysis of H3K9me3 in Skeletal muscle cells; Lib:XZ:20100628:20--ChIP:XZ:20100621:20:Skeletal muscle:H3K9Me3

description:
sample_term_id: UBERON_0001134
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib:XZ:20100628:20--ChIP:XZ:20100621:20:Skeletal muscle:H3K9Me3
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.3274
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.3355
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************
BED and WIG files were replaced on April 29, 2014

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

ANALYSIS FILE NAME: GSM621690_BI.Skeletal_Muscle.H3K9me3.63.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100628:20--ChIP:XZ:20100621:20:Skeletal muscle:H3K9Me3.hg19.level.1
ANALYSIS TITLE: Mapping of Skeletal Muscle Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K9me3 ChIP-Seq on Skeletal Muscle, Donor 63 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.4570
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 2

QUALITY SCORES:
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED: 59
FINDPEAKS_SCORE: 0.0179
FINDPEAKS_PERCENTILE: 7
HOTSPOT_SCORE: 0.0518
HOTSPOT_PERCENTILE: 12
IROC_SCORE: 0.7013
IROC_PERCENTILE: 14
POISSON_SCORE: 0.318
POISSON_PERCENTILE: 25

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

ANALYSIS FILE NAME: GSM621690_BI.Skeletal_Muscle.H3K9me3.63.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100628:20--ChIP:XZ:20100621:20:Skeletal muscle:H3K9Me3.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Skeletal Muscle Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K9me3 ChIP-Seq read mappings from Skeletal Muscle, Donor 63 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.4844
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: SM H3K9me3 63
BROWSER_TRACK_DESCRIPTION: BI Skeletal Muscle Histone H3K9me3 Donor 63 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED: 59
FINDPEAKS_SCORE: 0.0179
FINDPEAKS_PERCENTILE: 7
HOTSPOT_SCORE: 0.0518
HOTSPOT_PERCENTILE: 12
IROC_SCORE: 0.7013
IROC_PERCENTILE: 14
POISSON_SCORE: 0.318
POISSON_PERCENTILE: 25

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

source_name: Primary skeletal muscle tissue; Lib:XZ:20100628:20--ChIP:XZ:20100621:20:Skeletal muscle:H3K9Me3

extract_protocol: Library construction protocol: Single read - Illumina

value: "NL muscle,... Osteomylitis - BKA"

value: genomic DNA

value: Male

value: 54 years

value: Histone H3K9me3


title: ChIP-Seq analysis of H3K27me3 in Skeletal muscle cells; Lib:XZ:20100628:11--ChIP:XZ:20100621:11:Skeletal muscle:H3K27Me3

description:
sample_term_id: UBERON_0001134
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib:XZ:20100628:11--ChIP:XZ:20100621:11:Skeletal muscle:H3K27Me3
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.3267
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.3356
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************
BED and WIG files were replaced on April 29, 2014

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

ANALYSIS FILE NAME: GSM621683_BI.Skeletal_Muscle.H3K27me3.62.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100628:11--ChIP:XZ:20100621:11:Skeletal muscle:H3K27Me3.hg19.level.1
ANALYSIS TITLE: Mapping of Skeletal Muscle Histone H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K27me3 ChIP-Seq on Skeletal Muscle, Donor 62 were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.4661
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 2

QUALITY SCORES:
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED: 52
FINDPEAKS_SCORE: 0.0346
FINDPEAKS_PERCENTILE: 21
HOTSPOT_SCORE: 0.0918
HOTSPOT_PERCENTILE: 12
IROC_SCORE: 0.885
IROC_PERCENTILE: 35
POISSON_SCORE: 0.3881
POISSON_PERCENTILE: 29

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

ANALYSIS FILE NAME: GSM621683_BI.Skeletal_Muscle.H3K27me3.62.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100628:11--ChIP:XZ:20100621:11:Skeletal muscle:H3K27Me3.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Skeletal Muscle Histone H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K27me3 ChIP-Seq read mappings from Skeletal Muscle, Donor 62 were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.4935
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: SM H3K27me3 62
BROWSER_TRACK_DESCRIPTION: BI Skeletal Muscle Histone H3K27me3 Donor 62 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED: 52
FINDPEAKS_SCORE: 0.0346
FINDPEAKS_PERCENTILE: 21
HOTSPOT_SCORE: 0.0918
HOTSPOT_PERCENTILE: 12
IROC_SCORE: 0.885
IROC_PERCENTILE: 35
POISSON_SCORE: 0.3881
POISSON_PERCENTILE: 29

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

source_name: Primary skeletal muscle tissue; Lib:XZ:20100628:11--ChIP:XZ:20100621:11:Skeletal muscle:H3K27Me3

value: "NL muscle,... PVD - BKA"

value: Skeletal muscle

value: white

value: Female

value: Primary Tissue

value: unknown

value: Millipore

value: Histone H3K27me3


title: ChIP-Seq analysis of H3K9me3 in Skeletal muscle cells; Lib:XZ:20100628:13--ChIP:XZ:20100621:13:Skeletal muscle:H3K9Me3

description:
sample_term_id: UBERON_0001134
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib:XZ:20100628:13--ChIP:XZ:20100621:13:Skeletal muscle:H3K9Me3
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.3265
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.3356
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************
BED and WIG files were replaced on April 29, 2014

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

ANALYSIS FILE NAME: GSM621681_BI.Skeletal_Muscle.H3K9me3.62.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100628:13--ChIP:XZ:20100621:13:Skeletal muscle:H3K9Me3.hg19.level.1
ANALYSIS TITLE: Mapping of Skeletal Muscle Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K9me3 ChIP-Seq on Skeletal Muscle, Donor 62 were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.4562
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 2

QUALITY SCORES:
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED: 59
FINDPEAKS_SCORE: 0.0163
FINDPEAKS_PERCENTILE: 2
HOTSPOT_SCORE: 0.0487
HOTSPOT_PERCENTILE: 8
IROC_SCORE: 0.6288
IROC_PERCENTILE: 7
POISSON_SCORE: 0.3234
POISSON_PERCENTILE: 29

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

ANALYSIS FILE NAME: GSM621681_BI.Skeletal_Muscle.H3K9me3.62.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100628:13--ChIP:XZ:20100621:13:Skeletal muscle:H3K9Me3.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Skeletal Muscle Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K9me3 ChIP-Seq read mappings from Skeletal Muscle, Donor 62 were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.4836
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: SM H3K9me3 62
BROWSER_TRACK_DESCRIPTION: BI Skeletal Muscle Histone H3K9me3 Donor 62 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED: 59
FINDPEAKS_SCORE: 0.0163
FINDPEAKS_PERCENTILE: 2
HOTSPOT_SCORE: 0.0487
HOTSPOT_PERCENTILE: 8
IROC_SCORE: 0.6288
IROC_PERCENTILE: 7
POISSON_SCORE: 0.3234
POISSON_PERCENTILE: 29

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

source_name: Primary skeletal muscle tissue; Lib:XZ:20100628:13--ChIP:XZ:20100621:13:Skeletal muscle:H3K9Me3

value: MGH Pathology

value: 72 years

value: Protein A-Sepharose 4B

value: 10 million cells

value: SDS lysis

value: 70 ul bed volume

value: Abcam


title: ChIP-Seq analysis of WCE in human rectal mucosa cells; Lib:XZ:20100503:14--ChIP:XZ:20100420:14:rectal mucosa:WCE

description:
sample_term_id: UBERON_0003346
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib:XZ:20100503:14--ChIP:XZ:20100420:14:rectal mucosa:WCE
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.3261
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.3351
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib:XZ:20100503:14--ChIP:XZ:20100420:14:rectal mucosa:WCE
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.3261
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.3351
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************
BED and WIG files were replaced on April 29, 2014
BED and WIG files were replaced on April 29, 2014

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

ANALYSIS FILE NAME: GSM621677_BI.Rectal_Mucosa.Input.31.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100503:14--ChIP:XZ:20100420:14:rectal mucosa:WCE.hg19.level.1
ANALYSIS TITLE: Mapping of Rectal Mucosa ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina reads produced by ChIP-Seq Input on Rectal Mucosa, Donor 31 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.4649
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 2

QUALITY SCORES:
NUMBER_OF_Input_EXPERIMENTS_SCORED: 67
FINDPEAKS_SCORE: 0.0052
FINDPEAKS_PERCENTILE: 7
HOTSPOT_SCORE: 0.0034
HOTSPOT_PERCENTILE: 6
IROC_SCORE: 0.8115
IROC_PERCENTILE: 50
POISSON_SCORE: 0.2378
POISSON_PERCENTILE: 52

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

ANALYSIS FILE NAME: GSM621677_BI.Rectal_Mucosa.Input.31.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100503:14--ChIP:XZ:20100420:14:rectal mucosa:WCE.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Rectal Mucosa ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina ChIP-Seq Input read mappings from Rectal Mucosa, Donor 31 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.4923
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: RM Input 31
BROWSER_TRACK_DESCRIPTION: BI Rectal Mucosa ChIP-Seq Input Donor 31 EA Release 2

QUALITY SCORES:
NUMBER_OF_Input_EXPERIMENTS_SCORED: 67
FINDPEAKS_SCORE: 0.0052
FINDPEAKS_PERCENTILE: 7
HOTSPOT_SCORE: 0.0034
HOTSPOT_PERCENTILE: 6
IROC_SCORE: 0.8115
IROC_PERCENTILE: 50
POISSON_SCORE: 0.2378
POISSON_PERCENTILE: 52

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

source_name: Primary rectal mucosal tissue; Lib:XZ:20100503:14--ChIP:XZ:20100420:14:rectal mucosa:WCE

value: surgery

value: "normal mucosa, diverticular disease"

value: genomic DNA

value: mucosa

value: rectum

value: standard

value: ChIP-Seq Input

value: Input

value: Bioruptor


title: ChIP-Seq analysis of H3K4me1 in Skeletal muscle cells; Lib:XZ:20100628:15--ChIP:XZ:20100621:15:Skeletal muscle:H3K4Me1

description:
sample_term_id: UBERON_0001134
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib:XZ:20100628:15--ChIP:XZ:20100621:15:Skeletal muscle:H3K4Me1
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.3263
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.3355
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************
BED and WIG files were replaced on April 29, 2014

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

ANALYSIS FILE NAME: GSM621679_BI.Skeletal_Muscle.H3K4me1.63.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100628:15--ChIP:XZ:20100621:15:Skeletal muscle:H3K4Me1.hg19.level.1
ANALYSIS TITLE: Mapping of Skeletal Muscle Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me1 ChIP-Seq on Skeletal Muscle, Donor 63 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.4680
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 2

QUALITY SCORES:
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED: 43
FINDPEAKS_SCORE: 0.3759
FINDPEAKS_PERCENTILE: 56
HOTSPOT_SCORE: 0.3679
HOTSPOT_PERCENTILE: 47
IROC_SCORE: 0.9904
IROC_PERCENTILE: 64
POISSON_SCORE: 0.6153
POISSON_PERCENTILE: 72

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

ANALYSIS FILE NAME: GSM621679_BI.Skeletal_Muscle.H3K4me1.63.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100628:15--ChIP:XZ:20100621:15:Skeletal muscle:H3K4Me1.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Skeletal Muscle Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me1 ChIP-Seq read mappings from Skeletal Muscle, Donor 63 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.4954
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: SM H3K4me1 63
BROWSER_TRACK_DESCRIPTION: BI Skeletal Muscle Histone H3K4me1 Donor 63 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED: 43
FINDPEAKS_SCORE: 0.3759
FINDPEAKS_PERCENTILE: 56
HOTSPOT_SCORE: 0.3679
HOTSPOT_PERCENTILE: 47
IROC_SCORE: 0.9904
IROC_PERCENTILE: 64
POISSON_SCORE: 0.6153
POISSON_PERCENTILE: 72

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

source_name: Primary skeletal muscle tissue; Lib:XZ:20100628:15--ChIP:XZ:20100621:15:Skeletal muscle:H3K4Me1

value: "NL muscle,... Osteomylitis - BKA"

value: Skeletal muscle

value: white

value: Male

value: Primary Tissue

value: unknown

value: 54 years

value: Histone H3K4me1


title: ChIP-Seq analysis of H3K27me3 in rectal mucosa cells; Lib:XZ:20100503:11--ChIP:XZ:20100420:11:rectal mucosa:H3K27Me3

description:
sample_term_id: UBERON_0003346
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib:XZ:20100503:11--ChIP:XZ:20100420:11:rectal mucosa:H3K27Me3
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.3260
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.3351
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib:XZ:20100503:11--ChIP:XZ:20100420:11:rectal mucosa:H3K27Me3
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.3260
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.3351
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************
BED and WIG files were replaced on April 29, 2014
BED and WIG files were replaced on April 29, 2014

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

ANALYSIS FILE NAME: GSM621676_BI.Rectal_Mucosa.H3K27me3.31.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100503:11--ChIP:XZ:20100420:11:rectal mucosa:H3K27Me3.hg19.level.1
ANALYSIS TITLE: Mapping of Rectal Mucosa Histone H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K27me3 ChIP-Seq on Rectal Mucosa, Donor 31 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.4798
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 2

QUALITY SCORES:
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED: 52
FINDPEAKS_SCORE: 0.0115
FINDPEAKS_PERCENTILE: 4
HOTSPOT_SCORE: 0.0572
HOTSPOT_PERCENTILE: 2
IROC_SCORE: 0.9214
IROC_PERCENTILE: 54
POISSON_SCORE: 0.3775
POISSON_PERCENTILE: 19

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

ANALYSIS FILE NAME: GSM621676_BI.Rectal_Mucosa.H3K27me3.31.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100503:11--ChIP:XZ:20100420:11:rectal mucosa:H3K27Me3.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Rectal Mucosa Histone H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K27me3 ChIP-Seq read mappings from Rectal Mucosa, Donor 31 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.5072
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: RM H3K27me3 31
BROWSER_TRACK_DESCRIPTION: BI Rectal Mucosa Histone H3K27me3 Donor 31 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED: 52
FINDPEAKS_SCORE: 0.0115
FINDPEAKS_PERCENTILE: 4
HOTSPOT_SCORE: 0.0572
HOTSPOT_PERCENTILE: 2
IROC_SCORE: 0.9214
IROC_PERCENTILE: 54
POISSON_SCORE: 0.3775
POISSON_PERCENTILE: 19

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

source_name: Primary rectal mucosal tissue; Lib:XZ:20100503:11--ChIP:XZ:20100420:11:rectal mucosa:H3K27Me3

value: surgery

value: Female

value: MGH Pathology

value: Protein A-Sepharose 4B

value: 10 million cells

value: SDS lysis

value: 70 ul bed volume

value: Millipore

value: Histone H3K27me3


title: ChIP-Seq analysis of WCE in human Skeletal muscle cells; Lib:XZ:20100628:14--ChIP:XZ:20100621:14:Skeletal muscle:WCE

description:
sample_term_id: UBERON_0001134
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib:XZ:20100628:14--ChIP:XZ:20100621:14:Skeletal muscle:WCE
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.3264
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.3356
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************
BED and WIG files were replaced on April 29, 2014

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

ANALYSIS FILE NAME: GSM621680_BI.Skeletal_Muscle.Input.62.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100628:14--ChIP:XZ:20100621:14:Skeletal muscle:WCE.hg19.level.1
ANALYSIS TITLE: Mapping of Skeletal Muscle ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina reads produced by ChIP-Seq Input on Skeletal Muscle, Donor 62 were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.4801
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 2

QUALITY SCORES:
NUMBER_OF_Input_EXPERIMENTS_SCORED: 67
FINDPEAKS_SCORE: 0.0053
FINDPEAKS_PERCENTILE: 9
HOTSPOT_SCORE: 0.0033
HOTSPOT_PERCENTILE: 5
IROC_SCORE: 0.0
IROC_PERCENTILE: 18
POISSON_SCORE: 0.2472
POISSON_PERCENTILE: 66

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

ANALYSIS FILE NAME: GSM621680_BI.Skeletal_Muscle.Input.62.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100628:14--ChIP:XZ:20100621:14:Skeletal muscle:WCE.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Skeletal Muscle ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina ChIP-Seq Input read mappings from Skeletal Muscle, Donor 62 were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.5075
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: SM Input 62
BROWSER_TRACK_DESCRIPTION: BI Skeletal Muscle ChIP-Seq Input Donor 62 EA Release 2

QUALITY SCORES:
NUMBER_OF_Input_EXPERIMENTS_SCORED: 67
FINDPEAKS_SCORE: 0.0053
FINDPEAKS_PERCENTILE: 9
HOTSPOT_SCORE: 0.0033
HOTSPOT_PERCENTILE: 5
IROC_SCORE: 0.0
IROC_PERCENTILE: 18
POISSON_SCORE: 0.2472
POISSON_PERCENTILE: 66

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

source_name: Primary skeletal muscle tissue; Lib:XZ:20100628:14--ChIP:XZ:20100621:14:Skeletal muscle:WCE

value: "NL muscle,... PVD - BKA"

value: genomic DNA

value: 72 years

value: standard

value: ChIP-Seq Input

value: Input

value: Bioruptor


title: ChIP-Seq analysis of H3K9ac in colonic  mucosa cells; Lib:XZ:20100513:05--ChIP:XZ:20100503:05:colonic  mucosa:H3K9Ac

description:
sample_term_id: UBERON_0000317
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib:XZ:20100513:05--ChIP:XZ:20100503:05:colonic  mucosa:H3K9Ac
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.3258
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.3354
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************
BED and WIG files were replaced on April 29, 2014

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

ANALYSIS FILE NAME: GSM621674_BI.Colonic_Mucosa.H3K9ac.32.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100513:05--ChIP:XZ:20100503:05:colonic  mucosa:H3K9Ac.hg19.level.1
ANALYSIS TITLE: Mapping of Colonic Mucosa Histone H3K9ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K9ac ChIP-Seq on Colonic Mucosa, Donor 32 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.4674
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 2

QUALITY SCORES:
NUMBER_OF_H3K9ac_EXPERIMENTS_SCORED: 35
FINDPEAKS_SCORE: 0.2194
FINDPEAKS_PERCENTILE: 63
HOTSPOT_SCORE: 0.2838
HOTSPOT_PERCENTILE: 63
IROC_SCORE: 0.9855
IROC_PERCENTILE: 57
POISSON_SCORE: 0.3437
POISSON_PERCENTILE: 37

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

ANALYSIS FILE NAME: GSM621674_BI.Colonic_Mucosa.H3K9ac.32.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100513:05--ChIP:XZ:20100503:05:colonic  mucosa:H3K9Ac.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Colonic Mucosa Histone H3K9ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K9ac ChIP-Seq read mappings from Colonic Mucosa, Donor 32 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.4948
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: CM H3K9ac 32
BROWSER_TRACK_DESCRIPTION: BI Colonic Mucosa Histone H3K9ac Donor 32 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K9ac_EXPERIMENTS_SCORED: 35
FINDPEAKS_SCORE: 0.2194
FINDPEAKS_PERCENTILE: 63
HOTSPOT_SCORE: 0.2838
HOTSPOT_PERCENTILE: 63
IROC_SCORE: 0.9855
IROC_PERCENTILE: 57
POISSON_SCORE: 0.3437
POISSON_PERCENTILE: 37

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

source_name: Primary colonic mucosal tissue; Lib:XZ:20100513:05--ChIP:XZ:20100503:05:colonic  mucosa:H3K9Ac

value: "normal mucosa, adeno. CA of Cecum"

value: mucosa

value: white

value: Primary Tissue

value: colon

value: Abcam

value: Histone H3K9ac


title: ChIP-Seq analysis of H3K9me3 in human rectal mucosa cells; Lib:XZ:20100503:13--ChIP:XZ:20100420:13:rectal mucosa:H3K9Me3

description:
sample_term_id: UBERON_0003346
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib:XZ:20100503:13--ChIP:XZ:20100420:13:rectal mucosa:H3K9Me3
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.3262
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.3351
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib:XZ:20100503:13--ChIP:XZ:20100420:13:rectal mucosa:H3K9Me3
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.3262
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.3351
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************
BED and WIG files were replaced on April 29, 2014
BED and WIG files were replaced on April 29, 2014

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

ANALYSIS FILE NAME: GSM621678_BI.Rectal_Mucosa.H3K9me3.31.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100503:13--ChIP:XZ:20100420:13:rectal mucosa:H3K9Me3.hg19.level.1
ANALYSIS TITLE: Mapping of Rectal Mucosa Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K9me3 ChIP-Seq on Rectal Mucosa, Donor 31 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.4834
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 2

QUALITY SCORES:
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED: 59
FINDPEAKS_SCORE: 0.02
FINDPEAKS_PERCENTILE: 10
HOTSPOT_SCORE: 0.0407
HOTSPOT_PERCENTILE: 5
IROC_SCORE: 0.9982
IROC_PERCENTILE: 98
POISSON_SCORE: 0.345
POISSON_PERCENTILE: 39

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

ANALYSIS FILE NAME: GSM621678_BI.Rectal_Mucosa.H3K9me3.31.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100503:13--ChIP:XZ:20100420:13:rectal mucosa:H3K9Me3.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Rectal Mucosa Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K9me3 ChIP-Seq read mappings from Rectal Mucosa, Donor 31 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.5108
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: RM H3K9me3 31
BROWSER_TRACK_DESCRIPTION: BI Rectal Mucosa Histone H3K9me3 Donor 31 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED: 59
FINDPEAKS_SCORE: 0.02
FINDPEAKS_PERCENTILE: 10
HOTSPOT_SCORE: 0.0407
HOTSPOT_PERCENTILE: 5
IROC_SCORE: 0.9982
IROC_PERCENTILE: 98
POISSON_SCORE: 0.345
POISSON_PERCENTILE: 39

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

source_name: Primary rectal mucosal tissue; Lib:XZ:20100503:13--ChIP:XZ:20100420:13:rectal mucosa:H3K9Me3

value: surgery

value: "normal mucosa, diverticular disease"

value: Female

value: rectum

value: MGH Pathology

value: Protein A-Sepharose 4B

value: 10 million cells

value: SDS lysis

value: 70 ul bed volume

value: Histone H3K9me3


title: ChIP-Seq analysis of H3K27me3 in colonic  mucosa cells; Lib:XZ:20100513:04--ChIP:XZ:20100503:04:colonic  mucosa:H3K27Me3

description:
sample_term_id: UBERON_0000317
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib:XZ:20100513:04--ChIP:XZ:20100503:04:colonic  mucosa:H3K27Me3
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.3257
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.3354
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************
BED and WIG files were replaced on April 29, 2014

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

ANALYSIS FILE NAME: GSM621673_BI.Colonic_Mucosa.H3K27me3.32.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100513:04--ChIP:XZ:20100503:04:colonic  mucosa:H3K27Me3.hg19.level.1
ANALYSIS TITLE: Mapping of Colonic Mucosa Histone H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K27me3 ChIP-Seq on Colonic Mucosa, Donor 32 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.4613
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 2

QUALITY SCORES:
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED: 52
FINDPEAKS_SCORE: 0.0835
FINDPEAKS_PERCENTILE: 40
HOTSPOT_SCORE: 0.1847
HOTSPOT_PERCENTILE: 44
IROC_SCORE: 0.8615
IROC_PERCENTILE: 27
POISSON_SCORE: 0.349
POISSON_PERCENTILE: 8

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

ANALYSIS FILE NAME: GSM621673_BI.Colonic_Mucosa.H3K27me3.32.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100513:04--ChIP:XZ:20100503:04:colonic  mucosa:H3K27Me3.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Colonic Mucosa Histone H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K27me3 ChIP-Seq read mappings from Colonic Mucosa, Donor 32 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.4887
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: CM H3K27me3 32
BROWSER_TRACK_DESCRIPTION: BI Colonic Mucosa Histone H3K27me3 Donor 32 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED: 52
FINDPEAKS_SCORE: 0.0835
FINDPEAKS_PERCENTILE: 40
HOTSPOT_SCORE: 0.1847
HOTSPOT_PERCENTILE: 44
IROC_SCORE: 0.8615
IROC_PERCENTILE: 27
POISSON_SCORE: 0.349
POISSON_PERCENTILE: 8

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

source_name: Primary colonic mucosal tissue; Lib:XZ:20100513:04--ChIP:XZ:20100503:04:colonic  mucosa:H3K27Me3

value: "normal mucosa, adeno. CA of Cecum"

value: genomic DNA

value: Millipore

value: Histone H3K27me3

value: Bioruptor


title: ChIP-Seq analysis of H3K36me3 in colonic  mucosa cells; Lib:XZ:20100513:03--ChIP:XZ:20100503:03:colonic  mucosa:H3K36Me3

description:
sample_term_id: UBERON_0000317
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib:XZ:20100513:03--ChIP:XZ:20100503:03:colonic  mucosa:H3K36Me3
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.3256
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.3354
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************
BED and WIG files were replaced on April 29, 2014

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

ANALYSIS FILE NAME: GSM621672_BI.Colonic_Mucosa.H3K36me3.32.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100513:03--ChIP:XZ:20100503:03:colonic  mucosa:H3K36Me3.hg19.level.1
ANALYSIS TITLE: Mapping of Colonic Mucosa Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K36me3 ChIP-Seq on Colonic Mucosa, Donor 32 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.4695
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 2

QUALITY SCORES:
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED: 54
FINDPEAKS_SCORE: 0.2543
FINDPEAKS_PERCENTILE: 56
HOTSPOT_SCORE: 0.2745
HOTSPOT_PERCENTILE: 55
IROC_SCORE: 0.9718
IROC_PERCENTILE: 54
POISSON_SCORE: 0.4824
POISSON_PERCENTILE: 44

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

ANALYSIS FILE NAME: GSM621672_BI.Colonic_Mucosa.H3K36me3.32.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100513:03--ChIP:XZ:20100503:03:colonic  mucosa:H3K36Me3.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Colonic Mucosa Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K36me3 ChIP-Seq read mappings from Colonic Mucosa, Donor 32 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.4969
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: CM H3K36me3 32
BROWSER_TRACK_DESCRIPTION: BI Colonic Mucosa Histone H3K36me3 Donor 32 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED: 54
FINDPEAKS_SCORE: 0.2543
FINDPEAKS_PERCENTILE: 56
HOTSPOT_SCORE: 0.2745
HOTSPOT_PERCENTILE: 55
IROC_SCORE: 0.9718
IROC_PERCENTILE: 54
POISSON_SCORE: 0.4824
POISSON_PERCENTILE: 44

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

source_name: Primary colonic mucosal tissue; Lib:XZ:20100513:03--ChIP:XZ:20100503:03:colonic  mucosa:H3K36Me3

value: mucosa

value: white

value: Primary Tissue

value: colon

value: Abcam

value: Histone H3K36me3


title: ChIP-Seq analysis of H3K4me3 in colonic  mucosa cells; Lib:XZ:20100513:02--ChIP:XZ:20100503:02:colonic  mucosa:H3K4Me3

description:
sample_term_id: UBERON_0000317
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib:XZ:20100513:02--ChIP:XZ:20100503:02:colonic  mucosa:H3K4Me3
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.3255
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.3354
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************
BED and WIG files were replaced on April 29, 2014

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

ANALYSIS FILE NAME: GSM621671_BI.Colonic_Mucosa.H3K4me3.32.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100513:02--ChIP:XZ:20100503:02:colonic  mucosa:H3K4Me3.hg19.level.1
ANALYSIS TITLE: Mapping of Colonic Mucosa Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me3 ChIP-Seq on Colonic Mucosa, Donor 32 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.4683
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 2

QUALITY SCORES:
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED: 62
FINDPEAKS_SCORE: 0.4979
FINDPEAKS_PERCENTILE: 69
HOTSPOT_SCORE: 0.4897
HOTSPOT_PERCENTILE: 67
IROC_SCORE: 0.9922
IROC_PERCENTILE: 11
POISSON_SCORE: 0.5597
POISSON_PERCENTILE: 68

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

ANALYSIS FILE NAME: GSM621671_BI.Colonic_Mucosa.H3K4me3.32.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100513:02--ChIP:XZ:20100503:02:colonic  mucosa:H3K4Me3.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Colonic Mucosa Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me3 ChIP-Seq read mappings from Colonic Mucosa, Donor 32 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.4957
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: CM H3K4me3 32
BROWSER_TRACK_DESCRIPTION: BI Colonic Mucosa Histone H3K4me3 Donor 32 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED: 62
FINDPEAKS_SCORE: 0.4979
FINDPEAKS_PERCENTILE: 69
HOTSPOT_SCORE: 0.4897
HOTSPOT_PERCENTILE: 67
IROC_SCORE: 0.9922
IROC_PERCENTILE: 11
POISSON_SCORE: 0.5597
POISSON_PERCENTILE: 68

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

source_name: Primary colonic mucosal tissue; Lib:XZ:20100513:02--ChIP:XZ:20100503:02:colonic  mucosa:H3K4Me3

value: surgery

value: Female

value: MGH Pathology

value: Histone H3K4me3


title: ChIP-Seq analysis of H3K4me3 in Skeletal muscle cells; Lib:XZ:20100628:16--ChIP:XZ:20100621:16:Skeletal muscle:H3K4Me3

description:
sample_term_id: UBERON_0001134
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib:XZ:20100628:16--ChIP:XZ:20100621:16:Skeletal muscle:H3K4Me3
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.3278
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.3355
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************
BED and WIG files were replaced on April 29, 2014

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

ANALYSIS FILE NAME: GSM621694_BI.Skeletal_Muscle.H3K4me3.63.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100628:16--ChIP:XZ:20100621:16:Skeletal muscle:H3K4Me3.hg19.level.1
ANALYSIS TITLE: Mapping of Skeletal Muscle Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me3 ChIP-Seq on Skeletal Muscle, Donor 63 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.4795
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 2

QUALITY SCORES:
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED: 62
FINDPEAKS_SCORE: 0.2694
FINDPEAKS_PERCENTILE: 26
HOTSPOT_SCORE: 0.2763
HOTSPOT_PERCENTILE: 25
IROC_SCORE: 0.9986
IROC_PERCENTILE: 44
POISSON_SCORE: 0.395
POISSON_PERCENTILE: 31

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

ANALYSIS FILE NAME: GSM621694_BI.Skeletal_Muscle.H3K4me3.63.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100628:16--ChIP:XZ:20100621:16:Skeletal muscle:H3K4Me3.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Skeletal Muscle Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me3 ChIP-Seq read mappings from Skeletal Muscle, Donor 63 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.5069
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: SM H3K4me3 63
BROWSER_TRACK_DESCRIPTION: BI Skeletal Muscle Histone H3K4me3 Donor 63 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED: 62
FINDPEAKS_SCORE: 0.2694
FINDPEAKS_PERCENTILE: 26
HOTSPOT_SCORE: 0.2763
HOTSPOT_PERCENTILE: 25
IROC_SCORE: 0.9986
IROC_PERCENTILE: 44
POISSON_SCORE: 0.395
POISSON_PERCENTILE: 31

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

source_name: Primary skeletal muscle tissue; Lib:XZ:20100628:16--ChIP:XZ:20100621:16:Skeletal muscle:H3K4Me3

value: "NL muscle,... Osteomylitis - BKA"

value: Skeletal muscle

value: Male

value: unknown

value: 54 years

value: Protein A-Sepharose 4B

value: 10 million cells

value: SDS lysis

value: 70 ul bed volume


title: ChIP-Seq analysis of WCE in human colonic  mucosa cells; Lib:XZ:20100513:07--ChIP:XZ:20100503:07:colonic  mucosa:WCE

description:
sample_term_id: UBERON_0000317
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib:XZ:20100513:07--ChIP:XZ:20100503:07:colonic  mucosa:WCE
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.3253
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.3354
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************
BED and WIG files were replaced on April 29, 2014

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

ANALYSIS FILE NAME: GSM621669_BI.Colonic_Mucosa.Input.32.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100513:07--ChIP:XZ:20100503:07:colonic  mucosa:WCE.hg19.level.1
ANALYSIS TITLE: Mapping of Colonic Mucosa ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina reads produced by ChIP-Seq Input on Colonic Mucosa, Donor 32 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.4762
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 2

QUALITY SCORES:
NUMBER_OF_Input_EXPERIMENTS_SCORED: 67
FINDPEAKS_SCORE: 0.0059
FINDPEAKS_PERCENTILE: 19
HOTSPOT_SCORE: 0.0221
HOTSPOT_PERCENTILE: 36
IROC_SCORE: 0.9671
IROC_PERCENTILE: 79
POISSON_SCORE: 0.1808
POISSON_PERCENTILE: 15

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

ANALYSIS FILE NAME: GSM621669_BI.Colonic_Mucosa.Input.32.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100513:07--ChIP:XZ:20100503:07:colonic  mucosa:WCE.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Colonic Mucosa ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina ChIP-Seq Input read mappings from Colonic Mucosa, Donor 32 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.5036
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: CM Input 32
BROWSER_TRACK_DESCRIPTION: BI Colonic Mucosa ChIP-Seq Input Donor 32 EA Release 2

QUALITY SCORES:
NUMBER_OF_Input_EXPERIMENTS_SCORED: 67
FINDPEAKS_SCORE: 0.0059
FINDPEAKS_PERCENTILE: 19
HOTSPOT_SCORE: 0.0221
HOTSPOT_PERCENTILE: 36
IROC_SCORE: 0.9671
IROC_PERCENTILE: 79
POISSON_SCORE: 0.1808
POISSON_PERCENTILE: 15

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

source_name: Primary colonic mucosal tissue; Lib:XZ:20100513:07--ChIP:XZ:20100503:07:colonic  mucosa:WCE

value: "normal mucosa, adeno. CA of Cecum"

value: genomic DNA

value: mucosa

value: white

value: Primary Tissue

value: standard

value: ChIP-Seq Input

value: Input

value: Bioruptor


title: ChIP-Seq analysis of H3K4me1 in colonic  mucosa cells; Lib:XZ:20100513:01--ChIP:XZ:20100503:01:colonic  mucosa:H3K4Me1

description:
sample_term_id: UBERON_0000317
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib:XZ:20100513:01--ChIP:XZ:20100503:01:colonic  mucosa:H3K4Me1
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.3254
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.3354
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************
BED and WIG files were replaced on April 29, 2014

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

ANALYSIS FILE NAME: GSM621670_BI.Colonic_Mucosa.H3K4me1.32.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100513:01--ChIP:XZ:20100503:01:colonic  mucosa:H3K4Me1.hg19.level.1
ANALYSIS TITLE: Mapping of Colonic Mucosa Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me1 ChIP-Seq on Colonic Mucosa, Donor 32 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.4712
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 2

QUALITY SCORES:
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED: 43
FINDPEAKS_SCORE: 0.2514
FINDPEAKS_PERCENTILE: 33
HOTSPOT_SCORE: 0.31
HOTSPOT_PERCENTILE: 30
IROC_SCORE: 0.9708
IROC_PERCENTILE: 38
POISSON_SCORE: 0.456
POISSON_PERCENTILE: 14

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

ANALYSIS FILE NAME: GSM621670_BI.Colonic_Mucosa.H3K4me1.32.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100513:01--ChIP:XZ:20100503:01:colonic  mucosa:H3K4Me1.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Colonic Mucosa Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me1 ChIP-Seq read mappings from Colonic Mucosa, Donor 32 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.4986
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: CM H3K4me1 32
BROWSER_TRACK_DESCRIPTION: BI Colonic Mucosa Histone H3K4me1 Donor 32 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED: 43
FINDPEAKS_SCORE: 0.2514
FINDPEAKS_PERCENTILE: 33
HOTSPOT_SCORE: 0.31
HOTSPOT_PERCENTILE: 30
IROC_SCORE: 0.9708
IROC_PERCENTILE: 38
POISSON_SCORE: 0.456
POISSON_PERCENTILE: 14

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

source_name: Primary colonic mucosal tissue; Lib:XZ:20100513:01--ChIP:XZ:20100503:01:colonic  mucosa:H3K4Me1

value: surgery

value: Female

value: colon

value: MGH Pathology

value: Abcam

value: Histone H3K4me1


title: ChIP-Seq analysis of H3K9me3 rectal smooth muscle; Lib:XZ:20100503:06--ChIP:XZ:20100420:06:rectal smooth muscle:H3K9Me3

description:
sample_term_id: NTR_0001404
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib:XZ:20100503:06--ChIP:XZ:20100420:06:rectal smooth muscle:H3K9Me3
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.3244
EDACC Genboree Sample Page:

****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************
BED and WIG files were replaced on April 29, 2014

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

ANALYSIS FILE NAME: GSM621660_BI.Rectal_Smooth_Muscle.H3K9me3.30.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100503:06--ChIP:XZ:20100420:06:rectal smooth muscle:H3K9Me3.hg19.level.1
ANALYSIS TITLE: Mapping of Rectal Smooth Muscle Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K9me3 ChIP-Seq on Rectal Smooth Muscle, Donor 30 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.4622
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 2

QUALITY SCORES:
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED: 59
FINDPEAKS_SCORE: 0.0283
FINDPEAKS_PERCENTILE: 24
HOTSPOT_SCORE: 0.0815
HOTSPOT_PERCENTILE: 25
IROC_SCORE: 0.5161
IROC_PERCENTILE: 2
POISSON_SCORE: 0.2676
POISSON_PERCENTILE: 8

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

ANALYSIS FILE NAME: GSM621660_BI.Rectal_Smooth_Muscle.H3K9me3.30.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100503:06--ChIP:XZ:20100420:06:rectal smooth muscle:H3K9Me3.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Rectal Smooth Muscle Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K9me3 ChIP-Seq read mappings from Rectal Smooth Muscle, Donor 30 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.4896
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: RSM H3K9me3 30
BROWSER_TRACK_DESCRIPTION: BI Rectal Smooth Muscle Histone H3K9me3 Donor 30 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED: 59
FINDPEAKS_SCORE: 0.0283
FINDPEAKS_PERCENTILE: 24
HOTSPOT_SCORE: 0.0815
HOTSPOT_PERCENTILE: 25
IROC_SCORE: 0.5161
IROC_PERCENTILE: 2
POISSON_SCORE: 0.2676
POISSON_PERCENTILE: 8

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

source_name: Primary rectal smooth muscle tissue; Lib:XZ:20100503:06--ChIP:XZ:20100420:06:rectal smooth muscle:H3K9Me3

value: normal smooth muscle

value: smooth muscle

value: rectum

value: Protein A-Sepharose 4B

value: 10 million cells

value: SDS lysis

value: Histone H3K9me3


title: ChIP-Seq analysis of H3K9ac in rectal smooth muscle; Lib:XZ:20100503:05--ChIP:XZ:20100420:05:rectal smooth muscle:H3K9Ac

description:
sample_term_id: NTR_0001404
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib:XZ:20100503:05--ChIP:XZ:20100420:05:rectal smooth muscle:H3K9Ac
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.3245
EDACC Genboree Sample Page:

****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************
BED and WIG files were replaced on April 29, 2014

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

ANALYSIS FILE NAME: GSM621661_BI.Rectal_Smooth_Muscle.H3K9ac.30.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100503:05--ChIP:XZ:20100420:05:rectal smooth muscle:H3K9Ac.hg19.level.1
ANALYSIS TITLE: Mapping of Rectal Smooth Muscle Histone H3K9ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K9ac ChIP-Seq on Rectal Smooth Muscle, Donor 30 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.4710
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 2

QUALITY SCORES:
NUMBER_OF_H3K9ac_EXPERIMENTS_SCORED: 35
FINDPEAKS_SCORE: 0.0607
FINDPEAKS_PERCENTILE: 9
HOTSPOT_SCORE: 0.1036
HOTSPOT_PERCENTILE: 3
IROC_SCORE: 0.9804
IROC_PERCENTILE: 46
POISSON_SCORE: 0.2966
POISSON_PERCENTILE: 9

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

ANALYSIS FILE NAME: GSM621661_BI.Rectal_Smooth_Muscle.H3K9ac.30.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100503:05--ChIP:XZ:20100420:05:rectal smooth muscle:H3K9Ac.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Rectal Smooth Muscle Histone H3K9ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K9ac ChIP-Seq read mappings from Rectal Smooth Muscle, Donor 30 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.4984
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: RSM H3K9ac 30
BROWSER_TRACK_DESCRIPTION: BI Rectal Smooth Muscle Histone H3K9ac Donor 30 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K9ac_EXPERIMENTS_SCORED: 35
FINDPEAKS_SCORE: 0.0607
FINDPEAKS_PERCENTILE: 9
HOTSPOT_SCORE: 0.1036
HOTSPOT_PERCENTILE: 3
IROC_SCORE: 0.9804
IROC_PERCENTILE: 46
POISSON_SCORE: 0.2966
POISSON_PERCENTILE: 9

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

source_name: Primary rectal smooth muscle tissue; Lib:XZ:20100503:05--ChIP:XZ:20100420:05:rectal smooth muscle:H3K9Ac

value: genomic DNA

value: white

value: Primary Tissue

value: 70 ul bed volume

value: Histone H3K9ac


title: ChIP-Seq analysis of H3K9me3 in colonic  mucosa cells; Lib:XZ:20100513:06--ChIP:XZ:20100503:06:colonic  mucosa:H3K9Me3

description:
sample_term_id: UBERON_0000317
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib:XZ:20100513:06--ChIP:XZ:20100503:06:colonic  mucosa:H3K9Me3
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.3252
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.3354
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************
BED and WIG files were replaced on April 29, 2014

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

ANALYSIS FILE NAME: GSM621668_BI.Colonic_Mucosa.H3K9me3.32.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100513:06--ChIP:XZ:20100503:06:colonic  mucosa:H3K9Me3.hg19.level.1
ANALYSIS TITLE: Mapping of Colonic Mucosa Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K9me3 ChIP-Seq on Colonic Mucosa, Donor 32 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.4589
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 2

QUALITY SCORES:
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED: 59
FINDPEAKS_SCORE: 0.0675
FINDPEAKS_PERCENTILE: 41
HOTSPOT_SCORE: 0.1436
HOTSPOT_PERCENTILE: 42
IROC_SCORE: 0.7313
IROC_PERCENTILE: 24
POISSON_SCORE: 0.2785
POISSON_PERCENTILE: 12

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

ANALYSIS FILE NAME: GSM621668_BI.Colonic_Mucosa.H3K9me3.32.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100513:06--ChIP:XZ:20100503:06:colonic  mucosa:H3K9Me3.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Colonic Mucosa Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K9me3 ChIP-Seq read mappings from Colonic Mucosa, Donor 32 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.4863
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: CM H3K9me3 32
BROWSER_TRACK_DESCRIPTION: BI Colonic Mucosa Histone H3K9me3 Donor 32 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED: 59
FINDPEAKS_SCORE: 0.0675
FINDPEAKS_PERCENTILE: 41
HOTSPOT_SCORE: 0.1436
HOTSPOT_PERCENTILE: 42
IROC_SCORE: 0.7313
IROC_PERCENTILE: 24
POISSON_SCORE: 0.2785
POISSON_PERCENTILE: 12

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

source_name: Primary colonic mucosal tissue; Lib:XZ:20100513:06--ChIP:XZ:20100503:06:colonic  mucosa:H3K9Me3

value: surgery

value: "normal mucosa, adeno. CA of Cecum"

value: mucosa

value: Female

value: Bioruptor


title: ChIP-Seq analysis of H3K4me3 in human rectal mucosa cells; Lib:XZ:20100503:09--ChIP:XZ:20100420:09:rectal mucosa:H3K4Me3

description:
sample_term_id: UBERON_0003346
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib:XZ:20100503:09--ChIP:XZ:20100420:09:rectal mucosa:H3K4Me3
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.3242
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.3351
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib:XZ:20100503:09--ChIP:XZ:20100420:09:rectal mucosa:H3K4Me3
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.3242
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.3351
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************
BED and WIG files were replaced on April 29, 2014
BED and WIG files were replaced on April 29, 2014

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

ANALYSIS FILE NAME: GSM621658_BI.Rectal_Mucosa.H3K4me3.31.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100503:09--ChIP:XZ:20100420:09:rectal mucosa:H3K4Me3.hg19.level.1
ANALYSIS TITLE: Mapping of Rectal Mucosa Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me3 ChIP-Seq on Rectal Mucosa, Donor 31 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.4656
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 2

QUALITY SCORES:
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED: 62
FINDPEAKS_SCORE: 0.3203
FINDPEAKS_PERCENTILE: 37
HOTSPOT_SCORE: 0.3226
HOTSPOT_PERCENTILE: 34
IROC_SCORE: 0.9795
IROC_PERCENTILE: 2
POISSON_SCORE: 0.4212
POISSON_PERCENTILE: 35

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

ANALYSIS FILE NAME: GSM621658_BI.Rectal_Mucosa.H3K4me3.31.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100503:09--ChIP:XZ:20100420:09:rectal mucosa:H3K4Me3.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Rectal Mucosa Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me3 ChIP-Seq read mappings from Rectal Mucosa, Donor 31 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.4930
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: RM H3K4me3 31
BROWSER_TRACK_DESCRIPTION: BI Rectal Mucosa Histone H3K4me3 Donor 31 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED: 62
FINDPEAKS_SCORE: 0.3203
FINDPEAKS_PERCENTILE: 37
HOTSPOT_SCORE: 0.3226
HOTSPOT_PERCENTILE: 34
IROC_SCORE: 0.9795
IROC_PERCENTILE: 2
POISSON_SCORE: 0.4212
POISSON_PERCENTILE: 35

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

source_name: Primary rectal mucosal tissue; Lib:XZ:20100503:09--ChIP:XZ:20100420:09:rectal mucosa:H3K4Me3

value: "normal mucosa, diverticular disease"

value: MGH Pathology

value: Millipore

value: Histone H3K4me3