title: ChIP-Seq analysis of H3K4me2 in human hSKM cells; Lib:MC:20100511:10--ChIP:MC:20100505:10:hSKM:H3K4Me2

description:
sample_term_id: CL_0000594
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib:MC:20100511:10--ChIP:MC:20100505:10:hSKM:H3K4Me2
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.3174
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.3210
****************
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: GSM621750_BI.Muscle_Satellite_Cultured_Cells.H3K4me2.hSKM-2.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:MC:20100511:10--ChIP:MC:20100505:10:hSKM:H3K4Me2.hg19.level.1
ANALYSIS TITLE: Mapping of Muscle Satellite Cultured Cells Histone H3K4me2 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me2 ChIP-Seq on Muscle Satellite Cultured Cells, Donor hSKM-2 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.4787
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_H3K4me2_EXPERIMENTS_SCORED: 8
FINDPEAKS_SCORE: 0.582
FINDPEAKS_PERCENTILE: 50
HOTSPOT_SCORE: 0.5496
HOTSPOT_PERCENTILE: 38
IROC_SCORE: 0.9989
IROC_PERCENTILE: 25
POISSON_SCORE: 0.6669
POISSON_PERCENTILE: 50

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

ANALYSIS FILE NAME: GSM621750_BI.Muscle_Satellite_Cultured_Cells.H3K4me2.hSKM-2.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:MC:20100511:10--ChIP:MC:20100505:10:hSKM:H3K4Me2.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Muscle Satellite Cultured Cells Histone H3K4me2 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me2 ChIP-Seq read mappings from Muscle Satellite Cultured Cells, Donor hSKM-2 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.5061
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: MS H3K4me2 2
BROWSER_TRACK_DESCRIPTION: BI Muscle Satellite Cultured Cells Histone H3K4me2 Donor hSKM-2 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K4me2_EXPERIMENTS_SCORED: 8
FINDPEAKS_SCORE: 0.582
FINDPEAKS_PERCENTILE: 50
HOTSPOT_SCORE: 0.5496
HOTSPOT_PERCENTILE: 38
IROC_SCORE: 0.9989
IROC_PERCENTILE: 25
POISSON_SCORE: 0.6669
POISSON_PERCENTILE: 50

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

source_name: "Expanded from muscle spindle cells (Muoio et al; Diabetes 51, 901 (2002))"; Lib:MC:20100511:10--ChIP:MC:20100505:10:hSKM:H3K4Me2

value: genomic DNA

value: unknown

value: hSKM

value: Histone H3K4me2


title: ChIP-Seq analysis of H3K36me3 in human hSKM cells; Lib:MC:20100511:12--ChIP:MC:20100505:12:hSKM:H3K36Me3

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: CL_0000594
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib:MC:20100511:12--ChIP:MC:20100505:12:hSKM:H3K36Me3
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.3173
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.3210
****************
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: GSM621749_BI.Muscle_Satellite_Cultured_Cells.H3K36me3.hSKM-2.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:MC:20100511:12--ChIP:MC:20100505:12:hSKM:H3K36Me3.hg19.level.1
ANALYSIS TITLE: Mapping of Muscle Satellite Cultured Cells Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K36me3 ChIP-Seq on Muscle Satellite Cultured Cells, Donor hSKM-2 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.4650
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: 0.1903
FINDPEAKS_PERCENTILE: 37
HOTSPOT_SCORE: 0.1966
HOTSPOT_PERCENTILE: 28
IROC_SCORE: 0.8846
IROC_PERCENTILE: 22
POISSON_SCORE: 0.5351
POISSON_PERCENTILE: 61

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

ANALYSIS FILE NAME: GSM621749_BI.Muscle_Satellite_Cultured_Cells.H3K36me3.hSKM-2.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:MC:20100511:12--ChIP:MC:20100505:12:hSKM:H3K36Me3.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Muscle Satellite Cultured Cells Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K36me3 ChIP-Seq read mappings from Muscle Satellite Cultured Cells, Donor hSKM-2 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.4924
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: MS H3K36me3 2
BROWSER_TRACK_DESCRIPTION: BI Muscle Satellite Cultured Cells Histone H3K36me3 Donor hSKM-2 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED: 54
FINDPEAKS_SCORE: 0.1903
FINDPEAKS_PERCENTILE: 37
HOTSPOT_SCORE: 0.1966
HOTSPOT_PERCENTILE: 28
IROC_SCORE: 0.8846
IROC_PERCENTILE: 22
POISSON_SCORE: 0.5351
POISSON_PERCENTILE: 61

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

molecule: genomic DNA

organism: Homo sapiens

source_name: "Expanded from muscle spindle cells (Muoio et al; Diabetes 51, 901 (2002))"; Lib:MC:20100511:12--ChIP:MC:20100505:12:hSKM:H3K36Me3

extract_protocol: Library construction protocol: Single read - Illumina

tag: lineage

value: mesoderm

tag: medium

value: DMEM

tag: molecule

tag: disease

tag: passage

tag: line

value: in vivo

tag: batch

value: Cell Line

value: differentiated

tag: Sex

value: Unknown

value: Duke University

value: Protein A-Sepharose 4B

value: 10 million cells

value: SDS lysis

value: 70 ul bed volume

value: Abcam

value: Histone H3K36me3

value: Bioruptor


title: ChIP-Seq analysis of H3K27me3 in human hSKM cells; Lib:MC:20100511:13--ChIP:MC:20100505:13:hSKM:H3K27Me3

description:
sample_term_id: CL_0000594
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib:MC:20100511:13--ChIP:MC:20100505:13:hSKM:H3K27Me3
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.3175
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.3210
****************
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: GSM621751_BI.Muscle_Satellite_Cultured_Cells.H3K27me3.hSKM-2.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:MC:20100511:13--ChIP:MC:20100505:13:hSKM:H3K27Me3.hg19.level.1
ANALYSIS TITLE: Mapping of Muscle Satellite Cultured Cells Histone H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K27me3 ChIP-Seq on Muscle Satellite Cultured Cells, Donor hSKM-2 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.4600
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: 0.0251
FINDPEAKS_PERCENTILE: 13
HOTSPOT_SCORE: 0.113
HOTSPOT_PERCENTILE: 21
IROC_SCORE: 0.9109
IROC_PERCENTILE: 48
POISSON_SCORE: 0.5053
POISSON_PERCENTILE: 65

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

ANALYSIS FILE NAME: GSM621751_BI.Muscle_Satellite_Cultured_Cells.H3K27me3.hSKM-2.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:MC:20100511:13--ChIP:MC:20100505:13:hSKM:H3K27Me3.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Muscle Satellite Cultured Cells Histone H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K27me3 ChIP-Seq read mappings from Muscle Satellite Cultured Cells, Donor hSKM-2 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.4874
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: MS H3K27me3 2
BROWSER_TRACK_DESCRIPTION: BI Muscle Satellite Cultured Cells Histone H3K27me3 Donor hSKM-2 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED: 52
FINDPEAKS_SCORE: 0.0251
FINDPEAKS_PERCENTILE: 13
HOTSPOT_SCORE: 0.113
HOTSPOT_PERCENTILE: 21
IROC_SCORE: 0.9109
IROC_PERCENTILE: 48
POISSON_SCORE: 0.5053
POISSON_PERCENTILE: 65

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

source_name: "Expanded from muscle spindle cells (Muoio et al; Diabetes 51, 901 (2002))"; Lib:MC:20100511:13--ChIP:MC:20100505:13:hSKM:H3K27Me3

value: genomic DNA

value: unknown

value: Millipore

value: Histone H3K27me3


title: WD iPSC-3

status: Public on Dec 01 2010

type: RNA

city: Guangzhou

first: shiqiang

last: zhang

address: 190 Kai Yuan Avenue, Science Park

country: China

institute: Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences

description: WD iPSC-3(KSR+VPA)

hyb_protocol: Following fragmentation and labeling, 10 ug of cDNA were hybridized for 16 hr at 45C on GeneChip HuGene 1.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix Scanner 3000 7G.

data_processing: The data were analyzed with Robust Multichip Average (RMA) using Partek software.

label: biotin

molecule: total RNA

source_name: WD iPSC (passage 8)

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA (Whole Transcript (WT) Sense Target   Labeling Assay Manual, 2007, Affymetrix).

growth_protocol: WD fibroblasts were maintained in DMEM plus 10% fetal bovine serum (FBS),  WD iPSCs and H9 were maintained on Matrigel with mTESR1 culture medium

extract_protocol: Cells were collected by Accutase treatment. Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: WD fibroblasts (passage 5),  WD iPSCs (passage 8) and H9 (passage 40) were used for RNA extraction, spontaneously differentiated cells in WD iPSCs and H9 were removed manually before Trizol treatment.

tag: cell type

value: Wilson’s disease iPSC


title: hES H9

description: hES H9(Wicell)

source_name: hES H9 (passage 40)

value: hES H9


title: ChIP-Seq analysis of H3K4me3 in human hSKM cells; Lib:MC:20100511:11--ChIP:MC:20100505:11:hSKM:H3K4Me3

description:
sample_term_id: CL_0000594
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib:MC:20100511:11--ChIP:MC:20100505:11:hSKM:H3K4Me3
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.3169
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.3210
****************
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: GSM621745_BI.Muscle_Satellite_Cultured_Cells.H3K4me3.hSKM-2.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:MC:20100511:11--ChIP:MC:20100505:11:hSKM:H3K4Me3.hg19.level.1
ANALYSIS TITLE: Mapping of Muscle Satellite Cultured Cells Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me3 ChIP-Seq on Muscle Satellite Cultured Cells, Donor hSKM-2 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.4651
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: 0.4304
FINDPEAKS_PERCENTILE: 60
HOTSPOT_SCORE: 0.4229
HOTSPOT_PERCENTILE: 57
IROC_SCORE: 0.9916
IROC_PERCENTILE: 10
POISSON_SCORE: 0.5259
POISSON_PERCENTILE: 61

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

ANALYSIS FILE NAME: GSM621745_BI.Muscle_Satellite_Cultured_Cells.H3K4me3.hSKM-2.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:MC:20100511:11--ChIP:MC:20100505:11:hSKM:H3K4Me3.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Muscle Satellite Cultured Cells Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me3 ChIP-Seq read mappings from Muscle Satellite Cultured Cells, Donor hSKM-2 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.4925
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: MS H3K4me3 2
BROWSER_TRACK_DESCRIPTION: BI Muscle Satellite Cultured Cells Histone H3K4me3 Donor hSKM-2 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED: 62
FINDPEAKS_SCORE: 0.4304
FINDPEAKS_PERCENTILE: 60
HOTSPOT_SCORE: 0.4229
HOTSPOT_PERCENTILE: 57
IROC_SCORE: 0.9916
IROC_PERCENTILE: 10
POISSON_SCORE: 0.5259
POISSON_PERCENTILE: 61

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

source_name: "Expanded from muscle spindle cells (Muoio et al; Diabetes 51, 901 (2002))"; Lib:MC:20100511:11--ChIP:MC:20100505:11:hSKM:H3K4Me3

value: mesoderm

value: DMEM

value: hSKM

value: in vivo

value: Cell Line

value: Histone H3K4me3


title: ChIP-Seq analysis of WCE in human hSKM cells; Lib:MC:20100511:16--ChIP:MC:20100505:16:hSKM:WCE

description:
sample_term_id: CL_0000594
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib:MC:20100511:16--ChIP:MC:20100505:16:hSKM:WCE
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.3170
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.3210
****************
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: GSM621746_BI.Muscle_Satellite_Cultured_Cells.Input.hSKM-2.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:MC:20100511:16--ChIP:MC:20100505:16:hSKM:WCE.hg19.level.1
ANALYSIS TITLE: Mapping of Muscle Satellite Cultured Cells ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina reads produced by ChIP-Seq Input on Muscle Satellite Cultured Cells, Donor hSKM-2 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.4692
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 2

QUALITY SCORES:
NUMBER_OF_Input_EXPERIMENTS_SCORED: 67
FINDPEAKS_SCORE: 0.0052
FINDPEAKS_PERCENTILE: 7
HOTSPOT_SCORE: 0.0303
HOTSPOT_PERCENTILE: 41
IROC_SCORE: 0.9182
IROC_PERCENTILE: 68
POISSON_SCORE: 0.2244
POISSON_PERCENTILE: 45

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

ANALYSIS FILE NAME: GSM621746_BI.Muscle_Satellite_Cultured_Cells.Input.hSKM-2.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:MC:20100511:16--ChIP:MC:20100505:16:hSKM:WCE.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Muscle Satellite Cultured Cells ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina ChIP-Seq Input read mappings from Muscle Satellite Cultured Cells, Donor hSKM-2 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.4966
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: MS Input 2
BROWSER_TRACK_DESCRIPTION: BI Muscle Satellite Cultured Cells ChIP-Seq Input Donor hSKM-2 EA Release 2

QUALITY SCORES:
NUMBER_OF_Input_EXPERIMENTS_SCORED: 67
FINDPEAKS_SCORE: 0.0052
FINDPEAKS_PERCENTILE: 7
HOTSPOT_SCORE: 0.0303
HOTSPOT_PERCENTILE: 41
IROC_SCORE: 0.9182
IROC_PERCENTILE: 68
POISSON_SCORE: 0.2244
POISSON_PERCENTILE: 45

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

source_name: "Expanded from muscle spindle cells (Muoio et al; Diabetes 51, 901 (2002))"; Lib:MC:20100511:16--ChIP:MC:20100505:16:hSKM:WCE

value: differentiated

value: Unknown

value: Duke University

value: standard

value: SDS lysis

value: ChIP-Seq Input

value: Input


title: ChIP-Seq analysis of H3K9me3 in human hSKM cells; Lib:MC:20100511:15--ChIP:MC:20100505:15:hSKM:H3K9Me3

description:
sample_term_id: CL_0000594
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib:MC:20100511:15--ChIP:MC:20100505:15:hSKM:H3K9Me3
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.3171
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.3210
****************
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: GSM621747_BI.Muscle_Satellite_Cultured_Cells.H3K9me3.hSKM-2.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:MC:20100511:15--ChIP:MC:20100505:15:hSKM:H3K9Me3.hg19.level.1
ANALYSIS TITLE: Mapping of Muscle Satellite Cultured Cells Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K9me3 ChIP-Seq on Muscle Satellite Cultured Cells, Donor hSKM-2 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.4777
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: 0.0175
FINDPEAKS_PERCENTILE: 3
HOTSPOT_SCORE: 0.0538
HOTSPOT_PERCENTILE: 14
IROC_SCORE: 0.5805
IROC_PERCENTILE: 5
POISSON_SCORE: 0.3469
POISSON_PERCENTILE: 41

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

ANALYSIS FILE NAME: GSM621747_BI.Muscle_Satellite_Cultured_Cells.H3K9me3.hSKM-2.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:MC:20100511:15--ChIP:MC:20100505:15:hSKM:H3K9Me3.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Muscle Satellite Cultured Cells Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K9me3 ChIP-Seq read mappings from Muscle Satellite Cultured Cells, Donor hSKM-2 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.5051
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: MS H3K9me3 2
BROWSER_TRACK_DESCRIPTION: BI Muscle Satellite Cultured Cells Histone H3K9me3 Donor hSKM-2 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED: 59
FINDPEAKS_SCORE: 0.0175
FINDPEAKS_PERCENTILE: 3
HOTSPOT_SCORE: 0.0538
HOTSPOT_PERCENTILE: 14
IROC_SCORE: 0.5805
IROC_PERCENTILE: 5
POISSON_SCORE: 0.3469
POISSON_PERCENTILE: 41

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

source_name: "Expanded from muscle spindle cells (Muoio et al; Diabetes 51, 901 (2002))"; Lib:MC:20100511:15--ChIP:MC:20100505:15:hSKM:H3K9Me3

value: genomic DNA

value: unknown

value: Protein A-Sepharose 4B

value: 10 million cells

value: 70 ul bed volume

value: Abcam

value: Histone H3K9me3

value: Bioruptor


title: ChIP-Seq analysis of H3K9me3 in human hSKM cells; Lib:MC:20100222:07--ChIP:MC:20100216:07:hSKM:H3K9Me3

description:
sample_term_id: CL_0000594
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib:MC:20100222:07--ChIP:MC:20100216:07:hSKM:H3K9Me3
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.3168
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.3209
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************
BED and WIG files were replaced on April 29, 2014

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

ANALYSIS FILE NAME: GSM621744_BI.Muscle_Satellite_Cultured_Cells.H3K9me3.hSKM-1.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:MC:20100222:07--ChIP:MC:20100216:07:hSKM:H3K9Me3.hg19.level.1
ANALYSIS TITLE: Mapping of Muscle Satellite Cultured Cells Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K9me3 ChIP-Seq on Muscle Satellite Cultured Cells, Donor hSKM-1 were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.4772
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: 0.0176
FINDPEAKS_PERCENTILE: 5
HOTSPOT_SCORE: 0.0578
HOTSPOT_PERCENTILE: 17
IROC_SCORE: 0.9971
IROC_PERCENTILE: 97
POISSON_SCORE: 0.305
POISSON_PERCENTILE: 19

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

ANALYSIS FILE NAME: GSM621744_BI.Muscle_Satellite_Cultured_Cells.H3K9me3.hSKM-1.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:MC:20100222:07--ChIP:MC:20100216:07:hSKM:H3K9Me3.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Muscle Satellite Cultured Cells Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K9me3 ChIP-Seq read mappings from Muscle Satellite Cultured Cells, Donor hSKM-1 were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.5046
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: MS H3K9me3 1
BROWSER_TRACK_DESCRIPTION: BI Muscle Satellite Cultured Cells Histone H3K9me3 Donor hSKM-1 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED: 59
FINDPEAKS_SCORE: 0.0176
FINDPEAKS_PERCENTILE: 5
HOTSPOT_SCORE: 0.0578
HOTSPOT_PERCENTILE: 17
IROC_SCORE: 0.9971
IROC_PERCENTILE: 97
POISSON_SCORE: 0.305
POISSON_PERCENTILE: 19

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

source_name: "Expanded from muscle spindle cells (Muoio et al; Diabetes 51, 901 (2002))"; Lib:MC:20100222:07--ChIP:MC:20100216:07:hSKM:H3K9Me3

value: mesoderm

value: DMEM

value: hSKM

value: in vivo

value: Cell Line


title: ChIP-Seq analysis of H3K4me3 in human hSKM cells; Lib:MC:20100222:10--ChIP:MC:20100216:10:hSKM:H3K4Me3

description:
sample_term_id: CL_0000594
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib:MC:20100222:10--ChIP:MC:20100216:10:hSKM:H3K4Me3
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.3184
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.3211
****************
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: GSM621760_BI.Muscle_Satellite_Cultured_Cells.H3K4me3.hSKM-3.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:MC:20100222:10--ChIP:MC:20100216:10:hSKM:H3K4Me3.hg19.level.1
ANALYSIS TITLE: Mapping of Muscle Satellite Cultured Cells Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me3 ChIP-Seq on Muscle Satellite Cultured Cells, Donor hSKM-3 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.4658
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: 0.4334
FINDPEAKS_PERCENTILE: 61
HOTSPOT_SCORE: 0.4243
HOTSPOT_PERCENTILE: 59
IROC_SCORE: 0.9844
IROC_PERCENTILE: 3
POISSON_SCORE: 0.519
POISSON_PERCENTILE: 60

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

ANALYSIS FILE NAME: GSM621760_BI.Muscle_Satellite_Cultured_Cells.H3K4me3.hSKM-3.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:MC:20100222:10--ChIP:MC:20100216:10:hSKM:H3K4Me3.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Muscle Satellite Cultured Cells Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me3 ChIP-Seq read mappings from Muscle Satellite Cultured Cells, Donor hSKM-3 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.4932
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: MS H3K4me3 3
BROWSER_TRACK_DESCRIPTION: BI Muscle Satellite Cultured Cells Histone H3K4me3 Donor hSKM-3 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED: 62
FINDPEAKS_SCORE: 0.4334
FINDPEAKS_PERCENTILE: 61
HOTSPOT_SCORE: 0.4243
HOTSPOT_PERCENTILE: 59
IROC_SCORE: 0.9844
IROC_PERCENTILE: 3
POISSON_SCORE: 0.519
POISSON_PERCENTILE: 60

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

source_name: "Expanded from muscle spindle cells (Muoio et al; Diabetes 51, 901 (2002))"; Lib:MC:20100222:10--ChIP:MC:20100216:10:hSKM:H3K4Me3

value: differentiated

value: Unknown

value: Duke University

value: Millipore

value: Histone H3K4me3


title: ChIP-Seq analysis of H3K4me1 in human hSKM cells; Lib:MC:20100222:01--ChIP:MC:20100216:01:hSKM:H3K4Me1

description:
sample_term_id: CL_0000594
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib:MC:20100222:01--ChIP:MC:20100216:01:hSKM:H3K4Me1
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.3165
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.3209
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************
BED and WIG files were replaced on April 29, 2014

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

ANALYSIS FILE NAME: GSM621741_BI.Muscle_Satellite_Cultured_Cells.H3K4me1.hSKM-1.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:MC:20100222:01--ChIP:MC:20100216:01:hSKM:H3K4Me1.hg19.level.1
ANALYSIS TITLE: Mapping of Muscle Satellite Cultured Cells Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me1 ChIP-Seq on Muscle Satellite Cultured Cells, Donor hSKM-1 were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.4628
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: 0.5299
FINDPEAKS_PERCENTILE: 79
HOTSPOT_SCORE: 0.512
HOTSPOT_PERCENTILE: 79
IROC_SCORE: 0.9674
IROC_PERCENTILE: 33
POISSON_SCORE: 0.6907
POISSON_PERCENTILE: 86

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

ANALYSIS FILE NAME: GSM621741_BI.Muscle_Satellite_Cultured_Cells.H3K4me1.hSKM-1.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:MC:20100222:01--ChIP:MC:20100216:01:hSKM:H3K4Me1.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Muscle Satellite Cultured Cells Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me1 ChIP-Seq read mappings from Muscle Satellite Cultured Cells, Donor hSKM-1 were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.4902
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: MS H3K4me1 1
BROWSER_TRACK_DESCRIPTION: BI Muscle Satellite Cultured Cells Histone H3K4me1 Donor hSKM-1 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED: 43
FINDPEAKS_SCORE: 0.5299
FINDPEAKS_PERCENTILE: 79
HOTSPOT_SCORE: 0.512
HOTSPOT_PERCENTILE: 79
IROC_SCORE: 0.9674
IROC_PERCENTILE: 33
POISSON_SCORE: 0.6907
POISSON_PERCENTILE: 86

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

source_name: "Expanded from muscle spindle cells (Muoio et al; Diabetes 51, 901 (2002))"; Lib:MC:20100222:01--ChIP:MC:20100216:01:hSKM:H3K4Me1

value: genomic DNA

value: unknown

value: SDS lysis

value: Histone H3K4me1


title: ChIP-Seq analysis of H3K4me2 in human hSKM cells; Lib:MC:20100222:02--ChIP:MC:20100216:02:hSKM:H3K4Me2

description:
sample_term_id: CL_0000594
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib:MC:20100222:02--ChIP:MC:20100216:02:hSKM:H3K4Me2
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.3166
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.3209
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************
BED and WIG files were replaced on April 29, 2014

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

ANALYSIS FILE NAME: GSM621742_BI.Muscle_Satellite_Cultured_Cells.H3K4me2.hSKM-1.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:MC:20100222:02--ChIP:MC:20100216:02:hSKM:H3K4Me2.hg19.level.1
ANALYSIS TITLE: Mapping of Muscle Satellite Cultured Cells Histone H3K4me2 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me2 ChIP-Seq on Muscle Satellite Cultured Cells, Donor hSKM-1 were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.4782
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_H3K4me2_EXPERIMENTS_SCORED: 8
FINDPEAKS_SCORE: 0.5763
FINDPEAKS_PERCENTILE: 38
HOTSPOT_SCORE: 0.545
HOTSPOT_PERCENTILE: 25
IROC_SCORE: 0.9991
IROC_PERCENTILE: 50
POISSON_SCORE: 0.6488
POISSON_PERCENTILE: 38

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

ANALYSIS FILE NAME: GSM621742_BI.Muscle_Satellite_Cultured_Cells.H3K4me2.hSKM-1.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:MC:20100222:02--ChIP:MC:20100216:02:hSKM:H3K4Me2.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Muscle Satellite Cultured Cells Histone H3K4me2 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me2 ChIP-Seq read mappings from Muscle Satellite Cultured Cells, Donor hSKM-1 were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.5056
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: MS H3K4me2 1
BROWSER_TRACK_DESCRIPTION: BI Muscle Satellite Cultured Cells Histone H3K4me2 Donor hSKM-1 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K4me2_EXPERIMENTS_SCORED: 8
FINDPEAKS_SCORE: 0.5763
FINDPEAKS_PERCENTILE: 38
HOTSPOT_SCORE: 0.545
HOTSPOT_PERCENTILE: 25
IROC_SCORE: 0.9991
IROC_PERCENTILE: 50
POISSON_SCORE: 0.6488
POISSON_PERCENTILE: 38

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

source_name: "Expanded from muscle spindle cells (Muoio et al; Diabetes 51, 901 (2002))"; Lib:MC:20100222:02--ChIP:MC:20100216:02:hSKM:H3K4Me2

value: Protein A-Sepharose 4B

value: 10 million cells

value: 70 ul bed volume

value: Abcam

value: Histone H3K4me2


title: ChIP-Seq analysis of H3K27me3 in human hSKM cells; Lib:MC:20100222:05--ChIP:MC:20100216:05:hSKM:H3K27Me3

description:
sample_term_id: CL_0000594
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib:MC:20100222:05--ChIP:MC:20100216:05:hSKM:H3K27Me3
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.3164
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.3209
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************
BED and WIG files were replaced on April 29, 2014

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

ANALYSIS FILE NAME: GSM621740_BI.Muscle_Satellite_Cultured_Cells.H3K27me3.hSKM-1.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:MC:20100222:05--ChIP:MC:20100216:05:hSKM:H3K27Me3.hg19.level.1
ANALYSIS TITLE: Mapping of Muscle Satellite Cultured Cells Histone H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K27me3 ChIP-Seq on Muscle Satellite Cultured Cells, Donor hSKM-1 were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.4596
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: 0.0689
FINDPEAKS_PERCENTILE: 35
HOTSPOT_SCORE: 0.1512
HOTSPOT_PERCENTILE: 33
IROC_SCORE: 0.0
IROC_PERCENTILE: 4
POISSON_SCORE: 0.5356
POISSON_PERCENTILE: 79

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

ANALYSIS FILE NAME: GSM621740_BI.Muscle_Satellite_Cultured_Cells.H3K27me3.hSKM-1.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:MC:20100222:05--ChIP:MC:20100216:05:hSKM:H3K27Me3.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Muscle Satellite Cultured Cells Histone H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K27me3 ChIP-Seq read mappings from Muscle Satellite Cultured Cells, Donor hSKM-1 were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.4870
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: MS H3K27me3 1
BROWSER_TRACK_DESCRIPTION: BI Muscle Satellite Cultured Cells Histone H3K27me3 Donor hSKM-1 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED: 52
FINDPEAKS_SCORE: 0.0689
FINDPEAKS_PERCENTILE: 35
HOTSPOT_SCORE: 0.1512
HOTSPOT_PERCENTILE: 33
IROC_SCORE: 0.0
IROC_PERCENTILE: 4
POISSON_SCORE: 0.5356
POISSON_PERCENTILE: 79

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

source_name: "Expanded from muscle spindle cells (Muoio et al; Diabetes 51, 901 (2002))"; Lib:MC:20100222:05--ChIP:MC:20100216:05:hSKM:H3K27Me3

value: mesoderm

value: DMEM

value: hSKM

value: Histone H3K27me3

value: Bioruptor


title: ChIP-Seq analysis of H3K27me3 in human hSKM cells; Lib:MC:20100222:12--ChIP:MC:20100216:12:hSKM:H3K27Me3

description:
sample_term_id: CL_0000594
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib:MC:20100222:12--ChIP:MC:20100216:12:hSKM:H3K27Me3
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.3179
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.3211
****************
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: GSM621755_BI.Muscle_Satellite_Cultured_Cells.H3K27me3.hSKM-3.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:MC:20100222:12--ChIP:MC:20100216:12:hSKM:H3K27Me3.hg19.level.1
ANALYSIS TITLE: Mapping of Muscle Satellite Cultured Cells Histone H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K27me3 ChIP-Seq on Muscle Satellite Cultured Cells, Donor hSKM-3 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.4601
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: 0.1041
FINDPEAKS_PERCENTILE: 42
HOTSPOT_SCORE: 0.173
HOTSPOT_PERCENTILE: 40
IROC_SCORE: 0.8881
IROC_PERCENTILE: 38
POISSON_SCORE: 0.543
POISSON_PERCENTILE: 83

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

ANALYSIS FILE NAME: GSM621755_BI.Muscle_Satellite_Cultured_Cells.H3K27me3.hSKM-3.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:MC:20100222:12--ChIP:MC:20100216:12:hSKM:H3K27Me3.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Muscle Satellite Cultured Cells Histone H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K27me3 ChIP-Seq read mappings from Muscle Satellite Cultured Cells, Donor hSKM-3 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.4875
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: MS H3K27me3 3
BROWSER_TRACK_DESCRIPTION: BI Muscle Satellite Cultured Cells Histone H3K27me3 Donor hSKM-3 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED: 52
FINDPEAKS_SCORE: 0.1041
FINDPEAKS_PERCENTILE: 42
HOTSPOT_SCORE: 0.173
HOTSPOT_PERCENTILE: 40
IROC_SCORE: 0.8881
IROC_PERCENTILE: 38
POISSON_SCORE: 0.543
POISSON_PERCENTILE: 83

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

source_name: "Expanded from muscle spindle cells (Muoio et al; Diabetes 51, 901 (2002))"; Lib:MC:20100222:12--ChIP:MC:20100216:12:hSKM:H3K27Me3

value: in vivo

value: Cell Line

value: differentiated

value: Unknown

value: Duke University


title: ChIP-Seq analysis of H3K36me3 in human hSKM cells; Lib:MC:20100222:04--ChIP:MC:20100216:04:hSKM:H3K36Me3

description:
sample_term_id: CL_0000594
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib:MC:20100222:04--ChIP:MC:20100216:04:hSKM:H3K36Me3
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.3163
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.3209
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************
BED and WIG files were replaced on April 29, 2014

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

ANALYSIS FILE NAME: GSM621739_BI.Muscle_Satellite_Cultured_Cells.H3K36me3.hSKM-1.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:MC:20100222:04--ChIP:MC:20100216:04:hSKM:H3K36Me3.hg19.level.1
ANALYSIS TITLE: Mapping of Muscle Satellite Cultured Cells Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K36me3 ChIP-Seq on Muscle Satellite Cultured Cells, Donor hSKM-1 were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.4647
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: 0.078
FINDPEAKS_PERCENTILE: 19
HOTSPOT_SCORE: 0.1615
HOTSPOT_PERCENTILE: 17
IROC_SCORE: 0.8396
IROC_PERCENTILE: 15
POISSON_SCORE: 0.4217
POISSON_PERCENTILE: 26

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

ANALYSIS FILE NAME: GSM621739_BI.Muscle_Satellite_Cultured_Cells.H3K36me3.hSKM-1.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:MC:20100222:04--ChIP:MC:20100216:04:hSKM:H3K36Me3.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Muscle Satellite Cultured Cells Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K36me3 ChIP-Seq read mappings from Muscle Satellite Cultured Cells, Donor hSKM-1 were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.4921
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: MS H3K36me3 1
BROWSER_TRACK_DESCRIPTION: BI Muscle Satellite Cultured Cells Histone H3K36me3 Donor hSKM-1 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED: 54
FINDPEAKS_SCORE: 0.078
FINDPEAKS_PERCENTILE: 19
HOTSPOT_SCORE: 0.1615
HOTSPOT_PERCENTILE: 17
IROC_SCORE: 0.8396
IROC_PERCENTILE: 15
POISSON_SCORE: 0.4217
POISSON_PERCENTILE: 26

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

source_name: "Expanded from muscle spindle cells (Muoio et al; Diabetes 51, 901 (2002))"; Lib:MC:20100222:04--ChIP:MC:20100216:04:hSKM:H3K36Me3

value: genomic DNA

value: unknown

value: SDS lysis

value: Histone H3K36me3


title: ChIP-Seq analysis of H3K9ac in human hSKM cells; Lib:MC:20100222:06--ChIP:MC:20100216:06:hSKM:H3K9Ac

description:
sample_term_id: CL_0000594
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib:MC:20100222:06--ChIP:MC:20100216:06:hSKM:H3K9Ac
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.3162
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.3209
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************
BED and WIG files were replaced on April 29, 2014

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

ANALYSIS FILE NAME: GSM621738_BI.Muscle_Satellite_Cultured_Cells.H3K9ac.hSKM-1.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:MC:20100222:06--ChIP:MC:20100216:06:hSKM:H3K9Ac.hg19.level.1
ANALYSIS TITLE: Mapping of Muscle Satellite Cultured Cells Histone H3K9ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K9ac ChIP-Seq on Muscle Satellite Cultured Cells, Donor hSKM-1 were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.4781
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 2

QUALITY SCORES:
NUMBER_OF_H3K9ac_EXPERIMENTS_SCORED: 35
FINDPEAKS_SCORE: 0.5353
FINDPEAKS_PERCENTILE: 86
HOTSPOT_SCORE: 0.5427
HOTSPOT_PERCENTILE: 94
IROC_SCORE: 0.9868
IROC_PERCENTILE: 60
POISSON_SCORE: 0.6229
POISSON_PERCENTILE: 86

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

ANALYSIS FILE NAME: GSM621738_BI.Muscle_Satellite_Cultured_Cells.H3K9ac.hSKM-1.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:MC:20100222:06--ChIP:MC:20100216:06:hSKM:H3K9Ac.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Muscle Satellite Cultured Cells Histone H3K9ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K9ac ChIP-Seq read mappings from Muscle Satellite Cultured Cells, Donor hSKM-1 were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.5055
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: MS H3K9ac 1
BROWSER_TRACK_DESCRIPTION: BI Muscle Satellite Cultured Cells Histone H3K9ac Donor hSKM-1 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K9ac_EXPERIMENTS_SCORED: 35
FINDPEAKS_SCORE: 0.5353
FINDPEAKS_PERCENTILE: 86
HOTSPOT_SCORE: 0.5427
HOTSPOT_PERCENTILE: 94
IROC_SCORE: 0.9868
IROC_PERCENTILE: 60
POISSON_SCORE: 0.6229
POISSON_PERCENTILE: 86

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

source_name: "Expanded from muscle spindle cells (Muoio et al; Diabetes 51, 901 (2002))"; Lib:MC:20100222:06--ChIP:MC:20100216:06:hSKM:H3K9Ac

value: Protein A-Sepharose 4B

value: 10 million cells

value: 70 ul bed volume

value: Histone H3K9ac


title: ChIP-Seq analysis of H3K4me3 in human hSKM cells; Lib:MC:20100222:03--ChIP:MC:20100216:03:hSKM:H3K4Me3

description:
sample_term_id: CL_0000594
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib:MC:20100222:03--ChIP:MC:20100216:03:hSKM:H3K4Me3
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.3161
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.3209
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************
BED and WIG files were replaced on April 29, 2014

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

ANALYSIS FILE NAME: GSM621737_BI.Muscle_Satellite_Cultured_Cells.H3K4me3.hSKM-1.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:MC:20100222:03--ChIP:MC:20100216:03:hSKM:H3K4Me3.hg19.level.1
ANALYSIS TITLE: Mapping of Muscle Satellite Cultured Cells Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me3 ChIP-Seq on Muscle Satellite Cultured Cells, Donor hSKM-1 were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.4646
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: 0.5013
FINDPEAKS_PERCENTILE: 73
HOTSPOT_SCORE: 0.5469
HOTSPOT_PERCENTILE: 79
IROC_SCORE: 0.9991
IROC_PERCENTILE: 48
POISSON_SCORE: 0.7325
POISSON_PERCENTILE: 92

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

ANALYSIS FILE NAME: GSM621737_BI.Muscle_Satellite_Cultured_Cells.H3K4me3.hSKM-1.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:MC:20100222:03--ChIP:MC:20100216:03:hSKM:H3K4Me3.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Muscle Satellite Cultured Cells Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me3 ChIP-Seq read mappings from Muscle Satellite Cultured Cells, Donor hSKM-1 were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.4920
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: MS H3K4me3 1
BROWSER_TRACK_DESCRIPTION: BI Muscle Satellite Cultured Cells Histone H3K4me3 Donor hSKM-1 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED: 62
FINDPEAKS_SCORE: 0.5013
FINDPEAKS_PERCENTILE: 73
HOTSPOT_SCORE: 0.5469
HOTSPOT_PERCENTILE: 79
IROC_SCORE: 0.9991
IROC_PERCENTILE: 48
POISSON_SCORE: 0.7325
POISSON_PERCENTILE: 92

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

source_name: "Expanded from muscle spindle cells (Muoio et al; Diabetes 51, 901 (2002))"; Lib:MC:20100222:03--ChIP:MC:20100216:03:hSKM:H3K4Me3

value: mesoderm

value: DMEM

value: Millipore

value: Histone H3K4me3


title: ChIP-Seq analysis of H3K9ac in Skeletal muscle cells; Lib:XZ:20100628:19--ChIP:XZ:20100621:19:Skeletal muscle:H3K9Ac

description:
sample_term_id: UBERON_0001134
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib:XZ:20100628:19--ChIP:XZ:20100621:19:Skeletal muscle:H3K9Ac
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.3275
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.3355
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************
BED and WIG files were replaced on April 29, 2014

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

ANALYSIS FILE NAME: GSM621691_BI.Skeletal_Muscle.H3K9ac.63.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100628:19--ChIP:XZ:20100621:19:Skeletal muscle:H3K9Ac.hg19.level.1
ANALYSIS TITLE: Mapping of Skeletal Muscle Histone H3K9ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K9ac ChIP-Seq on Skeletal Muscle, Donor 63 were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.4778
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 2

QUALITY SCORES:
NUMBER_OF_H3K9ac_EXPERIMENTS_SCORED: 35
FINDPEAKS_SCORE: 0.5678
FINDPEAKS_PERCENTILE: 94
HOTSPOT_SCORE: 0.5013
HOTSPOT_PERCENTILE: 86
IROC_SCORE: 0.9836
IROC_PERCENTILE: 49
POISSON_SCORE: 0.83
POISSON_PERCENTILE: 100

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

ANALYSIS FILE NAME: GSM621691_BI.Skeletal_Muscle.H3K9ac.63.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100628:19--ChIP:XZ:20100621:19:Skeletal muscle:H3K9Ac.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Skeletal Muscle Histone H3K9ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K9ac ChIP-Seq read mappings from Skeletal Muscle, Donor 63 were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.5052
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: SM H3K9ac 63
BROWSER_TRACK_DESCRIPTION: BI Skeletal Muscle Histone H3K9ac Donor 63 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K9ac_EXPERIMENTS_SCORED: 35
FINDPEAKS_SCORE: 0.5678
FINDPEAKS_PERCENTILE: 94
HOTSPOT_SCORE: 0.5013
HOTSPOT_PERCENTILE: 86
IROC_SCORE: 0.9836
IROC_PERCENTILE: 49
POISSON_SCORE: 0.83
POISSON_PERCENTILE: 100

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

source_name: Primary skeletal muscle tissue; Lib:XZ:20100628:19--ChIP:XZ:20100621:19:Skeletal muscle:H3K9Ac

value: surgery

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

value: Skeletal muscle

value: white

value: Male

value: Primary Tissue

value: MGH Pathology

value: 54 years

value: Abcam

value: Bioruptor


title: ChIP-Seq analysis of H3K27me3 in Skeletal muscle cells; Lib:XZ:20100628:18--ChIP:XZ:20100621:18:Skeletal muscle:H3K27Me3

description:
sample_term_id: UBERON_0001134
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib:XZ:20100628:18--ChIP:XZ:20100621:18:Skeletal muscle:H3K27Me3
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.3276
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.3355
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************
BED and WIG files were replaced on April 29, 2014

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

ANALYSIS FILE NAME: GSM621692_BI.Skeletal_Muscle.H3K27me3.63.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100628:18--ChIP:XZ:20100621:18: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 63 were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.4664
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: 0.0571
FINDPEAKS_PERCENTILE: 29
HOTSPOT_SCORE: 0.1189
HOTSPOT_PERCENTILE: 23
IROC_SCORE: 0.7975
IROC_PERCENTILE: 17
POISSON_SCORE: 0.4398
POISSON_PERCENTILE: 46

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

ANALYSIS FILE NAME: GSM621692_BI.Skeletal_Muscle.H3K27me3.63.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100628:18--ChIP:XZ:20100621:18: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 63 were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.4938
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 63
BROWSER_TRACK_DESCRIPTION: BI Skeletal Muscle Histone H3K27me3 Donor 63 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED: 52
FINDPEAKS_SCORE: 0.0571
FINDPEAKS_PERCENTILE: 29
HOTSPOT_SCORE: 0.1189
HOTSPOT_PERCENTILE: 23
IROC_SCORE: 0.7975
IROC_PERCENTILE: 17
POISSON_SCORE: 0.4398
POISSON_PERCENTILE: 46

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

source_name: Primary skeletal muscle tissue; Lib:XZ:20100628:18--ChIP:XZ:20100621:18:Skeletal muscle:H3K27Me3

value: genomic DNA

value: unknown

value: Protein A-Sepharose 4B

value: 10 million cells

value: SDS lysis

value: Histone H3K27me3


title: ChIP-Seq analysis of H3K9ac in Skeletal muscle cells; Lib:XZ:20100423:06--ChIP:XZ:20100331:06:Skeletal muscle:H3K9Ac

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:20100423:06--ChIP:XZ:20100331:06:Skeletal muscle:H3K9Ac
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.3272
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: GSM621688_BI.Skeletal_Muscle.H3K9ac.19.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100423:06--ChIP:XZ:20100331:06:Skeletal muscle:H3K9Ac.hg19.level.1
ANALYSIS TITLE: Mapping of Skeletal Muscle Histone H3K9ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K9ac ChIP-Seq on Skeletal Muscle, Donor 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.4679
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 2

QUALITY SCORES:
NUMBER_OF_H3K9ac_EXPERIMENTS_SCORED: 35
FINDPEAKS_SCORE: 0.3962
FINDPEAKS_PERCENTILE: 71
HOTSPOT_SCORE: 0.4472
HOTSPOT_PERCENTILE: 77
IROC_SCORE: 0.9656
IROC_PERCENTILE: 29
POISSON_SCORE: 0.8216
POISSON_PERCENTILE: 97

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

ANALYSIS FILE NAME: GSM621688_BI.Skeletal_Muscle.H3K9ac.19.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100423:06--ChIP:XZ:20100331:06:Skeletal muscle:H3K9Ac.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Skeletal Muscle Histone H3K9ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K9ac ChIP-Seq read mappings from Skeletal Muscle, Donor 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.4953
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: SM H3K9ac 19
BROWSER_TRACK_DESCRIPTION: BI Skeletal Muscle Histone H3K9ac Donor 19 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K9ac_EXPERIMENTS_SCORED: 35
FINDPEAKS_SCORE: 0.3962
FINDPEAKS_PERCENTILE: 71
HOTSPOT_SCORE: 0.4472
HOTSPOT_PERCENTILE: 77
IROC_SCORE: 0.9656
IROC_PERCENTILE: 29
POISSON_SCORE: 0.8216
POISSON_PERCENTILE: 97

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

source_name: Primary skeletal muscle tissue; Lib:XZ:20100423:06--ChIP:XZ:20100331:06:Skeletal muscle:H3K9Ac

value: Unknown

value: 70 ul bed volume

value: Histone H3K9ac


title: ChIP-Seq analysis of H3K4me3 in Skeletal muscle cells; Lib:XZ:20100628:09--ChIP:XZ:20100621:09:Skeletal muscle:H3K4Me3

description:
sample_term_id: UBERON_0001134
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib:XZ:20100628:09--ChIP:XZ:20100621:09:Skeletal muscle:H3K4Me3
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.3269
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.3356
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************
BED and WIG files were replaced on April 29, 2014

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

ANALYSIS FILE NAME: GSM621685_BI.Skeletal_Muscle.H3K4me3.62.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100628:09--ChIP:XZ:20100621:09: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 62 were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.4790
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: 0.3112
FINDPEAKS_PERCENTILE: 35
HOTSPOT_SCORE: 0.3359
HOTSPOT_PERCENTILE: 38
IROC_SCORE: 0.9973
IROC_PERCENTILE: 27
POISSON_SCORE: 0.496
POISSON_PERCENTILE: 55

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

ANALYSIS FILE NAME: GSM621685_BI.Skeletal_Muscle.H3K4me3.62.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100628:09--ChIP:XZ:20100621:09: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 62 were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.5064
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 62
BROWSER_TRACK_DESCRIPTION: BI Skeletal Muscle Histone H3K4me3 Donor 62 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED: 62
FINDPEAKS_SCORE: 0.3112
FINDPEAKS_PERCENTILE: 35
HOTSPOT_SCORE: 0.3359
HOTSPOT_PERCENTILE: 38
IROC_SCORE: 0.9973
IROC_PERCENTILE: 27
POISSON_SCORE: 0.496
POISSON_PERCENTILE: 55

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

source_name: Primary skeletal muscle tissue; Lib:XZ:20100628:09--ChIP:XZ:20100621:09:Skeletal muscle:H3K4Me3

extract_protocol: Library construction protocol: not specified

value: surgery

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

value: Skeletal muscle

value: Female

value: 72 years

value: Millipore

value: Histone H3K4me3


title: ChIP-Seq analysis of H3K36me3 in Skeletal muscle cells; Lib:XZ:20100628:17--ChIP:XZ:20100621:17:Skeletal muscle:H3K36Me3

description:
sample_term_id: UBERON_0001134
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib:XZ:20100628:17--ChIP:XZ:20100621:17:Skeletal muscle:H3K36Me3
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.3277
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.3355
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************
BED and WIG files were replaced on April 29, 2014

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

ANALYSIS FILE NAME: GSM621693_BI.Skeletal_Muscle.H3K36me3.63.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100628:17--ChIP:XZ:20100621:17: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 63 were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.4711
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: 0.1074
FINDPEAKS_PERCENTILE: 22
HOTSPOT_SCORE: 0.1734
HOTSPOT_PERCENTILE: 21
IROC_SCORE: 0.9435
IROC_PERCENTILE: 41
POISSON_SCORE: 0.4489
POISSON_PERCENTILE: 33

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

ANALYSIS FILE NAME: GSM621693_BI.Skeletal_Muscle.H3K36me3.63.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100628:17--ChIP:XZ:20100621:17: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 63 were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.4985
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 63
BROWSER_TRACK_DESCRIPTION: BI Skeletal Muscle Histone H3K36me3 Donor 63 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED: 54
FINDPEAKS_SCORE: 0.1074
FINDPEAKS_PERCENTILE: 22
HOTSPOT_SCORE: 0.1734
HOTSPOT_PERCENTILE: 21
IROC_SCORE: 0.9435
IROC_PERCENTILE: 41
POISSON_SCORE: 0.4489
POISSON_PERCENTILE: 33

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

source_name: Primary skeletal muscle tissue; Lib:XZ:20100628:17--ChIP:XZ:20100621:17:Skeletal muscle:H3K36Me3

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

value: white

value: Male

value: Primary Tissue

value: MGH Pathology

value: 54 years

value: Abcam

value: Histone H3K36me3

value: Bioruptor


title: ChIP-Seq analysis of H3K36me3 in rectal mucosa cells; Lib:XZ:20100503:10--ChIP:XZ:20100420:10:rectal mucosa:H3K36Me3

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:20100503:10--ChIP:XZ:20100420:10:rectal mucosa:H3K36Me3
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.3271
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:20100503:10--ChIP:XZ:20100420:10:rectal mucosa:H3K36Me3
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.3271
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: GSM621687_BI.Rectal_Mucosa.H3K36me3.31.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100503:10--ChIP:XZ:20100420:10:rectal mucosa:H3K36Me3.hg19.level.1
ANALYSIS TITLE: Mapping of Rectal Mucosa Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K36me3 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.4591
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: 0.1493
FINDPEAKS_PERCENTILE: 28
HOTSPOT_SCORE: 0.1942
HOTSPOT_PERCENTILE: 26
IROC_SCORE: 0.7714
IROC_PERCENTILE: 9
POISSON_SCORE: 0.4934
POISSON_PERCENTILE: 48

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

ANALYSIS FILE NAME: GSM621687_BI.Rectal_Mucosa.H3K36me3.31.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100503:10--ChIP:XZ:20100420:10:rectal mucosa:H3K36Me3.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Rectal Mucosa Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K36me3 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.4865
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 H3K36me3 31
BROWSER_TRACK_DESCRIPTION: BI Rectal Mucosa Histone H3K36me3 Donor 31 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED: 54
FINDPEAKS_SCORE: 0.1493
FINDPEAKS_PERCENTILE: 28
HOTSPOT_SCORE: 0.1942
HOTSPOT_PERCENTILE: 26
IROC_SCORE: 0.7714
IROC_PERCENTILE: 9
POISSON_SCORE: 0.4934
POISSON_PERCENTILE: 48

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

source_name: Primary rectal mucosal tissue; Lib:XZ:20100503:10--ChIP:XZ:20100420:10:rectal mucosa:H3K36Me3

value: "normal mucosa, diverticular disease"

value: genomic DNA

value: mucosa

value: rectum

value: Protein A-Sepharose 4B

value: 10 million cells

value: SDS lysis

value: 70 ul bed volume


title: ChIP-Seq analysis of H3K4me1 in Skeletal muscle cells; Lib:XZ:20100628:08--ChIP:XZ:20100621:08:Skeletal muscle:H3K4Me1

description:
sample_term_id: UBERON_0001134
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib:XZ:20100628:08--ChIP:XZ:20100621:08:Skeletal muscle:H3K4Me1
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.3270
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.3356
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************
BED and WIG files were replaced on April 29, 2014

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

ANALYSIS FILE NAME: GSM621686_BI.Skeletal_Muscle.H3K4me1.62.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100628:08--ChIP:XZ:20100621:08:Skeletal muscle:H3K4Me1.hg19.level.1
ANALYSIS TITLE: Mapping of Skeletal Muscle Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me1 ChIP-Seq on Skeletal Muscle, Donor 62 were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.4676
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: 0.3687
FINDPEAKS_PERCENTILE: 51
HOTSPOT_SCORE: 0.363
HOTSPOT_PERCENTILE: 44
IROC_SCORE: 0.9904
IROC_PERCENTILE: 64
POISSON_SCORE: 0.61
POISSON_PERCENTILE: 70

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

ANALYSIS FILE NAME: GSM621686_BI.Skeletal_Muscle.H3K4me1.62.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100628:08--ChIP:XZ:20100621:08:Skeletal muscle:H3K4Me1.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Skeletal Muscle Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me1 ChIP-Seq read mappings from Skeletal Muscle, Donor 62 were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.4950
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: SM H3K4me1 62
BROWSER_TRACK_DESCRIPTION: BI Skeletal Muscle Histone H3K4me1 Donor 62 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED: 43
FINDPEAKS_SCORE: 0.3687
FINDPEAKS_PERCENTILE: 51
HOTSPOT_SCORE: 0.363
HOTSPOT_PERCENTILE: 44
IROC_SCORE: 0.9904
IROC_PERCENTILE: 64
POISSON_SCORE: 0.61
POISSON_PERCENTILE: 70

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

source_name: Primary skeletal muscle tissue; Lib:XZ:20100628:08--ChIP:XZ:20100621:08:Skeletal muscle:H3K4Me1

value: surgery

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

value: Skeletal muscle

value: Female

value: unknown

value: 72 years

value: Histone H3K4me1