title: ChIP-Seq analysis of WCE in rectal smooth muscle cells; Lib:XZ:20100503:07--ChIP:XZ:20100420:07:rectal smooth muscle:WCE

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:20100503:07--ChIP:XZ:20100420:07:rectal smooth muscle:WCE
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.3241
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: GSM621657_BI.Rectal_Smooth_Muscle.Input.30.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100503:07--ChIP:XZ:20100420:07:rectal smooth muscle:WCE.hg19.level.1
ANALYSIS TITLE: Mapping of Rectal Smooth Muscle ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina reads produced by ChIP-Seq Input 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.4717
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: 0.0063
FINDPEAKS_PERCENTILE: 21
HOTSPOT_SCORE: 0.0061
HOTSPOT_PERCENTILE: 18
IROC_SCORE: 0.9714
IROC_PERCENTILE: 81
POISSON_SCORE: 0.2001
POISSON_PERCENTILE: 28

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

ANALYSIS FILE NAME: GSM621657_BI.Rectal_Smooth_Muscle.Input.30.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100503:07--ChIP:XZ:20100420:07:rectal smooth muscle:WCE.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Rectal Smooth Muscle ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina ChIP-Seq Input 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.4991
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 Input 30
BROWSER_TRACK_DESCRIPTION: BI Rectal Smooth Muscle ChIP-Seq Input Donor 30 EA Release 2

QUALITY SCORES:
NUMBER_OF_Input_EXPERIMENTS_SCORED: 67
FINDPEAKS_SCORE: 0.0063
FINDPEAKS_PERCENTILE: 21
HOTSPOT_SCORE: 0.0061
HOTSPOT_PERCENTILE: 18
IROC_SCORE: 0.9714
IROC_PERCENTILE: 81
POISSON_SCORE: 0.2001
POISSON_PERCENTILE: 28

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

source_name: Primary rectal smooth muscle tissue; Lib:XZ:20100503:07--ChIP:XZ:20100420:07:rectal smooth muscle:WCE

value: normal smooth muscle

value: smooth muscle

value: rectum

value: standard

value: ChIP-Seq Input

value: Input


title: ChIP-Seq analysis of H3K27me3 rectal smooth muscle;Lib:XZ:20100503:04--ChIP:XZ:20100420:04:rectal smooth muscle:H3K27Me3

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: 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:20100503:04--ChIP:XZ:20100420:04:rectal smooth muscle:H3K27Me3
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.3239
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

library_source: genomic

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

ANALYSIS FILE NAME: GSM621655_BI.Rectal_Smooth_Muscle.H3K27me3.30.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100503:04--ChIP:XZ:20100420:04:rectal smooth muscle:H3K27Me3.hg19.level.1
ANALYSIS TITLE: Mapping of Rectal Smooth Muscle Histone H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K27me3 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.4750
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: 0.0164
FINDPEAKS_PERCENTILE: 10
HOTSPOT_SCORE: 0.0781
HOTSPOT_PERCENTILE: 8
IROC_SCORE: 0.7033
IROC_PERCENTILE: 8
POISSON_SCORE: 0.3509
POISSON_PERCENTILE: 10

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

ANALYSIS FILE NAME: GSM621655_BI.Rectal_Smooth_Muscle.H3K27me3.30.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100503:04--ChIP:XZ:20100420:04:rectal smooth muscle:H3K27Me3.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Rectal Smooth Muscle Histone H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K27me3 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.5024
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 H3K27me3 30
BROWSER_TRACK_DESCRIPTION: BI Rectal Smooth Muscle Histone H3K27me3 Donor 30 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED: 52
FINDPEAKS_SCORE: 0.0164
FINDPEAKS_PERCENTILE: 10
HOTSPOT_SCORE: 0.0781
HOTSPOT_PERCENTILE: 8
IROC_SCORE: 0.7033
IROC_PERCENTILE: 8
POISSON_SCORE: 0.3509
POISSON_PERCENTILE: 10

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

molecule: genomic DNA

organism: Homo sapiens

source_name: Primary rectal smooth muscle tissue; Lib:XZ:20100503:04--ChIP:XZ:20100420:04:rectal smooth muscle:H3K27Me3

extract_protocol: Library construction protocol: Single read - Illumina

value: surgery

tag: molecule

value: genomic DNA

tag: disease

value: white

value: Female

value: Primary Tissue

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

value: Bioruptor


title: ChIP-Seq analysis of H3K36me3 rectal smooth muscle;Lib:XZ:20100503:03--ChIP:XZ:20100420:03:rectal smooth muscle:H3K36Me3

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:20100503:03--ChIP:XZ:20100420:03:rectal smooth muscle:H3K36Me3
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.3240
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: GSM621656_BI.Rectal_Smooth_Muscle.H3K36me3.30.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100503:03--ChIP:XZ:20100420:03:rectal smooth muscle:H3K36Me3.hg19.level.1
ANALYSIS TITLE: Mapping of Rectal Smooth Muscle Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K36me3 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.4630
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: 0.0711
FINDPEAKS_PERCENTILE: 17
HOTSPOT_SCORE: 0.1552
HOTSPOT_PERCENTILE: 15
IROC_SCORE: 0.9058
IROC_PERCENTILE: 26
POISSON_SCORE: 0.4139
POISSON_PERCENTILE: 24

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

ANALYSIS FILE NAME: GSM621656_BI.Rectal_Smooth_Muscle.H3K36me3.30.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100503:03--ChIP:XZ:20100420:03:rectal smooth muscle:H3K36Me3.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Rectal Smooth Muscle Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K36me3 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.4904
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 H3K36me3 30
BROWSER_TRACK_DESCRIPTION: BI Rectal Smooth Muscle Histone H3K36me3 Donor 30 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED: 54
FINDPEAKS_SCORE: 0.0711
FINDPEAKS_PERCENTILE: 17
HOTSPOT_SCORE: 0.1552
HOTSPOT_PERCENTILE: 15
IROC_SCORE: 0.9058
IROC_PERCENTILE: 26
POISSON_SCORE: 0.4139
POISSON_PERCENTILE: 24

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

source_name: Primary rectal smooth muscle tissue; Lib:XZ:20100503:03--ChIP:XZ:20100420:03:rectal smooth muscle:H3K36Me3

value: normal smooth muscle

value: smooth muscle

value: rectum

value: Abcam

value: Histone H3K36me3


title: ChIP-Seq analysis H3K36me3 stomach smooth muscle;Lib:XZ:20100423:21--ChIP:XZ:70100407:10:stomach smooth muscle:H3K36Me3

description:
sample_term_id: UBERON_0008856
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib:XZ:20100423:21--ChIP:XZ:70100407:10:stomach smooth muscle:H3K36Me3
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.3233
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.3346
****************
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: GSM621649_BI.Stomach_Smooth_Muscle.H3K36me3.28.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100423:21--ChIP:XZ:70100407:10:stomach smooth muscle:H3K36Me3.hg19.level.1
ANALYSIS TITLE: Mapping of Stomach Smooth Muscle Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K36me3 ChIP-Seq on Stomach Smooth Muscle, Donor 28 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.4575
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: 0.2172
FINDPEAKS_PERCENTILE: 43
HOTSPOT_SCORE: 0.2366
HOTSPOT_PERCENTILE: 40
IROC_SCORE: 0.9721
IROC_PERCENTILE: 57
POISSON_SCORE: 0.5173
POISSON_PERCENTILE: 56

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

ANALYSIS FILE NAME: GSM621649_BI.Stomach_Smooth_Muscle.H3K36me3.28.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100423:21--ChIP:XZ:70100407:10:stomach smooth muscle:H3K36Me3.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Stomach Smooth Muscle Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K36me3 ChIP-Seq read mappings from Stomach Smooth Muscle, Donor 28 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.4849
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: SSM H3K36me3 28
BROWSER_TRACK_DESCRIPTION: BI Stomach Smooth Muscle Histone H3K36me3 Donor 28 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED: 54
FINDPEAKS_SCORE: 0.2172
FINDPEAKS_PERCENTILE: 43
HOTSPOT_SCORE: 0.2366
HOTSPOT_PERCENTILE: 40
IROC_SCORE: 0.9721
IROC_PERCENTILE: 57
POISSON_SCORE: 0.5173
POISSON_PERCENTILE: 56

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

source_name: Primary gastric smooth muscle tissue; Lib:XZ:20100423:21--ChIP:XZ:70100407:10:stomach smooth muscle:H3K36Me3

value: surgery

value: genomic DNA

value: stomach


title: ChIP-Seq analysis of H3K9me3 in human adult kidney cells; Lib:XZ:20100423:17--ChIP:XZ:70100407:06:adult kidney:H3K9Me3

description:
sample_term_id: UBERON_0002113
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib:XZ:20100423:17--ChIP:XZ:70100407:06:adult kidney:H3K9Me3
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.3235
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.3349
****************
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: GSM621651_BI.Adult_Kidney.H3K9me3.27.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100423:17--ChIP:XZ:70100407:06:adult kidney:H3K9Me3.hg19.level.1
ANALYSIS TITLE: Mapping of Adult Kidney Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K9me3 ChIP-Seq on Adult Kidney, Donor 27 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.4607
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: 0.0209
FINDPEAKS_PERCENTILE: 14
HOTSPOT_SCORE: 0.0388
HOTSPOT_PERCENTILE: 3
IROC_SCORE: 0.8653
IROC_PERCENTILE: 64
POISSON_SCORE: 0.3071
POISSON_PERCENTILE: 22

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

ANALYSIS FILE NAME: GSM621651_BI.Adult_Kidney.H3K9me3.27.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100423:17--ChIP:XZ:70100407:06:adult kidney:H3K9Me3.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Adult Kidney Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K9me3 ChIP-Seq read mappings from Adult Kidney, Donor 27 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.4881
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: AK H3K9me3 27
BROWSER_TRACK_DESCRIPTION: BI Adult Kidney Histone H3K9me3 Donor 27 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED: 59
FINDPEAKS_SCORE: 0.0209
FINDPEAKS_PERCENTILE: 14
HOTSPOT_SCORE: 0.0388
HOTSPOT_PERCENTILE: 3
IROC_SCORE: 0.8653
IROC_PERCENTILE: 64
POISSON_SCORE: 0.3071
POISSON_PERCENTILE: 22

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

source_name: Primary kidney tissue; Lib:XZ:20100423:17--ChIP:XZ:70100407:06:adult kidney:H3K9Me3

value: "normal, renal cell CA (clear cell type)"

value: Adult Kidney

value: white

value: Male

value: Primary Tissue

value: kidney

value: Histone H3K9me3


title: ChIP-Seq analysis of H3K4me1 in human rectal mucosa cells; Lib:XZ:20100503:08--ChIP:XZ:20100420:08:rectal mucosa:H3K4Me1

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:20100503:08--ChIP:XZ:20100420:08:rectal mucosa:H3K4Me1
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.3243
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:20100503:08--ChIP:XZ:20100420:08:rectal mucosa:H3K4Me1
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.3243
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: GSM621659_BI.Rectal_Mucosa.H3K4me1.31.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100503:08--ChIP:XZ:20100420:08:rectal mucosa:H3K4Me1.hg19.level.1
ANALYSIS TITLE: Mapping of Rectal Mucosa Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me1 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.4771
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: 0.2398
FINDPEAKS_PERCENTILE: 28
HOTSPOT_SCORE: 0.2865
HOTSPOT_PERCENTILE: 23
IROC_SCORE: 0.96
IROC_PERCENTILE: 29
POISSON_SCORE: 0.4953
POISSON_PERCENTILE: 30

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

ANALYSIS FILE NAME: GSM621659_BI.Rectal_Mucosa.H3K4me1.31.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100503:08--ChIP:XZ:20100420:08:rectal mucosa:H3K4Me1.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Rectal Mucosa Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me1 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.5045
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 H3K4me1 31
BROWSER_TRACK_DESCRIPTION: BI Rectal Mucosa Histone H3K4me1 Donor 31 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED: 43
FINDPEAKS_SCORE: 0.2398
FINDPEAKS_PERCENTILE: 28
HOTSPOT_SCORE: 0.2865
HOTSPOT_PERCENTILE: 23
IROC_SCORE: 0.96
IROC_PERCENTILE: 29
POISSON_SCORE: 0.4953
POISSON_PERCENTILE: 30

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

source_name: Primary rectal mucosal tissue; Lib:XZ:20100503:08--ChIP:XZ:20100420:08:rectal mucosa:H3K4Me1

value: "normal mucosa, diverticular disease"

value: mucosa

value: Female

value: MGH Pathology

value: Protein A-Sepharose 4B

value: 10 million cells

value: SDS lysis

value: 70 ul bed volume

value: Histone H3K4me1


title: ChIP-Seq analysis of H3K4me3 stomach smooth muscle;Lib:XZ:20100423:20--ChIP:XZ:70100407:09:stomach smooth muscle:H3K4Me3

description:
sample_term_id: UBERON_0008856
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib:XZ:20100423:20--ChIP:XZ:70100407:09:stomach smooth muscle:H3K4Me3
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.3229
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.3346
****************
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: GSM621645_BI.Stomach_Smooth_Muscle.H3K4me3.28.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100423:20--ChIP:XZ:70100407:09:stomach smooth muscle:H3K4Me3.hg19.level.1
ANALYSIS TITLE: Mapping of Stomach Smooth Muscle Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me3 ChIP-Seq on Stomach Smooth Muscle, Donor 28 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.4615
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: 0.4652
FINDPEAKS_PERCENTILE: 63
HOTSPOT_SCORE: 0.4503
HOTSPOT_PERCENTILE: 62
IROC_SCORE: 0.9925
IROC_PERCENTILE: 13
POISSON_SCORE: 0.5499
POISSON_PERCENTILE: 63

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

ANALYSIS FILE NAME: GSM621645_BI.Stomach_Smooth_Muscle.H3K4me3.28.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100423:20--ChIP:XZ:70100407:09:stomach smooth muscle:H3K4Me3.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Stomach Smooth Muscle Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me3 ChIP-Seq read mappings from Stomach Smooth Muscle, Donor 28 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.4889
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: SSM H3K4me3 28
BROWSER_TRACK_DESCRIPTION: BI Stomach Smooth Muscle Histone H3K4me3 Donor 28 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED: 62
FINDPEAKS_SCORE: 0.4652
FINDPEAKS_PERCENTILE: 63
HOTSPOT_SCORE: 0.4503
HOTSPOT_PERCENTILE: 62
IROC_SCORE: 0.9925
IROC_PERCENTILE: 13
POISSON_SCORE: 0.5499
POISSON_PERCENTILE: 63

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

source_name: Primary gastric smooth muscle tissue; Lib:XZ:20100423:20--ChIP:XZ:70100407:09:stomach smooth muscle:H3K4Me3

value: surgery

value: normal smooth muscle

value: genomic DNA

value: smooth muscle

value: stomach

value: Millipore

value: Histone H3K4me3

value: Bioruptor


title: ChIP-Seq analysis of WCE in human adult kidney cells; Lib:XZ:20100423:18--ChIP:XZ:70100407:07:adult kidney:WCE

description:
sample_term_id: UBERON_0002113
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib:XZ:20100423:18--ChIP:XZ:70100407:07:adult kidney:WCE
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.3222
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.3349
****************
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: GSM621638_BI.Adult_Kidney.Input.27.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100423:18--ChIP:XZ:70100407:07:adult kidney:WCE.hg19.level.1
ANALYSIS TITLE: Mapping of Adult Kidney ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina reads produced by ChIP-Seq Input on Adult Kidney, Donor 27 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.4754
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: 0.0068
FINDPEAKS_PERCENTILE: 31
HOTSPOT_SCORE: 0.006
HOTSPOT_PERCENTILE: 17
IROC_SCORE: 0.0
IROC_PERCENTILE: 18
POISSON_SCORE: 0.1934
POISSON_PERCENTILE: 22

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

ANALYSIS FILE NAME: GSM621638_BI.Adult_Kidney.Input.27.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100423:18--ChIP:XZ:70100407:07:adult kidney:WCE.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Adult Kidney ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina ChIP-Seq Input read mappings from Adult Kidney, Donor 27 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.5028
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: AK Input 27
BROWSER_TRACK_DESCRIPTION: BI Adult Kidney ChIP-Seq Input Donor 27 EA Release 2

QUALITY SCORES:
NUMBER_OF_Input_EXPERIMENTS_SCORED: 67
FINDPEAKS_SCORE: 0.0068
FINDPEAKS_PERCENTILE: 31
HOTSPOT_SCORE: 0.006
HOTSPOT_PERCENTILE: 17
IROC_SCORE: 0.0
IROC_PERCENTILE: 18
POISSON_SCORE: 0.1934
POISSON_PERCENTILE: 22

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

source_name: Primary kidney tissue; Lib:XZ:20100423:18--ChIP:XZ:70100407:07:adult kidney:WCE

value: "normal, renal cell CA (clear cell type)"

value: Adult Kidney

value: white

value: Male

value: Primary Tissue

value: kidney

value: standard

value: ChIP-Seq Input

value: Input


title: ChIP-Seq analysis of H3K36me3 in Skeletal muscle cells; Lib:XZ:20100423:04--ChIP:XZ:20100331:04: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:20100423:04--ChIP:XZ:20100331:04:Skeletal muscle:H3K36Me3
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.3228
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.3347
****************
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: GSM621644_BI.Skeletal_Muscle.H3K36me3.19.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100423:04--ChIP:XZ:20100331:04: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 19 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.4611
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: 0.2779
FINDPEAKS_PERCENTILE: 63
HOTSPOT_SCORE: 0.2706
HOTSPOT_PERCENTILE: 51
IROC_SCORE: 0.861
IROC_PERCENTILE: 19
POISSON_SCORE: 0.5584
POISSON_PERCENTILE: 65

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

ANALYSIS FILE NAME: GSM621644_BI.Skeletal_Muscle.H3K36me3.19.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100423:04--ChIP:XZ:20100331:04: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 19 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.4885
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 19
BROWSER_TRACK_DESCRIPTION: BI Skeletal Muscle Histone H3K36me3 Donor 19 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED: 54
FINDPEAKS_SCORE: 0.2779
FINDPEAKS_PERCENTILE: 63
HOTSPOT_SCORE: 0.2706
HOTSPOT_PERCENTILE: 51
IROC_SCORE: 0.861
IROC_PERCENTILE: 19
POISSON_SCORE: 0.5584
POISSON_PERCENTILE: 65

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

source_name: Primary skeletal muscle tissue; Lib:XZ:20100423:04--ChIP:XZ:20100331:04:Skeletal muscle:H3K36Me3

value: surgery

value: Skeletal muscle

value: Unknown

value: unknown

value: MGH Pathology

value: Protein A-Sepharose 4B

value: 10 million cells

value: SDS lysis

value: 70 ul bed volume

value: Abcam

value: Histone H3K36me3


title: ChIP-Seq analysis of H3K27me3 in Skeletal muscle cells; Lib:XZ:20100423:01--ChIP:XZ:20100331:01: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:20100423:01--ChIP:XZ:20100331:01:Skeletal muscle:H3K27Me3
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.3237
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.3347
****************
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: GSM621653_BI.Skeletal_Muscle.H3K27me3.19.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100423:01--ChIP:XZ:20100331:01: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 19 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.4583
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: 0.0823
FINDPEAKS_PERCENTILE: 38
HOTSPOT_SCORE: 0.1542
HOTSPOT_PERCENTILE: 35
IROC_SCORE: 0.0
IROC_PERCENTILE: 4
POISSON_SCORE: 0.4738
POISSON_PERCENTILE: 56

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

ANALYSIS FILE NAME: GSM621653_BI.Skeletal_Muscle.H3K27me3.19.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100423:01--ChIP:XZ:20100331:01: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 19 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.4857
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 19
BROWSER_TRACK_DESCRIPTION: BI Skeletal Muscle Histone H3K27me3 Donor 19 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED: 52
FINDPEAKS_SCORE: 0.0823
FINDPEAKS_PERCENTILE: 38
HOTSPOT_SCORE: 0.1542
HOTSPOT_PERCENTILE: 35
IROC_SCORE: 0.0
IROC_PERCENTILE: 4
POISSON_SCORE: 0.4738
POISSON_PERCENTILE: 56

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

source_name: Primary skeletal muscle tissue; Lib:XZ:20100423:01--ChIP:XZ:20100331:01:Skeletal muscle:H3K27Me3

value: genomic DNA

value: Millipore

value: Histone H3K27me3

value: Bioruptor


title: ChIP-Seq analysis of H3K4me3 in human adult kidney cells; Lib:XZ:20100423:13--ChIP:XZ:70100407:02:adult kidney:H3K4Me3

description:
sample_term_id: UBERON_0002113
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib:XZ:20100423:13--ChIP:XZ:70100407:02:adult kidney:H3K4Me3
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.3232
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.3349
****************
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: GSM621648_BI.Adult_Kidney.H3K4me3.27.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100423:13--ChIP:XZ:70100407:02:adult kidney:H3K4Me3.hg19.level.1
ANALYSIS TITLE: Mapping of Adult Kidney Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me3 ChIP-Seq on Adult Kidney, Donor 27 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.4722
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: 0.2039
FINDPEAKS_PERCENTILE: 13
HOTSPOT_SCORE: 0.2112
HOTSPOT_PERCENTILE: 8
IROC_SCORE: 0.9995
IROC_PERCENTILE: 60
POISSON_SCORE: 0.3449
POISSON_PERCENTILE: 15

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

ANALYSIS FILE NAME: GSM621648_BI.Adult_Kidney.H3K4me3.27.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100423:13--ChIP:XZ:70100407:02:adult kidney:H3K4Me3.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Adult Kidney Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me3 ChIP-Seq read mappings from Adult Kidney, Donor 27 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.4996
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: AK H3K4me3 27
BROWSER_TRACK_DESCRIPTION: BI Adult Kidney Histone H3K4me3 Donor 27 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED: 62
FINDPEAKS_SCORE: 0.2039
FINDPEAKS_PERCENTILE: 13
HOTSPOT_SCORE: 0.2112
HOTSPOT_PERCENTILE: 8
IROC_SCORE: 0.9995
IROC_PERCENTILE: 60
POISSON_SCORE: 0.3449
POISSON_PERCENTILE: 15

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

source_name: Primary kidney tissue; Lib:XZ:20100423:13--ChIP:XZ:70100407:02:adult kidney:H3K4Me3

value: "normal, renal cell CA (clear cell type)"

value: Adult Kidney

value: white

value: Male

value: Primary Tissue

value: kidney

value: Histone H3K4me3


title: ChIP-Seq analysis H3K27me3 stomach smooth muscle; Lib:XZ:20100423:22--ChIP:XZ:70100407:11:stomach smooth muscle:H3K27Me3

description:
sample_term_id: UBERON_0008856
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib:XZ:20100423:22--ChIP:XZ:70100407:11:stomach smooth muscle:H3K27Me3
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.3219
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.3346
****************
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: GSM621635_BI.Stomach_Smooth_Muscle.H3K27me3.28.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100423:22--ChIP:XZ:70100407:11:stomach smooth muscle:H3K27Me3.hg19.level.1
ANALYSIS TITLE: Mapping of Stomach Smooth Muscle Histone H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K27me3 ChIP-Seq on Stomach Smooth Muscle, Donor 28 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.4749
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: 0.0324
FINDPEAKS_PERCENTILE: 17
HOTSPOT_SCORE: 0.1122
HOTSPOT_PERCENTILE: 19
IROC_SCORE: 0.7898
IROC_PERCENTILE: 15
POISSON_SCORE: 0.4388
POISSON_PERCENTILE: 44

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

ANALYSIS FILE NAME: GSM621635_BI.Stomach_Smooth_Muscle.H3K27me3.28.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100423:22--ChIP:XZ:70100407:11:stomach smooth muscle:H3K27Me3.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Stomach Smooth Muscle Histone H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K27me3 ChIP-Seq read mappings from Stomach Smooth Muscle, Donor 28 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.5023
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: SSM H3K27me3 28
BROWSER_TRACK_DESCRIPTION: BI Stomach Smooth Muscle Histone H3K27me3 Donor 28 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED: 52
FINDPEAKS_SCORE: 0.0324
FINDPEAKS_PERCENTILE: 17
HOTSPOT_SCORE: 0.1122
HOTSPOT_PERCENTILE: 19
IROC_SCORE: 0.7898
IROC_PERCENTILE: 15
POISSON_SCORE: 0.4388
POISSON_PERCENTILE: 44

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

source_name: Primary gastric smooth muscle tissue; Lib:XZ:20100423:22--ChIP:XZ:70100407:11:stomach smooth muscle:H3K27Me3

value: surgery

value: normal smooth muscle

value: smooth muscle

value: Female

value: stomach

value: MGH Pathology

value: Protein A-Sepharose 4B


title: ChIP-Seq analysis of WCE in human Skeletal muscle cells; Lib:XZ:20100423:11--ChIP:XZ:20100331:11: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:20100423:11--ChIP:XZ:20100331:11:Skeletal muscle:WCE
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.3225
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.3347
****************
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: GSM621641_BI.Skeletal_Muscle.Input.19.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100423:11--ChIP:XZ:20100331:11: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 19 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.4699
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: 0.0073
FINDPEAKS_PERCENTILE: 34
HOTSPOT_SCORE: 0.0047
HOTSPOT_PERCENTILE: 12
IROC_SCORE: 0.9885
IROC_PERCENTILE: 90
POISSON_SCORE: 0.2577
POISSON_PERCENTILE: 67

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

ANALYSIS FILE NAME: GSM621641_BI.Skeletal_Muscle.Input.19.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100423:11--ChIP:XZ:20100331:11: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 19 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.4973
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 19
BROWSER_TRACK_DESCRIPTION: BI Skeletal Muscle ChIP-Seq Input Donor 19 EA Release 2

QUALITY SCORES:
NUMBER_OF_Input_EXPERIMENTS_SCORED: 67
FINDPEAKS_SCORE: 0.0073
FINDPEAKS_PERCENTILE: 34
HOTSPOT_SCORE: 0.0047
HOTSPOT_PERCENTILE: 12
IROC_SCORE: 0.9885
IROC_PERCENTILE: 90
POISSON_SCORE: 0.2577
POISSON_PERCENTILE: 67

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

source_name: Primary skeletal muscle tissue; Lib:XZ:20100423:11--ChIP:XZ:20100331:11:Skeletal muscle:WCE

value: genomic DNA

value: Skeletal muscle

value: Unknown

value: unknown

value: standard

value: SDS lysis

value: ChIP-Seq Input

value: Input


title: ChIP-Seq analysis of H3K4me1 stomach smooth muscle;Lib:XZ:20100423:19--ChIP:XZ:70100407:08:stomach smooth muscle:H3K4Me1

description:
sample_term_id: UBERON_0008856
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib:XZ:20100423:19--ChIP:XZ:70100407:08:stomach smooth muscle:H3K4Me1
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.3226
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.3346
****************
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: GSM621642_BI.Stomach_Smooth_Muscle.H3K4me1.28.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100423:19--ChIP:XZ:70100407:08:stomach smooth muscle:H3K4Me1.hg19.level.1
ANALYSIS TITLE: Mapping of Stomach Smooth Muscle Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me1 ChIP-Seq on Stomach Smooth Muscle, Donor 28 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.4804
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: 0.3289
FINDPEAKS_PERCENTILE: 42
HOTSPOT_SCORE: 0.354
HOTSPOT_PERCENTILE: 40
IROC_SCORE: 0.9854
IROC_PERCENTILE: 50
POISSON_SCORE: 0.5238
POISSON_PERCENTILE: 40

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

ANALYSIS FILE NAME: GSM621642_BI.Stomach_Smooth_Muscle.H3K4me1.28.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100423:19--ChIP:XZ:70100407:08:stomach smooth muscle:H3K4Me1.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Stomach Smooth Muscle Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me1 ChIP-Seq read mappings from Stomach Smooth Muscle, Donor 28 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.5078
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: SSM H3K4me1 28
BROWSER_TRACK_DESCRIPTION: BI Stomach Smooth Muscle Histone H3K4me1 Donor 28 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED: 43
FINDPEAKS_SCORE: 0.3289
FINDPEAKS_PERCENTILE: 42
HOTSPOT_SCORE: 0.354
HOTSPOT_PERCENTILE: 40
IROC_SCORE: 0.9854
IROC_PERCENTILE: 50
POISSON_SCORE: 0.5238
POISSON_PERCENTILE: 40

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

source_name: Primary gastric smooth muscle tissue; Lib:XZ:20100423:19--ChIP:XZ:70100407:08:stomach smooth muscle:H3K4Me1

value: white

value: Primary Tissue

value: 10 million cells

value: 70 ul bed volume

value: Abcam

value: Histone H3K4me1

value: Bioruptor


title: ChIP-Seq analysis of H3K9me3 in Skeletal muscle cells; Lib:XZ:20100423:05--ChIP:XZ:20100331:05: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:20100423:05--ChIP:XZ:20100331:05:Skeletal muscle:H3K9Me3
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.3216
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.3347
****************
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: GSM621632_BI.Skeletal_Muscle.H3K9me3.19.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100423:05--ChIP:XZ:20100331:05: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 19 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.4757
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: 0.0521
FINDPEAKS_PERCENTILE: 37
HOTSPOT_SCORE: 0.1044
HOTSPOT_PERCENTILE: 36
IROC_SCORE: 0.6763
IROC_PERCENTILE: 12
POISSON_SCORE: 0.3785
POISSON_PERCENTILE: 49

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

ANALYSIS FILE NAME: GSM621632_BI.Skeletal_Muscle.H3K9me3.19.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100423:05--ChIP:XZ:20100331:05: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 19 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.5031
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 19
BROWSER_TRACK_DESCRIPTION: BI Skeletal Muscle Histone H3K9me3 Donor 19 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED: 59
FINDPEAKS_SCORE: 0.0521
FINDPEAKS_PERCENTILE: 37
HOTSPOT_SCORE: 0.1044
HOTSPOT_PERCENTILE: 36
IROC_SCORE: 0.6763
IROC_PERCENTILE: 12
POISSON_SCORE: 0.3785
POISSON_PERCENTILE: 49

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

source_name: Primary skeletal muscle tissue; Lib:XZ:20100423:05--ChIP:XZ:20100331:05:Skeletal muscle:H3K9Me3

value: surgery

value: MGH Pathology

value: Histone H3K9me3


title: ChIP-Seq analysis of H3K36me3 in human adult kidney cells; Lib:XZ:20100423:14--ChIP:XZ:70100407:03:adult kidney:H3K36Me3

description:
sample_term_id: UBERON_0002113
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib:XZ:20100423:14--ChIP:XZ:70100407:03:adult kidney:H3K36Me3
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.3218
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.3349
****************
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: GSM621634_BI.Adult_Kidney.H3K36me3.27.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100423:14--ChIP:XZ:70100407:03:adult kidney:H3K36Me3.hg19.level.1
ANALYSIS TITLE: Mapping of Adult Kidney Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K36me3 ChIP-Seq on Adult Kidney, Donor 27 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.4770
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: 0.0655
FINDPEAKS_PERCENTILE: 13
HOTSPOT_SCORE: 0.1515
HOTSPOT_PERCENTILE: 11
IROC_SCORE: 0.9069
IROC_PERCENTILE: 30
POISSON_SCORE: 0.4372
POISSON_PERCENTILE: 30

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

ANALYSIS FILE NAME: GSM621634_BI.Adult_Kidney.H3K36me3.27.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100423:14--ChIP:XZ:70100407:03:adult kidney:H3K36Me3.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Adult Kidney Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K36me3 ChIP-Seq read mappings from Adult Kidney, Donor 27 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.5044
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: AK H3K36me3 27
BROWSER_TRACK_DESCRIPTION: BI Adult Kidney Histone H3K36me3 Donor 27 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED: 54
FINDPEAKS_SCORE: 0.0655
FINDPEAKS_PERCENTILE: 13
HOTSPOT_SCORE: 0.1515
HOTSPOT_PERCENTILE: 11
IROC_SCORE: 0.9069
IROC_PERCENTILE: 30
POISSON_SCORE: 0.4372
POISSON_PERCENTILE: 30

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

source_name: Primary kidney tissue; Lib:XZ:20100423:14--ChIP:XZ:70100407:03:adult kidney:H3K36Me3

value: "normal, renal cell CA (clear cell type)"

value: genomic DNA

value: Adult Kidney

value: Male

value: kidney

value: Protein A-Sepharose 4B

value: Histone H3K36me3


title: ChIP-Seq analysis of WCE stomach smooth muscle cells; Lib:XZ:20100423:25--ChIP:XZ:70100407:14:stomach smooth muscle:WCE

description:
sample_term_id: UBERON_0008856
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib:XZ:20100423:25--ChIP:XZ:70100407:14:stomach smooth muscle:WCE
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.3236
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.3346
****************
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: GSM621652_BI.Stomach_Smooth_Muscle.Input.28.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100423:25--ChIP:XZ:70100407:14:stomach smooth muscle:WCE.hg19.level.1
ANALYSIS TITLE: Mapping of Stomach Smooth Muscle ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina reads produced by ChIP-Seq Input on Stomach Smooth Muscle, Donor 28 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.4636
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: 0.0094
FINDPEAKS_PERCENTILE: 48
HOTSPOT_SCORE: 0.0611
HOTSPOT_PERCENTILE: 50
IROC_SCORE: 0.0
IROC_PERCENTILE: NA
POISSON_SCORE: 0.4703
POISSON_PERCENTILE: 97

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

ANALYSIS FILE NAME: GSM621652_BI.Stomach_Smooth_Muscle.Input.28.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100423:25--ChIP:XZ:70100407:14:stomach smooth muscle:WCE.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Stomach Smooth Muscle ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina ChIP-Seq Input read mappings from Stomach Smooth Muscle, Donor 28 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.4910
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: SSM Input 28
BROWSER_TRACK_DESCRIPTION: BI Stomach Smooth Muscle ChIP-Seq Input Donor 28 EA Release 2

QUALITY SCORES:
NUMBER_OF_Input_EXPERIMENTS_SCORED: 67
FINDPEAKS_SCORE: 0.0094
FINDPEAKS_PERCENTILE: 48
HOTSPOT_SCORE: 0.0611
HOTSPOT_PERCENTILE: 50
IROC_SCORE: 0.0
IROC_PERCENTILE: NA
POISSON_SCORE: 0.4703
POISSON_PERCENTILE: 97

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

source_name: Primary gastric smooth muscle tissue; Lib:XZ:20100423:25--ChIP:XZ:70100407:14:stomach smooth muscle:WCE

value: normal smooth muscle

value: smooth muscle

value: white

value: Female

value: stomach

value: standard

value: SDS lysis

value: ChIP-Seq Input

value: Input


title: ChIP-Seq analysis of H3K4me3 rectal smooth muscle; Lib:XZ:20100503:02--ChIP:XZ:20100420:02:rectal smooth muscle:H3K4Me3

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:20100503:02--ChIP:XZ:20100420:02:rectal smooth muscle:H3K4Me3
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.3246
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: GSM621662_BI.Rectal_Smooth_Muscle.H3K4me3.30.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100503:02--ChIP:XZ:20100420:02:rectal smooth muscle:H3K4Me3.hg19.level.1
ANALYSIS TITLE: Mapping of Rectal Smooth Muscle Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me3 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.4815
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: 0.2962
FINDPEAKS_PERCENTILE: 32
HOTSPOT_SCORE: 0.3023
HOTSPOT_PERCENTILE: 31
IROC_SCORE: 0.9994
IROC_PERCENTILE: 56
POISSON_SCORE: 0.4328
POISSON_PERCENTILE: 42

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

ANALYSIS FILE NAME: GSM621662_BI.Rectal_Smooth_Muscle.H3K4me3.30.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100503:02--ChIP:XZ:20100420:02:rectal smooth muscle:H3K4Me3.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Rectal Smooth Muscle Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me3 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.5089
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 H3K4me3 30
BROWSER_TRACK_DESCRIPTION: BI Rectal Smooth Muscle Histone H3K4me3 Donor 30 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED: 62
FINDPEAKS_SCORE: 0.2962
FINDPEAKS_PERCENTILE: 32
HOTSPOT_SCORE: 0.3023
HOTSPOT_PERCENTILE: 31
IROC_SCORE: 0.9994
IROC_PERCENTILE: 56
POISSON_SCORE: 0.4328
POISSON_PERCENTILE: 42

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

source_name: Primary rectal smooth muscle tissue; Lib:XZ:20100503:02--ChIP:XZ:20100420:02:rectal smooth muscle:H3K4Me3

value: surgery

value: Primary Tissue

value: rectum

value: MGH Pathology

value: 10 million cells

value: 70 ul bed volume

value: Millipore

value: Histone H3K4me3

value: Bioruptor


title: ChIP-Seq analysis of H3K4me3 in Skeletal muscle cells; Lib:XZ:20100423:02--ChIP:XZ:20100331:02: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:20100423:02--ChIP:XZ:20100331:02:Skeletal muscle:H3K4Me3
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.3221
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.3347
****************
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: GSM621637_BI.Skeletal_Muscle.H3K4me3.19.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100423:02--ChIP:XZ:20100331:02: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 19 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.4689
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: 0.2774
FINDPEAKS_PERCENTILE: 27
HOTSPOT_SCORE: 0.2829
HOTSPOT_PERCENTILE: 26
IROC_SCORE: 0.9975
IROC_PERCENTILE: 31
POISSON_SCORE: 0.4227
POISSON_PERCENTILE: 37

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

ANALYSIS FILE NAME: GSM621637_BI.Skeletal_Muscle.H3K4me3.19.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100423:02--ChIP:XZ:20100331:02: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 19 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.4963
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 19
BROWSER_TRACK_DESCRIPTION: BI Skeletal Muscle Histone H3K4me3 Donor 19 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED: 62
FINDPEAKS_SCORE: 0.2774
FINDPEAKS_PERCENTILE: 27
HOTSPOT_SCORE: 0.2829
HOTSPOT_PERCENTILE: 26
IROC_SCORE: 0.9975
IROC_PERCENTILE: 31
POISSON_SCORE: 0.4227
POISSON_PERCENTILE: 37

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

source_name: Primary skeletal muscle tissue; Lib:XZ:20100423:02--ChIP:XZ:20100331:02:Skeletal muscle:H3K4Me3

value: genomic DNA

value: Skeletal muscle

value: Unknown

value: unknown

value: Protein A-Sepharose 4B


title: ChIP-Seq analysis of H3K9me3 stomach smooth muscle;Lib:XZ:20100423:24--ChIP:XZ:70100407:13:stomach smooth muscle:H3K9Me3

description:
sample_term_id: UBERON_0008856
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib:XZ:20100423:24--ChIP:XZ:70100407:13:stomach smooth muscle:H3K9Me3
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.3215
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.3346
****************
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: GSM621631_BI.Stomach_Smooth_Muscle.H3K9me3.28.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100423:24--ChIP:XZ:70100407:13:stomach smooth muscle:H3K9Me3.hg19.level.1
ANALYSIS TITLE: Mapping of Stomach Smooth Muscle Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K9me3 ChIP-Seq on Stomach Smooth Muscle, Donor 28 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.4800
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: 0.03
FINDPEAKS_PERCENTILE: 27
HOTSPOT_SCORE: 0.0863
HOTSPOT_PERCENTILE: 31
IROC_SCORE: 0.6425
IROC_PERCENTILE: 8
POISSON_SCORE: 0.4127
POISSON_PERCENTILE: 59

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

ANALYSIS FILE NAME: GSM621631_BI.Stomach_Smooth_Muscle.H3K9me3.28.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100423:24--ChIP:XZ:70100407:13:stomach smooth muscle:H3K9Me3.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Stomach Smooth Muscle Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K9me3 ChIP-Seq read mappings from Stomach Smooth Muscle, Donor 28 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.5074
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: SSM H3K9me3 28
BROWSER_TRACK_DESCRIPTION: BI Stomach Smooth Muscle Histone H3K9me3 Donor 28 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED: 59
FINDPEAKS_SCORE: 0.03
FINDPEAKS_PERCENTILE: 27
HOTSPOT_SCORE: 0.0863
HOTSPOT_PERCENTILE: 31
IROC_SCORE: 0.6425
IROC_PERCENTILE: 8
POISSON_SCORE: 0.4127
POISSON_PERCENTILE: 59

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

source_name: Primary gastric smooth muscle tissue; Lib:XZ:20100423:24--ChIP:XZ:70100407:13:stomach smooth muscle:H3K9Me3

value: normal smooth muscle

value: smooth muscle

value: white

value: Female

value: stomach

value: SDS lysis

value: Abcam

value: Histone H3K9me3


title: ChIP-Seq analysis of H3K27me3 in Duodenum mucosa cells; Lib:XZ:20100628:04--ChIP:XZ:20100621:04:Duodenum mucosa:H3K27Me3

description:
sample_term_id: UBERON_0000320
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib:XZ:20100628:04--ChIP:XZ:20100621:04:Duodenum mucosa:H3K27Me3
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.3800
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.3882
****************
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: GSM621460_BI.Duodenum_Mucosa.H3K27me3.61.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100628:04--ChIP:XZ:20100621:04:Duodenum mucosa:H3K27Me3.hg19.level.1
ANALYSIS TITLE: Mapping of Duodenum Mucosa Histone H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K27me3 ChIP-Seq on Duodenum Mucosa, Donor 61 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.4582
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: 0.0131
FINDPEAKS_PERCENTILE: 6
HOTSPOT_SCORE: 0.0622
HOTSPOT_PERCENTILE: 4
IROC_SCORE: 0.7119
IROC_PERCENTILE: 10
POISSON_SCORE: 0.3827
POISSON_PERCENTILE: 23

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

ANALYSIS FILE NAME: GSM621460_BI.Duodenum_Mucosa.H3K27me3.61.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100628:04--ChIP:XZ:20100621:04:Duodenum mucosa:H3K27Me3.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Duodenum Mucosa Histone H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K27me3 ChIP-Seq read mappings from Duodenum Mucosa, Donor 61 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.4856
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: DM H3K27me3 61
BROWSER_TRACK_DESCRIPTION: BI Duodenum Mucosa Histone H3K27me3 Donor 61 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED: 52
FINDPEAKS_SCORE: 0.0131
FINDPEAKS_PERCENTILE: 6
HOTSPOT_SCORE: 0.0622
HOTSPOT_PERCENTILE: 4
IROC_SCORE: 0.7119
IROC_PERCENTILE: 10
POISSON_SCORE: 0.3827
POISSON_PERCENTILE: 23

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

source_name: Primary duodenum mucosa tissue; Lib:XZ:20100628:04--ChIP:XZ:20100621:04:Duodenum mucosa:H3K27Me3

value: surgery

value: "NL mucosa,... Pancreatitis/IPMN"

value: mucosa

value: Male

value: Primary Tissue

value: duodenum

value: MGH Pathology

value: 76 years

value: 10 million cells

value: 70 ul bed volume

value: Histone H3K27me3


title: ChIP-Seq analysis of H3K27me3 in human Treg cells; Lib:RI:20100422:19--ChIP:MA:20100416:19:Treg:H3K27Me3

description:
sample_term_id: CL_0000815
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib:RI:20100422:19--ChIP:MA:20100416:19:Treg:H3K27Me3
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.3788
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.3893
****************
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: GSM621448_BI.Treg_Primary_Cells.H3K27me3.20.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:RI:20100422:19--ChIP:MA:20100416:19:Treg:H3K27Me3.hg19.level.1
ANALYSIS TITLE: Mapping of Treg Primary Cells Histone H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K27me3 ChIP-Seq on Treg Primary Cells, Donor 20 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.4719
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: 0.0227
FINDPEAKS_PERCENTILE: 12
HOTSPOT_SCORE: 0.1272
HOTSPOT_PERCENTILE: 25
IROC_SCORE: 0.8282
IROC_PERCENTILE: 19
POISSON_SCORE: 0.5451
POISSON_PERCENTILE: 85

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

ANALYSIS FILE NAME: GSM621448_BI.Treg_Primary_Cells.H3K27me3.20.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:RI:20100422:19--ChIP:MA:20100416:19:Treg:H3K27Me3.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Treg Primary Cells Histone H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K27me3 ChIP-Seq read mappings from Treg Primary Cells, Donor 20 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.4993
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: Treg H3K27me3 20
BROWSER_TRACK_DESCRIPTION: BI Treg Primary Cells Histone H3K27me3 Donor 20 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED: 52
FINDPEAKS_SCORE: 0.0227
FINDPEAKS_PERCENTILE: 12
HOTSPOT_SCORE: 0.1272
HOTSPOT_PERCENTILE: 25
IROC_SCORE: 0.8282
IROC_PERCENTILE: 19
POISSON_SCORE: 0.5451
POISSON_PERCENTILE: 85

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

source_name: "Treg cells derived from fom pooled leukopacks by Ficoll sedimentation, magnetic bead purification, and FACS"; Lib:RI:20100422:19--ChIP:MA:20100416:19:Treg:H3K27Me3

value: genomic DNA

tag: markers

value: CD4+ CD25high IL7R-

value: Treg

value: Unknown

value: Primary Cell

value: Whitehead Institute

value: Protein A-Sepharose 4B

value: Millipore

value: Bioruptor


title: ChIP-Seq analysis of H3K36me3 in human Treg cells; Lib:RI:20100422:20--ChIP:MA:20100416:20:Treg:H3K36Me3

description:
sample_term_id: CL_0000815
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib:RI:20100422:20--ChIP:MA:20100416:20:Treg:H3K36Me3
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.3789
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.3893
****************
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: GSM621449_BI.Treg_Primary_Cells.H3K36me3.20.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:RI:20100422:20--ChIP:MA:20100416:20:Treg:H3K36Me3.hg19.level.1
ANALYSIS TITLE: Mapping of Treg Primary Cells Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K36me3 ChIP-Seq on Treg Primary Cells, Donor 20 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.4803
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: 0.5507
FINDPEAKS_PERCENTILE: 89
HOTSPOT_SCORE: 0.4144
HOTSPOT_PERCENTILE: 89
IROC_SCORE: 0.9988
IROC_PERCENTILE: 100
POISSON_SCORE: 0.7036
POISSON_PERCENTILE: 89

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

ANALYSIS FILE NAME: GSM621449_BI.Treg_Primary_Cells.H3K36me3.20.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:RI:20100422:20--ChIP:MA:20100416:20:Treg:H3K36Me3.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Treg Primary Cells Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K36me3 ChIP-Seq read mappings from Treg Primary Cells, Donor 20 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.5077
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: Treg H3K36me3 20
BROWSER_TRACK_DESCRIPTION: BI Treg Primary Cells Histone H3K36me3 Donor 20 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED: 54
FINDPEAKS_SCORE: 0.5507
FINDPEAKS_PERCENTILE: 89
HOTSPOT_SCORE: 0.4144
HOTSPOT_PERCENTILE: 89
IROC_SCORE: 0.9988
IROC_PERCENTILE: 100
POISSON_SCORE: 0.7036
POISSON_PERCENTILE: 89

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

source_name: "Treg cells derived from fom pooled leukopacks by Ficoll sedimentation, magnetic bead purification, and FACS"; Lib:RI:20100422:20--ChIP:MA:20100416:20:Treg:H3K36Me3

value: SDS lysis

value: Abcam

value: Histone H3K36me3