title: ChIP-Seq analysis of WCE in human kidney cells; DNA_Lib 341

description:
sample_term_id: UBERON_0002113
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 341
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8715
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.9455
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

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

ANALYSIS FILE NAME: GSM773025_BI.Adult_Kidney.Input.153.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 341-DNA_Lib 341-DNA_Lib 341-DNA_Lib 341.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of Adult Kidney ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina reads produced by ChIP-Seq Input on Adult Kidney, Donor 153, 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.10838
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 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 39,947,186
NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 56
FINDPEAKS_SCORE: 0.0047
FINDPEAKS_PERCENTILE: 34
HOTSPOT_SCORE: 0.0044
HOTSPOT_PERCENTILE: 23
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.0417
POISSON_PERCENTILE: 33
MAXIMUM_REPLICATE_CORRELATION: 0.93

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

ANALYSIS FILE NAME: GSM773025_BI.Adult_Kidney.Input.153.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 341-DNA_Lib 341-DNA_Lib 341-DNA_Lib 341.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of Adult Kidney ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina ChIP-Seq Input read mappings from Adult Kidney, Donor 153, 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.11102
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 5
BROWSER_TRACK_NAME: AK Input 53 41
BROWSER_TRACK_DESCRIPTION: BI Adult Kidney ChIP-Seq Input Donor 153 Library DNA_Lib 341 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 39,947,186
NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 56
FINDPEAKS_SCORE: 0.0047
FINDPEAKS_PERCENTILE: 34
HOTSPOT_SCORE: 0.0044
HOTSPOT_PERCENTILE: 23
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.0417
POISSON_PERCENTILE: 33
MAXIMUM_REPLICATE_CORRELATION: 0.93

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

source_name: Primary kidney tissue; DNA_Lib 341

value: standard

value: cell/nuclei lysis

value: ChIP-Seq Input

value: Input

value: Branson


title: ChIP-Seq analysis of H3K9me3 in human kidney cells; DNA_Lib 340

status: Public on Dec 28 2011

type: SRA

city: Cambridge

first: BROAD

last: INSTITUTE

state: MA

country: USA

institute: Broad Institute

description:
sample_term_id: UBERON_0002113
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 340
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8716
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.9455
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

library_source: genomic

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

ANALYSIS FILE NAME: GSM773026_BI.Adult_Kidney.H3K9me3.153.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 340-DNA_Lib 340-DNA_Lib 340-DNA_Lib 340.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of Adult Kidney Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K9me3 ChIP-Seq on Adult Kidney, Donor 153, 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.10620
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 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 32,596,430
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 49
FINDPEAKS_SCORE: 0.0268
FINDPEAKS_PERCENTILE: 45
HOTSPOT_SCORE: 0.0801
HOTSPOT_PERCENTILE: 31
IROC_SCORE: 0.8589
IROC_PERCENTILE: 59
POISSON_SCORE: 0.2005
POISSON_PERCENTILE: 37
MAXIMUM_REPLICATE_CORRELATION: 0.95

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

ANALYSIS FILE NAME: GSM773026_BI.Adult_Kidney.H3K9me3.153.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 340-DNA_Lib 340-DNA_Lib 340-DNA_Lib 340.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of Adult Kidney Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K9me3 ChIP-Seq read mappings from Adult Kidney, Donor 153, 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.10884
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 5
BROWSER_TRACK_NAME: AK H3K9me3 53 40
BROWSER_TRACK_DESCRIPTION: BI Adult Kidney Histone H3K9me3 Donor 153 Library DNA_Lib 340 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 32,596,430
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 49
FINDPEAKS_SCORE: 0.0268
FINDPEAKS_PERCENTILE: 45
HOTSPOT_SCORE: 0.0801
HOTSPOT_PERCENTILE: 31
IROC_SCORE: 0.8589
IROC_PERCENTILE: 59
POISSON_SCORE: 0.2005
POISSON_PERCENTILE: 37
MAXIMUM_REPLICATE_CORRELATION: 0.95

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

molecule: genomic DNA

organism: Homo sapiens

source_name: Primary kidney tissue; DNA_Lib 340

extract_protocol: Library construction protocol: Single read - Illumina

tag: sample alias

tag: sample common name

value: Adult Kidney

value: Surgery

value: NL kidney,right kidney resection for RCC

tag: molecule

value: genomic DNA

tag: disease

value: Caucasian

value: Male

value: Primary Tissue

value: Kidney

value: MGH

value: 50.0 Years

value: Protein A-Sepharose 4B

value: 0.5 to 3 million cells

value: ~1 ug

value: 10 ul bed volume

value: Abcam

value: Histone H3K9me3


title: ChIP-Seq analysis of WCE in human CD45RO CD8 cells; DNA_Lib 534

description:
sample_term_id: CL_0000909
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 534
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8642
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.9465
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

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

ANALYSIS FILE NAME: GSM772952_BI.CD8_Memory_Primary_Cells.Input.Donor_101_8_pooled_leukopaks_Jan_20_2011.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 534-DNA_Lib 534-DNA_Lib 534.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of CD8 Memory Primary Cells ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina reads produced by ChIP-Seq Input on CD8 Memory Primary Cells, Donor Donor 101 8 pooled leukopaks Jan 20 2011, 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.10767
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 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 28,412,499
NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 56
FINDPEAKS_SCORE: 0.0063
FINDPEAKS_PERCENTILE: 72
HOTSPOT_SCORE: 0.0166
HOTSPOT_PERCENTILE: 61
IROC_SCORE: 0.0
IROC_PERCENTILE: 33
POISSON_SCORE: 0.0645
POISSON_PERCENTILE: 61
MAXIMUM_REPLICATE_CORRELATION: 0.93

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

ANALYSIS FILE NAME: GSM772952_BI.CD8_Memory_Primary_Cells.Input.Donor_101_8_pooled_leukopaks_Jan_20_2011.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 534-DNA_Lib 534-DNA_Lib 534.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of CD8 Memory Primary Cells ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina ChIP-Seq Input read mappings from CD8 Memory Primary Cells, Donor Donor 101 8 pooled leukopaks Jan 20 2011, 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.11031
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 5
BROWSER_TRACK_NAME: CD8M Input 01 34
BROWSER_TRACK_DESCRIPTION: BI CD8 Memory Primary Cells ChIP-Seq Input Donor 101 8 pooled leukopaks Jan 20 2011 Library DNA_Lib 534 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 28,412,499
NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 56
FINDPEAKS_SCORE: 0.0063
FINDPEAKS_PERCENTILE: 72
HOTSPOT_SCORE: 0.0166
HOTSPOT_PERCENTILE: 61
IROC_SCORE: 0.0
IROC_PERCENTILE: 33
POISSON_SCORE: 0.0645
POISSON_PERCENTILE: 61
MAXIMUM_REPLICATE_CORRELATION: 0.93

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

source_name: Memory CD8+ T cells; DNA_Lib 534

value: BioSam 186

value: CD8 Memory Primary Cells

value: presumed normal

tag: markers

value: CD45RO CD8

value: Unknown

value: Primary Cell

value: Dana Farber

value: standard

value: cell/nuclei lysis

value: ChIP-Seq Input

value: Input

value: Branson


title: ChIP-Seq analysis of H3K9me3 in human CD45RO CD8 cells; DNA_Lib 533

description:
sample_term_id: CL_0000909
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 533
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8648
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.9465
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

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

ANALYSIS FILE NAME: GSM772958_BI.CD8_Memory_Primary_Cells.H3K9me3.Donor_101_8_pooled_leukopaks_Jan_20_2011.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 533-DNA_Lib 533-DNA_Lib 533.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of CD8 Memory Primary Cells Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K9me3 ChIP-Seq on CD8 Memory Primary Cells, Donor Donor 101 8 pooled leukopaks Jan 20 2011, 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.10589
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 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 24,741,704
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 49
FINDPEAKS_SCORE: 0.0155
FINDPEAKS_PERCENTILE: 20
HOTSPOT_SCORE: 0.0536
HOTSPOT_PERCENTILE: 14
IROC_SCORE: 0.9098
IROC_PERCENTILE: 84
POISSON_SCORE: 0.1232
POISSON_PERCENTILE: 10
MAXIMUM_REPLICATE_CORRELATION: 0.95

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

ANALYSIS FILE NAME: GSM772958_BI.CD8_Memory_Primary_Cells.H3K9me3.Donor_101_8_pooled_leukopaks_Jan_20_2011.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 533-DNA_Lib 533-DNA_Lib 533.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of CD8 Memory Primary Cells Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K9me3 ChIP-Seq read mappings from CD8 Memory Primary Cells, Donor Donor 101 8 pooled leukopaks Jan 20 2011, 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.10853
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 5
BROWSER_TRACK_NAME: CD8M H3K9me3 01 33
BROWSER_TRACK_DESCRIPTION: BI CD8 Memory Primary Cells Histone H3K9me3 Donor 101 8 pooled leukopaks Jan 20 2011 Library DNA_Lib 533 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 24,741,704
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 49
FINDPEAKS_SCORE: 0.0155
FINDPEAKS_PERCENTILE: 20
HOTSPOT_SCORE: 0.0536
HOTSPOT_PERCENTILE: 14
IROC_SCORE: 0.9098
IROC_PERCENTILE: 84
POISSON_SCORE: 0.1232
POISSON_PERCENTILE: 10
MAXIMUM_REPLICATE_CORRELATION: 0.95

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

source_name: Memory CD8+ T cells; DNA_Lib 533

value: genomic DNA

value: Protein A-Sepharose 4B

value: 0.5 to 3 million cells


title: ChIP-Seq analysis of H3K27me3 in human colon smooth muscle cells; DNA_Lib 327

description:
sample_term_id: UBERON_0012489
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 327
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8664
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.7505
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

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

ANALYSIS FILE NAME: GSM772974_BI.Colon_Smooth_Muscle.H3K27me3.Donor_83_REMC_18.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 327-DNA_Lib 327-DNA_Lib 327-DNA_Lib 327.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of Colon Smooth Muscle Histone H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K27me3 ChIP-Seq on Colon Smooth Muscle, Donor Donor 83 REMC 18, 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.10797
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 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 31,716,947
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 49
FINDPEAKS_SCORE: 0.0065
FINDPEAKS_PERCENTILE: 8
HOTSPOT_SCORE: 0.0381
HOTSPOT_PERCENTILE: 6
IROC_SCORE: 0.843
IROC_PERCENTILE: 57
POISSON_SCORE: 0.107
POISSON_PERCENTILE: 4
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM772974_BI.Colon_Smooth_Muscle.H3K27me3.Donor_83_REMC_18.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 327-DNA_Lib 327-DNA_Lib 327-DNA_Lib 327.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of Colon Smooth Muscle Histone H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K27me3 ChIP-Seq read mappings from Colon Smooth Muscle, Donor Donor 83 REMC 18, 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.11061
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 5
BROWSER_TRACK_NAME: CSM H3K27me3 83 27
BROWSER_TRACK_DESCRIPTION: BI Colon Smooth Muscle Histone H3K27me3 Donor 83 REMC 18 Library DNA_Lib 327 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 31,716,947
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 49
FINDPEAKS_SCORE: 0.0065
FINDPEAKS_PERCENTILE: 8
HOTSPOT_SCORE: 0.0381
HOTSPOT_PERCENTILE: 6
IROC_SCORE: 0.843
IROC_PERCENTILE: 57
POISSON_SCORE: 0.107
POISSON_PERCENTILE: 4
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: Primary colonic smooth muscle tissue; DNA_Lib 327

value: BioSam 156 REMC 18

value: Colon Smooth Muscle

value: surgery

value: NL smooth muscle, colon rsctn for Adeno CA of cecum

value: smooth muscle

value: caucasian

value: Female

value: Primary Tissue

value: colon

value: Donor 83 REMC 18

value: MGH Pathology

value: 77 years

value: ~1 ug

value: 10 ul bed volume

value: Millipore

value: Histone H3K27me3


title: ChIP-Seq analysis of H3K9ac in human colon smooth muscle cells; DNA_Lib 323

description:
sample_term_id: UBERON_0012489
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 323
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8660
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.7505
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

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

ANALYSIS FILE NAME: GSM772970_BI.Colon_Smooth_Muscle.H3K9ac.Donor_83_REMC_18.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 323-DNA_Lib 323-DNA_Lib 323-DNA_Lib 323.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of Colon Smooth Muscle Histone H3K9ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K9ac ChIP-Seq on Colon Smooth Muscle, Donor Donor 83 REMC 18, 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.10843
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 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 29,514,083
NUMBER_OF_H3K9ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 19
FINDPEAKS_SCORE: 0.0525
FINDPEAKS_PERCENTILE: 16
HOTSPOT_SCORE: 0.101
HOTSPOT_PERCENTILE: 16
IROC_SCORE: 0.9687
IROC_PERCENTILE: 16
POISSON_SCORE: 0.1556
POISSON_PERCENTILE: 16
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM772970_BI.Colon_Smooth_Muscle.H3K9ac.Donor_83_REMC_18.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 323-DNA_Lib 323-DNA_Lib 323-DNA_Lib 323.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of Colon Smooth Muscle Histone H3K9ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K9ac ChIP-Seq read mappings from Colon Smooth Muscle, Donor Donor 83 REMC 18, 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.11107
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 5
BROWSER_TRACK_NAME: CSM H3K9ac 83 23
BROWSER_TRACK_DESCRIPTION: BI Colon Smooth Muscle Histone H3K9ac Donor 83 REMC 18 Library DNA_Lib 323 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 29,514,083
NUMBER_OF_H3K9ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 19
FINDPEAKS_SCORE: 0.0525
FINDPEAKS_PERCENTILE: 16
HOTSPOT_SCORE: 0.101
HOTSPOT_PERCENTILE: 16
IROC_SCORE: 0.9687
IROC_PERCENTILE: 16
POISSON_SCORE: 0.1556
POISSON_PERCENTILE: 16
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: Primary colonic smooth muscle tissue; DNA_Lib 323

value: genomic DNA

value: Protein A-Sepharose 4B

value: 0.5 to 3 million cells

value: cell/nuclei lysis

value: Abcam

value: Histone H3K9ac

value: Branson


title: ChIP-Seq analysis of H3K36me3 in human CD45RO CD8 cells; DNA_Lib 532

description:
sample_term_id: CL_0000909
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 532
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8647
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.9465
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

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

ANALYSIS FILE NAME: GSM772957_BI.CD8_Memory_Primary_Cells.H3K36me3.Donor_101_8_pooled_leukopaks_Jan_20_2011.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 532-DNA_Lib 532-DNA_Lib 532.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of CD8 Memory Primary Cells Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K36me3 ChIP-Seq on CD8 Memory Primary Cells, Donor Donor 101 8 pooled leukopaks Jan 20 2011, 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.10613
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 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 18,034,578
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 49
FINDPEAKS_SCORE: 0.0651
FINDPEAKS_PERCENTILE: 31
HOTSPOT_SCORE: 0.1669
HOTSPOT_PERCENTILE: 31
IROC_SCORE: 0.8614
IROC_PERCENTILE: 20
POISSON_SCORE: 0.2953
POISSON_PERCENTILE: 24
MAXIMUM_REPLICATE_CORRELATION: 0.94

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

ANALYSIS FILE NAME: GSM772957_BI.CD8_Memory_Primary_Cells.H3K36me3.Donor_101_8_pooled_leukopaks_Jan_20_2011.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 532-DNA_Lib 532-DNA_Lib 532.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of CD8 Memory Primary Cells Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K36me3 ChIP-Seq read mappings from CD8 Memory Primary Cells, Donor Donor 101 8 pooled leukopaks Jan 20 2011, 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.10877
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 5
BROWSER_TRACK_NAME: CD8M H3K36me3 01 32
BROWSER_TRACK_DESCRIPTION: BI CD8 Memory Primary Cells Histone H3K36me3 Donor 101 8 pooled leukopaks Jan 20 2011 Library DNA_Lib 532 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 18,034,578
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 49
FINDPEAKS_SCORE: 0.0651
FINDPEAKS_PERCENTILE: 31
HOTSPOT_SCORE: 0.1669
HOTSPOT_PERCENTILE: 31
IROC_SCORE: 0.8614
IROC_PERCENTILE: 20
POISSON_SCORE: 0.2953
POISSON_PERCENTILE: 24
MAXIMUM_REPLICATE_CORRELATION: 0.94

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

source_name: Memory CD8+ T cells; DNA_Lib 532

value: BioSam 186

value: CD8 Memory Primary Cells

value: presumed normal

value: CD45RO CD8

value: Unknown

value: Primary Cell

value: Dana Farber

value: Histone H3K36me3


title: ChIP-Seq analysis of H3K36me3 in human colon smooth muscle cells; DNA_Lib 326

description:
sample_term_id: UBERON_0012489
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 326
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8665
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.7505
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

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

ANALYSIS FILE NAME: GSM772975_BI.Colon_Smooth_Muscle.H3K36me3.Donor_83_REMC_18.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 326-DNA_Lib 326-DNA_Lib 326-DNA_Lib 326.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of Colon Smooth Muscle Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K36me3 ChIP-Seq on Colon Smooth Muscle, Donor Donor 83 REMC 18, 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.10794
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 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 31,157,050
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 49
FINDPEAKS_SCORE: 0.0951
FINDPEAKS_PERCENTILE: 43
HOTSPOT_SCORE: 0.183
HOTSPOT_PERCENTILE: 39
IROC_SCORE: 0.9247
IROC_PERCENTILE: 49
POISSON_SCORE: 0.3704
POISSON_PERCENTILE: 47
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM772975_BI.Colon_Smooth_Muscle.H3K36me3.Donor_83_REMC_18.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 326-DNA_Lib 326-DNA_Lib 326-DNA_Lib 326.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of Colon Smooth Muscle Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K36me3 ChIP-Seq read mappings from Colon Smooth Muscle, Donor Donor 83 REMC 18, 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.11058
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 5
BROWSER_TRACK_NAME: CSM H3K36me3 83 26
BROWSER_TRACK_DESCRIPTION: BI Colon Smooth Muscle Histone H3K36me3 Donor 83 REMC 18 Library DNA_Lib 326 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 31,157,050
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 49
FINDPEAKS_SCORE: 0.0951
FINDPEAKS_PERCENTILE: 43
HOTSPOT_SCORE: 0.183
HOTSPOT_PERCENTILE: 39
IROC_SCORE: 0.9247
IROC_PERCENTILE: 49
POISSON_SCORE: 0.3704
POISSON_PERCENTILE: 47
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: Primary colonic smooth muscle tissue; DNA_Lib 326

value: BioSam 156 REMC 18

value: Colon Smooth Muscle

value: surgery

value: NL smooth muscle, colon rsctn for Adeno CA of cecum

value: smooth muscle

value: caucasian

value: Female

value: Primary Tissue

value: colon

value: Donor 83 REMC 18

value: MGH Pathology

value: 77 years

value: ~1 ug

value: 10 ul bed volume


title: ChIP-Seq analysis of H3K36me3 in human CD45RO CD4 cells; DNA_Lib 539

description:
sample_term_id: CL_0000897
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 539
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8654
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.9467
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

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

ANALYSIS FILE NAME: GSM772964_BI.CD4_Memory_Primary_Cells.H3K36me3.Donor_100_7_pooled_leukopaks_Jan_7_2011.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 539-DNA_Lib 539-DNA_Lib 539.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of CD4 Memory Primary Cells Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K36me3 ChIP-Seq on CD4 Memory Primary Cells, Donor Donor 100 7 pooled leukopaks Jan 7 2011, 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.10711
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 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 31,191,113
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 49
FINDPEAKS_SCORE: 0.0662
FINDPEAKS_PERCENTILE: 35
HOTSPOT_SCORE: 0.1505
HOTSPOT_PERCENTILE: 20
IROC_SCORE: 0.9131
IROC_PERCENTILE: 43
POISSON_SCORE: 0.3012
POISSON_PERCENTILE: 29
MAXIMUM_REPLICATE_CORRELATION: 0.89

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

ANALYSIS FILE NAME: GSM772964_BI.CD4_Memory_Primary_Cells.H3K36me3.Donor_100_7_pooled_leukopaks_Jan_7_2011.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 539-DNA_Lib 539-DNA_Lib 539.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of CD4 Memory Primary Cells Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K36me3 ChIP-Seq read mappings from CD4 Memory Primary Cells, Donor Donor 100 7 pooled leukopaks Jan 7 2011, 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.10975
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 5
BROWSER_TRACK_NAME: CD4M H3K36me3 00 39
BROWSER_TRACK_DESCRIPTION: BI CD4 Memory Primary Cells Histone H3K36me3 Donor 100 7 pooled leukopaks Jan 7 2011 Library DNA_Lib 539 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 31,191,113
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 49
FINDPEAKS_SCORE: 0.0662
FINDPEAKS_PERCENTILE: 35
HOTSPOT_SCORE: 0.1505
HOTSPOT_PERCENTILE: 20
IROC_SCORE: 0.9131
IROC_PERCENTILE: 43
POISSON_SCORE: 0.3012
POISSON_PERCENTILE: 29
MAXIMUM_REPLICATE_CORRELATION: 0.89

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

source_name: Memory CD4+ T cells; DNA_Lib 539

value: BioSam 181

value: CD4 Memory Primary Cells

value: presumed normal

value: genomic DNA

value: CD45RO CD4

value: Unknown

value: Primary Cell

value: Donor 100 7 pooled leukopaks Jan 7 2011

value: Protein A-Sepharose 4B

value: 0.5 to 3 million cells

value: cell/nuclei lysis

value: Abcam

value: Branson


title: ChIP-Seq analysis of H3K27me3 in human stomach mucosa cells; DNA_Lib 320

description:
sample_term_id: UBERON_0001199
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 320
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8659
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.9453
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

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

ANALYSIS FILE NAME: GSM772969_BI.Stomach_Mucosa.H3K27me3.157.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 320-DNA_Lib 320-DNA_Lib 320-DNA_Lib 320.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of Stomach Mucosa Histone H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K27me3 ChIP-Seq on Stomach Mucosa, Donor 157, 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.10813
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 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 30,608,614
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 49
FINDPEAKS_SCORE: 0.0489
FINDPEAKS_PERCENTILE: 59
HOTSPOT_SCORE: 0.111
HOTSPOT_PERCENTILE: 45
IROC_SCORE: 0.9566
IROC_PERCENTILE: 73
POISSON_SCORE: 0.2385
POISSON_PERCENTILE: 39
MAXIMUM_REPLICATE_CORRELATION: 0.83

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

ANALYSIS FILE NAME: GSM772969_BI.Stomach_Mucosa.H3K27me3.157.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 320-DNA_Lib 320-DNA_Lib 320-DNA_Lib 320.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of Stomach Mucosa Histone H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K27me3 ChIP-Seq read mappings from Stomach Mucosa, Donor 157, 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.11077
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 5
BROWSER_TRACK_NAME: SM H3K27me3 57 20
BROWSER_TRACK_DESCRIPTION: BI Stomach Mucosa Histone H3K27me3 Donor 157 Library DNA_Lib 320 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 30,608,614
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 49
FINDPEAKS_SCORE: 0.0489
FINDPEAKS_PERCENTILE: 59
HOTSPOT_SCORE: 0.111
HOTSPOT_PERCENTILE: 45
IROC_SCORE: 0.9566
IROC_PERCENTILE: 73
POISSON_SCORE: 0.2385
POISSON_PERCENTILE: 39
MAXIMUM_REPLICATE_CORRELATION: 0.83

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

source_name: Primary stomach mucosal tissue; DNA_Lib 320

value: Stomach Mucosa

value: Surgery

value: NK stomach mucosa, stomach rmvd as part of pancr. CA

value: Caucasian

value: Male

value: Primary Tissue

value: Stomach

value: MGH

value: 59.0 Years

value: Millipore

value: Histone H3K27me3


title: ChIP-Seq analysis of H3K27ac in human CD45RO CD4 cells; DNA_Lib 538

description:
sample_term_id: CL_0000897
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 538
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8653
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.9467
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

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

ANALYSIS FILE NAME: GSM772963_BI.CD4_Memory_Primary_Cells.H3K27ac.Donor_100_7_pooled_leukopaks_Jan_7_2011.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 538-DNA_Lib 538-DNA_Lib 538.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of CD4 Memory Primary Cells Histone H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K27ac ChIP-Seq on CD4 Memory Primary Cells, Donor Donor 100 7 pooled leukopaks Jan 7 2011, 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.10629
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 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 15,022,887
NUMBER_OF_H3K27ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 34
FINDPEAKS_SCORE: 0.4456
FINDPEAKS_PERCENTILE: 91
HOTSPOT_SCORE: 0.4878
HOTSPOT_PERCENTILE: 94
IROC_SCORE: 0.9952
IROC_PERCENTILE: 65
POISSON_SCORE: 0.5292
POISSON_PERCENTILE: 91
MAXIMUM_REPLICATE_CORRELATION: 0.88

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

ANALYSIS FILE NAME: GSM772963_BI.CD4_Memory_Primary_Cells.H3K27ac.Donor_100_7_pooled_leukopaks_Jan_7_2011.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 538-DNA_Lib 538-DNA_Lib 538.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of CD4 Memory Primary Cells Histone H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K27ac ChIP-Seq read mappings from CD4 Memory Primary Cells, Donor Donor 100 7 pooled leukopaks Jan 7 2011, 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.10893
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 5
BROWSER_TRACK_NAME: CD4M H3K27ac 00 38
BROWSER_TRACK_DESCRIPTION: BI CD4 Memory Primary Cells Histone H3K27ac Donor 100 7 pooled leukopaks Jan 7 2011 Library DNA_Lib 538 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 15,022,887
NUMBER_OF_H3K27ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 34
FINDPEAKS_SCORE: 0.4456
FINDPEAKS_PERCENTILE: 91
HOTSPOT_SCORE: 0.4878
HOTSPOT_PERCENTILE: 94
IROC_SCORE: 0.9952
IROC_PERCENTILE: 65
POISSON_SCORE: 0.5292
POISSON_PERCENTILE: 91
MAXIMUM_REPLICATE_CORRELATION: 0.88

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

source_name: Memory CD4+ T cells; DNA_Lib 538

value: BioSam 181

value: CD4 Memory Primary Cells

value: presumed normal

value: genomic DNA

value: CD45RO CD4

value: Unknown

value: Primary Cell

value: Donor 100 7 pooled leukopaks Jan 7 2011

value: Dana Farber

value: ~1 ug

value: 10 ul bed volume

value: Histone H3K27ac


title: ChIP-Seq analysis of H3K4me1 in human colon smooth muscle cells; DNA_Lib 325

description:
sample_term_id: UBERON_0012489
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 325
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8662
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.7505
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

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

ANALYSIS FILE NAME: GSM772972_BI.Colon_Smooth_Muscle.H3K4me1.Donor_83_REMC_18.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 325-DNA_Lib 325-DNA_Lib 325-DNA_Lib 325.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of Colon Smooth Muscle Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me1 ChIP-Seq on Colon Smooth Muscle, Donor Donor 83 REMC 18, 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.10841
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 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 34,917,453
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 54
FINDPEAKS_SCORE: 0.1579
FINDPEAKS_PERCENTILE: 24
HOTSPOT_SCORE: 0.2555
HOTSPOT_PERCENTILE: 22
IROC_SCORE: 0.9505
IROC_PERCENTILE: 31
POISSON_SCORE: 0.4338
POISSON_PERCENTILE: 41
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM772972_BI.Colon_Smooth_Muscle.H3K4me1.Donor_83_REMC_18.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 325-DNA_Lib 325-DNA_Lib 325-DNA_Lib 325.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of Colon Smooth Muscle Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me1 ChIP-Seq read mappings from Colon Smooth Muscle, Donor Donor 83 REMC 18, 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.11105
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 5
BROWSER_TRACK_NAME: CSM H3K4me1 83 25
BROWSER_TRACK_DESCRIPTION: BI Colon Smooth Muscle Histone H3K4me1 Donor 83 REMC 18 Library DNA_Lib 325 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 34,917,453
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 54
FINDPEAKS_SCORE: 0.1579
FINDPEAKS_PERCENTILE: 24
HOTSPOT_SCORE: 0.2555
HOTSPOT_PERCENTILE: 22
IROC_SCORE: 0.9505
IROC_PERCENTILE: 31
POISSON_SCORE: 0.4338
POISSON_PERCENTILE: 41
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: Primary colonic smooth muscle tissue; DNA_Lib 325

value: BioSam 156 REMC 18

value: Colon Smooth Muscle

value: surgery

value: NL smooth muscle, colon rsctn for Adeno CA of cecum

value: smooth muscle

value: caucasian

value: Female

value: Primary Tissue

value: colon

value: Donor 83 REMC 18

value: MGH Pathology

value: 77 years

value: Protein A-Sepharose 4B

value: 0.5 to 3 million cells

value: cell/nuclei lysis

value: Abcam

value: Histone H3K4me1

value: Branson


title: ChIP-Seq analysis of H3K27me3 in human CD45RO CD8 cells; DNA_Lib 531

description:
sample_term_id: CL_0000909
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 531
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8646
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.9465
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

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

ANALYSIS FILE NAME: GSM772956_BI.CD8_Memory_Primary_Cells.H3K27me3.Donor_101_8_pooled_leukopaks_Jan_20_2011.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 531-DNA_Lib 531-DNA_Lib 531.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of CD8 Memory Primary Cells Histone H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K27me3 ChIP-Seq on CD8 Memory Primary Cells, Donor Donor 101 8 pooled leukopaks Jan 20 2011, 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.10614
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 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 15,085,902
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 49
FINDPEAKS_SCORE: 0.0107
FINDPEAKS_PERCENTILE: 20
HOTSPOT_SCORE: 0.1079
HOTSPOT_PERCENTILE: 41
IROC_SCORE: 0.5167
IROC_PERCENTILE: 4
POISSON_SCORE: 0.1746
POISSON_PERCENTILE: 14
MAXIMUM_REPLICATE_CORRELATION: 0.82

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

ANALYSIS FILE NAME: GSM772956_BI.CD8_Memory_Primary_Cells.H3K27me3.Donor_101_8_pooled_leukopaks_Jan_20_2011.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 531-DNA_Lib 531-DNA_Lib 531.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of CD8 Memory Primary Cells Histone H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K27me3 ChIP-Seq read mappings from CD8 Memory Primary Cells, Donor Donor 101 8 pooled leukopaks Jan 20 2011, 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.10878
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 5
BROWSER_TRACK_NAME: CD8M H3K27me3 01 31
BROWSER_TRACK_DESCRIPTION: BI CD8 Memory Primary Cells Histone H3K27me3 Donor 101 8 pooled leukopaks Jan 20 2011 Library DNA_Lib 531 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 15,085,902
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 49
FINDPEAKS_SCORE: 0.0107
FINDPEAKS_PERCENTILE: 20
HOTSPOT_SCORE: 0.1079
HOTSPOT_PERCENTILE: 41
IROC_SCORE: 0.5167
IROC_PERCENTILE: 4
POISSON_SCORE: 0.1746
POISSON_PERCENTILE: 14
MAXIMUM_REPLICATE_CORRELATION: 0.82

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

source_name: Memory CD8+ T cells; DNA_Lib 531

value: BioSam 186

value: CD8 Memory Primary Cells

value: presumed normal

value: genomic DNA

value: CD45RO CD8

value: Unknown

value: Primary Cell

value: Dana Farber

value: ~1 ug

value: 10 ul bed volume

value: Millipore

value: Histone H3K27me3


title: ChIP-Seq analysis of H3K9me3 in human CD45RO CD4 cells; DNA_Lib 540

description:
sample_term_id: CL_0000897
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 540
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8656
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.9467
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

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

ANALYSIS FILE NAME: GSM772966_BI.CD4_Memory_Primary_Cells.H3K9me3.Donor_100_7_pooled_leukopaks_Jan_7_2011.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 540-DNA_Lib 540-DNA_Lib 540.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of CD4 Memory Primary Cells Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K9me3 ChIP-Seq on CD4 Memory Primary Cells, Donor Donor 100 7 pooled leukopaks Jan 7 2011, 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.10803
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 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 27,997,744
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 49
FINDPEAKS_SCORE: 0.0219
FINDPEAKS_PERCENTILE: 31
HOTSPOT_SCORE: 0.0739
HOTSPOT_PERCENTILE: 24
IROC_SCORE: 0.8443
IROC_PERCENTILE: 51
POISSON_SCORE: 0.1993
POISSON_PERCENTILE: 33
MAXIMUM_REPLICATE_CORRELATION: 0.93

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

ANALYSIS FILE NAME: GSM772966_BI.CD4_Memory_Primary_Cells.H3K9me3.Donor_100_7_pooled_leukopaks_Jan_7_2011.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 540-DNA_Lib 540-DNA_Lib 540.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of CD4 Memory Primary Cells Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K9me3 ChIP-Seq read mappings from CD4 Memory Primary Cells, Donor Donor 100 7 pooled leukopaks Jan 7 2011, 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.11067
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 5
BROWSER_TRACK_NAME: CD4M H3K9me3 00 40
BROWSER_TRACK_DESCRIPTION: BI CD4 Memory Primary Cells Histone H3K9me3 Donor 100 7 pooled leukopaks Jan 7 2011 Library DNA_Lib 540 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 27,997,744
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 49
FINDPEAKS_SCORE: 0.0219
FINDPEAKS_PERCENTILE: 31
HOTSPOT_SCORE: 0.0739
HOTSPOT_PERCENTILE: 24
IROC_SCORE: 0.8443
IROC_PERCENTILE: 51
POISSON_SCORE: 0.1993
POISSON_PERCENTILE: 33
MAXIMUM_REPLICATE_CORRELATION: 0.93

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

source_name: Memory CD4+ T cells; DNA_Lib 540

value: BioSam 181

value: CD4 Memory Primary Cells

value: CD45RO CD4

value: Donor 100 7 pooled leukopaks Jan 7 2011

value: Protein A-Sepharose 4B

value: 0.5 to 3 million cells

value: Histone H3K9me3


title: ChIP-Seq analysis of WCE in human colon smooth muscle cells; DNA_Lib 321

description:
sample_term_id: UBERON_0012489
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 321
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8658
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.7505
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

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

ANALYSIS FILE NAME: GSM772968_BI.Colon_Smooth_Muscle.Input.Donor_83_REMC_18.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 321-DNA_Lib 321-DNA_Lib 321-DNA_Lib 321.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of Colon Smooth Muscle ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina reads produced by ChIP-Seq Input on Colon Smooth Muscle, Donor Donor 83 REMC 18, 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.10612
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 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 57,055,650
NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 56
FINDPEAKS_SCORE: 0.0039
FINDPEAKS_PERCENTILE: 21
HOTSPOT_SCORE: 0.0023
HOTSPOT_PERCENTILE: 2
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.0178
POISSON_PERCENTILE: 2
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM772968_BI.Colon_Smooth_Muscle.Input.Donor_83_REMC_18.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 321-DNA_Lib 321-DNA_Lib 321-DNA_Lib 321.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of Colon Smooth Muscle ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina ChIP-Seq Input read mappings from Colon Smooth Muscle, Donor Donor 83 REMC 18, 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.10876
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 5
BROWSER_TRACK_NAME: CSM Input 83 21
BROWSER_TRACK_DESCRIPTION: BI Colon Smooth Muscle ChIP-Seq Input Donor 83 REMC 18 Library DNA_Lib 321 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 57,055,650
NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 56
FINDPEAKS_SCORE: 0.0039
FINDPEAKS_PERCENTILE: 21
HOTSPOT_SCORE: 0.0023
HOTSPOT_PERCENTILE: 2
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.0178
POISSON_PERCENTILE: 2
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: Primary colonic smooth muscle tissue; DNA_Lib 321

value: BioSam 156 REMC 18

value: Colon Smooth Muscle

value: surgery

value: NL smooth muscle, colon rsctn for Adeno CA of cecum

value: smooth muscle

value: caucasian

value: Female

value: Primary Tissue

value: colon

value: Donor 83 REMC 18

value: MGH Pathology

value: 77 years

value: standard

value: cell/nuclei lysis

value: ChIP-Seq Input

value: Input

value: Branson


title: ChIP-Seq analysis of WCE in human stomach mucosa cells; DNA_Lib 314

description:
sample_term_id: UBERON_0001199
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 314
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8629
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.9453
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

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

ANALYSIS FILE NAME: GSM772939_BI.Stomach_Mucosa.Input.157.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 314-DNA_Lib 314-DNA_Lib 314-DNA_Lib 314.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of Stomach Mucosa ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina reads produced by ChIP-Seq Input on Stomach Mucosa, Donor 157, 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.10782
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 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 35,935,095
NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 56
FINDPEAKS_SCORE: 0.0049
FINDPEAKS_PERCENTILE: 39
HOTSPOT_SCORE: 0.0049
HOTSPOT_PERCENTILE: 30
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.0419
POISSON_PERCENTILE: 34
MAXIMUM_REPLICATE_CORRELATION: 0.9

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

ANALYSIS FILE NAME: GSM772939_BI.Stomach_Mucosa.Input.157.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 314-DNA_Lib 314-DNA_Lib 314-DNA_Lib 314.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of Stomach Mucosa ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina ChIP-Seq Input read mappings from Stomach Mucosa, Donor 157, 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.11046
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 5
BROWSER_TRACK_NAME: SM Input 57 14
BROWSER_TRACK_DESCRIPTION: BI Stomach Mucosa ChIP-Seq Input Donor 157 Library DNA_Lib 314 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 35,935,095
NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 56
FINDPEAKS_SCORE: 0.0049
FINDPEAKS_PERCENTILE: 39
HOTSPOT_SCORE: 0.0049
HOTSPOT_PERCENTILE: 30
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.0419
POISSON_PERCENTILE: 34
MAXIMUM_REPLICATE_CORRELATION: 0.9

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

source_name: Primary stomach mucosal tissue; DNA_Lib 314

value: Stomach Mucosa

value: Surgery

value: NK stomach mucosa, stomach rmvd as part of pancr. CA

value: genomic DNA

value: Caucasian

value: Male

value: Stomach

value: MGH

value: 59.0 Years


title: ChIP-Seq analysis of H3K9ac in human stomach mucosa cells; DNA_Lib 316

description:
sample_term_id: UBERON_0001199
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 316
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8631
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.9453
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

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

ANALYSIS FILE NAME: GSM772941_BI.Stomach_Mucosa.H3K9ac.157.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 316-DNA_Lib 316-DNA_Lib 316-DNA_Lib 316.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of Stomach Mucosa Histone H3K9ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K9ac ChIP-Seq on Stomach Mucosa, Donor 157, 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.10757
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 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 26,963,346
NUMBER_OF_H3K9ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 19
FINDPEAKS_SCORE: 0.1758
FINDPEAKS_PERCENTILE: 53
HOTSPOT_SCORE: 0.2287
HOTSPOT_PERCENTILE: 47
IROC_SCORE: 0.997
IROC_PERCENTILE: 79
POISSON_SCORE: 0.2923
POISSON_PERCENTILE: 53
MAXIMUM_REPLICATE_CORRELATION: 0.47

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

ANALYSIS FILE NAME: GSM772941_BI.Stomach_Mucosa.H3K9ac.157.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 316-DNA_Lib 316-DNA_Lib 316-DNA_Lib 316.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of Stomach Mucosa Histone H3K9ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K9ac ChIP-Seq read mappings from Stomach Mucosa, Donor 157, 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.11021
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 5
BROWSER_TRACK_NAME: SM H3K9ac 57 16
BROWSER_TRACK_DESCRIPTION: BI Stomach Mucosa Histone H3K9ac Donor 157 Library DNA_Lib 316 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 26,963,346
NUMBER_OF_H3K9ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 19
FINDPEAKS_SCORE: 0.1758
FINDPEAKS_PERCENTILE: 53
HOTSPOT_SCORE: 0.2287
HOTSPOT_PERCENTILE: 47
IROC_SCORE: 0.997
IROC_PERCENTILE: 79
POISSON_SCORE: 0.2923
POISSON_PERCENTILE: 53
MAXIMUM_REPLICATE_CORRELATION: 0.47

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

source_name: Primary stomach mucosal tissue; DNA_Lib 316

value: Primary Tissue

value: Protein A-Sepharose 4B

value: 0.5 to 3 million cells

value: ~1 ug

value: 10 ul bed volume

value: Abcam

value: Histone H3K9ac


title: ChIP-Seq analysis of H3K4me3 in human stomach mucosa cells; DNA_Lib 317

description:
sample_term_id: UBERON_0001199
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 317
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8632
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.9453
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

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

ANALYSIS FILE NAME: GSM772942_BI.Stomach_Mucosa.H3K4me3.157.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 317-DNA_Lib 317-DNA_Lib 317-DNA_Lib 317.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of Stomach Mucosa Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me3 ChIP-Seq on Stomach Mucosa, Donor 157, 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.10630
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 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 23,997,237
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 54
FINDPEAKS_SCORE: 0.0722
FINDPEAKS_PERCENTILE: 7
HOTSPOT_SCORE: 0.1282
HOTSPOT_PERCENTILE: 7
IROC_SCORE: 0.984
IROC_PERCENTILE: 20
POISSON_SCORE: 0.176
POISSON_PERCENTILE: 6
MAXIMUM_REPLICATE_CORRELATION: 0.75

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

ANALYSIS FILE NAME: GSM772942_BI.Stomach_Mucosa.H3K4me3.157.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 317-DNA_Lib 317-DNA_Lib 317-DNA_Lib 317.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of Stomach Mucosa Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me3 ChIP-Seq read mappings from Stomach Mucosa, Donor 157, 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.10894
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 5
BROWSER_TRACK_NAME: SM H3K4me3 57 17
BROWSER_TRACK_DESCRIPTION: BI Stomach Mucosa Histone H3K4me3 Donor 157 Library DNA_Lib 317 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 23,997,237
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 54
FINDPEAKS_SCORE: 0.0722
FINDPEAKS_PERCENTILE: 7
HOTSPOT_SCORE: 0.1282
HOTSPOT_PERCENTILE: 7
IROC_SCORE: 0.984
IROC_PERCENTILE: 20
POISSON_SCORE: 0.176
POISSON_PERCENTILE: 6
MAXIMUM_REPLICATE_CORRELATION: 0.75

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

source_name: Primary stomach mucosal tissue; DNA_Lib 317

value: cell/nuclei lysis

value: Millipore

value: Histone H3K4me3

value: Branson


title: Normal Breast Sample [ATM_7]

status: Public on Feb 01 2012

type: RNA

first: Ana Teresa

last: Maia

state: Cambridgeshire

address: Robinson Way

department: Department of Oncology

country: United Kingdom

institute: University of Cambridge

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The bead-level data were preprocessed using BASH (Cairns et al. (2008) Bioinformatics 24(24):2921-2), a function from the beadarray package (Dunning et al (2007) Bioinformatics 23(16):2183-4) in Bioconductor, and also log base 2 transformed and quantile normalised using the beadarray package.

label: biotin

molecule: total RNA

source_name: Normal Breast Sample

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina

extract_protocol: Total RNA was extracted from all samples using Qiazol (Invitrogen, Carlsbad, CA, USA) following manufacturer's instructions. The RNA was subsequently treated with DNaseI and repurified using acidic phenol-chlorophorm, and ethanol precipitation. DNA and RNA integrity were checked using the Agilent Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).

tag: tissue

value: breast

tag: gender

value: female


title: ChIP-Seq analysis of H3K36me3 in human stomach mucosa cells; DNA_Lib 319

description:
sample_term_id: UBERON_0001199
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 319
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8626
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.9453
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

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

ANALYSIS FILE NAME: GSM772936_BI.Stomach_Mucosa.H3K36me3.157.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 319-DNA_Lib 319-DNA_Lib 319-DNA_Lib 319.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of Stomach Mucosa Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K36me3 ChIP-Seq on Stomach Mucosa, Donor 157, 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.10760
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 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 33,363,481
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 49
FINDPEAKS_SCORE: 0.0049
FINDPEAKS_PERCENTILE: 4
HOTSPOT_SCORE: 0.0598
HOTSPOT_PERCENTILE: 4
IROC_SCORE: 0.6016
IROC_PERCENTILE: 2
POISSON_SCORE: 0.1785
POISSON_PERCENTILE: 6
MAXIMUM_REPLICATE_CORRELATION: 0.8

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

ANALYSIS FILE NAME: GSM772936_BI.Stomach_Mucosa.H3K36me3.157.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 319-DNA_Lib 319-DNA_Lib 319-DNA_Lib 319.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of Stomach Mucosa Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K36me3 ChIP-Seq read mappings from Stomach Mucosa, Donor 157, 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.11024
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 5
BROWSER_TRACK_NAME: SM H3K36me3 57 19
BROWSER_TRACK_DESCRIPTION: BI Stomach Mucosa Histone H3K36me3 Donor 157 Library DNA_Lib 319 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 33,363,481
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 49
FINDPEAKS_SCORE: 0.0049
FINDPEAKS_PERCENTILE: 4
HOTSPOT_SCORE: 0.0598
HOTSPOT_PERCENTILE: 4
IROC_SCORE: 0.6016
IROC_PERCENTILE: 2
POISSON_SCORE: 0.1785
POISSON_PERCENTILE: 6
MAXIMUM_REPLICATE_CORRELATION: 0.8

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

source_name: Primary stomach mucosal tissue; DNA_Lib 319

value: Stomach Mucosa

value: Surgery

value: NK stomach mucosa, stomach rmvd as part of pancr. CA

value: genomic DNA

value: Caucasian

value: Male

value: Histone H3K36me3


title: Normal Breast Sample [ATM_5]


title: ChIP-Seq analysis of WCE in human CD45RO CD4 cells; DNA_Lib 487

description:
sample_term_id: CL_0000897
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 487
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8620
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.9464
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

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

ANALYSIS FILE NAME: GSM772930_BI.CD4_Memory_Primary_Cells.Input.Donor_101_8_pooled_leukopaks_Jan_20_2011.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 487-DNA_Lib 487-DNA_Lib 487-DNA_Lib 487.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of CD4 Memory Primary Cells ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina reads produced by ChIP-Seq Input on CD4 Memory Primary Cells, Donor Donor 101 8 pooled leukopaks Jan 20 2011, 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.10615
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 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 35,187,187
NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 56
FINDPEAKS_SCORE: 0.0053
FINDPEAKS_PERCENTILE: 52
HOTSPOT_SCORE: 0.0048
HOTSPOT_PERCENTILE: 28
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.0364
POISSON_PERCENTILE: 26
MAXIMUM_REPLICATE_CORRELATION: 0.96

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

ANALYSIS FILE NAME: GSM772930_BI.CD4_Memory_Primary_Cells.Input.Donor_101_8_pooled_leukopaks_Jan_20_2011.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 487-DNA_Lib 487-DNA_Lib 487-DNA_Lib 487.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of CD4 Memory Primary Cells ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina ChIP-Seq Input read mappings from CD4 Memory Primary Cells, Donor Donor 101 8 pooled leukopaks Jan 20 2011, 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.10879
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 5
BROWSER_TRACK_NAME: CD4M Input 01 87
BROWSER_TRACK_DESCRIPTION: BI CD4 Memory Primary Cells ChIP-Seq Input Donor 101 8 pooled leukopaks Jan 20 2011 Library DNA_Lib 487 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 35,187,187
NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 56
FINDPEAKS_SCORE: 0.0053
FINDPEAKS_PERCENTILE: 52
HOTSPOT_SCORE: 0.0048
HOTSPOT_PERCENTILE: 28
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.0364
POISSON_PERCENTILE: 26
MAXIMUM_REPLICATE_CORRELATION: 0.96

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

source_name: Memory CD4+ T cells; DNA_Lib 487

value: BioSam 185

value: CD4 Memory Primary Cells

value: presumed normal

value: CD45RO CD4

value: Unknown

value: Primary Cell

value: Dana Farber

value: standard

value: ChIP-Seq Input

value: Input


title: ChIP-Seq analysis of H3K36me3 in human CD45RO CD4 cells; DNA_Lib 483

description:
sample_term_id: CL_0000897
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 483
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8616
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.9464
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

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

ANALYSIS FILE NAME: GSM772926_BI.CD4_Memory_Primary_Cells.H3K36me3.Donor_101_8_pooled_leukopaks_Jan_20_2011.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 483-DNA_Lib 483-DNA_Lib 483-DNA_Lib 483.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of CD4 Memory Primary Cells Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K36me3 ChIP-Seq on CD4 Memory Primary Cells, Donor Donor 101 8 pooled leukopaks Jan 20 2011, 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.10736
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 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 26,809,321
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 49
FINDPEAKS_SCORE: 0.0063
FINDPEAKS_PERCENTILE: 6
HOTSPOT_SCORE: 0.0641
HOTSPOT_PERCENTILE: 6
IROC_SCORE: 0.6196
IROC_PERCENTILE: 4
POISSON_SCORE: 0.1647
POISSON_PERCENTILE: 4
MAXIMUM_REPLICATE_CORRELATION: 0.89

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

ANALYSIS FILE NAME: GSM772926_BI.CD4_Memory_Primary_Cells.H3K36me3.Donor_101_8_pooled_leukopaks_Jan_20_2011.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 483-DNA_Lib 483-DNA_Lib 483-DNA_Lib 483.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of CD4 Memory Primary Cells Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K36me3 ChIP-Seq read mappings from CD4 Memory Primary Cells, Donor Donor 101 8 pooled leukopaks Jan 20 2011, 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.11000
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 5
BROWSER_TRACK_NAME: CD4M H3K36me3 01 83
BROWSER_TRACK_DESCRIPTION: BI CD4 Memory Primary Cells Histone H3K36me3 Donor 101 8 pooled leukopaks Jan 20 2011 Library DNA_Lib 483 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 26,809,321
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 49
FINDPEAKS_SCORE: 0.0063
FINDPEAKS_PERCENTILE: 6
HOTSPOT_SCORE: 0.0641
HOTSPOT_PERCENTILE: 6
IROC_SCORE: 0.6196
IROC_PERCENTILE: 4
POISSON_SCORE: 0.1647
POISSON_PERCENTILE: 4
MAXIMUM_REPLICATE_CORRELATION: 0.89

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

source_name: Memory CD4+ T cells; DNA_Lib 483

value: Protein A-Sepharose 4B

value: 0.5 to 3 million cells

value: cell/nuclei lysis

value: ~1 ug

value: 10 ul bed volume

value: Abcam

value: Branson


title: Normal Breast Sample [ATM_4]

value: breast

value: female


title: ChIP-Seq analysis of H3K9me3 in human stomach mucosa cells; DNA_Lib 315

description:
sample_term_id: UBERON_0001199
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 315
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8630
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.9453
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

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

ANALYSIS FILE NAME: GSM772940_BI.Stomach_Mucosa.H3K9me3.157.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 315-DNA_Lib 315-DNA_Lib 315-DNA_Lib 315.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of Stomach Mucosa Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K9me3 ChIP-Seq on Stomach Mucosa, Donor 157, 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.10710
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 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 20,940,784
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 49
FINDPEAKS_SCORE: 0.0132
FINDPEAKS_PERCENTILE: 8
HOTSPOT_SCORE: 0.052
HOTSPOT_PERCENTILE: 12
IROC_SCORE: 0.9092
IROC_PERCENTILE: 82
POISSON_SCORE: 0.1074
POISSON_PERCENTILE: 2
MAXIMUM_REPLICATE_CORRELATION: 0.86

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

ANALYSIS FILE NAME: GSM772940_BI.Stomach_Mucosa.H3K9me3.157.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 315-DNA_Lib 315-DNA_Lib 315-DNA_Lib 315.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of Stomach Mucosa Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K9me3 ChIP-Seq read mappings from Stomach Mucosa, Donor 157, 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.10974
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 5
BROWSER_TRACK_NAME: SM H3K9me3 57 15
BROWSER_TRACK_DESCRIPTION: BI Stomach Mucosa Histone H3K9me3 Donor 157 Library DNA_Lib 315 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 20,940,784
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 49
FINDPEAKS_SCORE: 0.0132
FINDPEAKS_PERCENTILE: 8
HOTSPOT_SCORE: 0.052
HOTSPOT_PERCENTILE: 12
IROC_SCORE: 0.9092
IROC_PERCENTILE: 82
POISSON_SCORE: 0.1074
POISSON_PERCENTILE: 2
MAXIMUM_REPLICATE_CORRELATION: 0.86

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

source_name: Primary stomach mucosal tissue; DNA_Lib 315

value: Stomach Mucosa

value: Surgery

value: NK stomach mucosa, stomach rmvd as part of pancr. CA

value: genomic DNA

value: Caucasian

value: Male

value: Primary Tissue

value: Stomach

value: MGH

value: 59.0 Years

value: Histone H3K9me3


title: Normal Breast Sample [ATM_3]


title: Normal Breast Sample [ATM_1]


title: Normal Breast Sample [ATM_2]