title: Reference Epigenome: ChIP-Seq Analysis of H3K36me3 in Human Small Bowel Tissue; renlab.H3K36me3.STL001SB.01.01

description:
sample_term_id: UBERON_0002108
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K36me3 in Human Small Bowel Tissue. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: AK327
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.12251
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.12250
****************
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: GSM910565_UCSD.Small_Intestine.H3K36me3.STL001.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K36me3.STL001SB.01.01.hg19.level.1.release.8
ANALYSIS TITLE: Mapping of Small Intestine H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K36me3 ChIP-Seq on Small Intestine, Donor STL001, 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.13523
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 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 8,458,906
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 12
FINDPEAKS_SCORE: 0.2054
FINDPEAKS_PERCENTILE: 42
HOTSPOT_SCORE: 0.326
HOTSPOT_PERCENTILE: 42
IROC_SCORE: 0.9434
IROC_PERCENTILE: 17
POISSON_SCORE: 0.441
POISSON_PERCENTILE: 42
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM910565_UCSD.Small_Intestine.H3K36me3.STL001.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K36me3.STL001SB.01.01.hg19.level.2.release.8
ANALYSIS TITLE: Raw Signal Density Graphs of Small Intestine H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K36me3 ChIP-Seq read mappings from Small Intestine, Donor STL001, 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.13643
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 8
BROWSER_TRACK_NAME: SI H3K36me3 01 27
BROWSER_TRACK_DESCRIPTION: UCSD Small Intestine Histone H3K36me3 Donor STL001 Library AK327 EA Release 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 8,458,906
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 12
FINDPEAKS_SCORE: 0.2054
FINDPEAKS_PERCENTILE: 42
HOTSPOT_SCORE: 0.326
HOTSPOT_PERCENTILE: 42
IROC_SCORE: 0.9434
IROC_PERCENTILE: 17
POISSON_SCORE: 0.441
POISSON_PERCENTILE: 42
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: Small Intestine tissue; renlab.H3K36me3.STL001SB.01.01

value: Small Intestine

value: healthy, no prior medical history (NO diabetes, hypertension, coronary artery disease, cancer)

value: Male

value: Caucasian and African American

value: Histone H3K36me3

value: Abcam


title: Reference Epigenome: ChIP-Seq Analysis of H3K27me3 in Human Sigmoid Colon Tissue; renlab.H3K27me3.STL003SG.01.01

status: Public on Jul 12 2012

type: SRA

city: La Jolla

first: UCSD AND

last: SALK

state: CA

address: Health Sciences Drive

country: USA

institute: University of California, San Diego

description:
sample_term_id: UBERON_0001159
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K27me3 in Human Sigmoid Colon Tissue. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: AY95
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.12227
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.11872
****************
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: GSM910564_UCSD.Sigmoid_Colon.H3K27me3.STL003.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K27me3.STL003SG.01.01.hg19.level.1.release.8
ANALYSIS TITLE: Mapping of Sigmoid Colon H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K27me3 ChIP-Seq on Sigmoid Colon, Donor STL003, 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.13513
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 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 16,923,598
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 19
FINDPEAKS_SCORE: 0.0872
FINDPEAKS_PERCENTILE: 74
HOTSPOT_SCORE: 0.253
HOTSPOT_PERCENTILE: 74
IROC_SCORE: 0.8544
IROC_PERCENTILE: 47
POISSON_SCORE: 0.4207
POISSON_PERCENTILE: 79
MAXIMUM_REPLICATE_CORRELATION: 0.97

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

ANALYSIS FILE NAME: GSM910564_UCSD.Sigmoid_Colon.H3K27me3.STL003.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K27me3.STL003SG.01.01.hg19.level.2.release.8
ANALYSIS TITLE: Raw Signal Density Graphs of Sigmoid Colon H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K27me3 ChIP-Seq read mappings from Sigmoid Colon, Donor STL003, 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.13633
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 8
BROWSER_TRACK_NAME: SC H3K27me3 03 95
BROWSER_TRACK_DESCRIPTION: UCSD Sigmoid Colon Histone H3K27me3 Donor STL003 Library AY95 EA Release 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 16,923,598
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 19
FINDPEAKS_SCORE: 0.0872
FINDPEAKS_PERCENTILE: 74
HOTSPOT_SCORE: 0.253
HOTSPOT_PERCENTILE: 74
IROC_SCORE: 0.8544
IROC_PERCENTILE: 47
POISSON_SCORE: 0.4207
POISSON_PERCENTILE: 79
MAXIMUM_REPLICATE_CORRELATION: 0.97

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

molecule: genomic DNA

organism: Homo sapiens

source_name: Sigmoid Colon tissue; renlab.H3K27me3.STL003SG.01.01

extract_protocol: Library construction protocol: See http://bioinformatics-renlab.ucsd.edu/RenLabLibraryProtocolV1.pdf

tag: sample alias

tag: sample common name

value: Sigmoid Colon

tag: molecule

value: genomic DNA

tag: disease

value: Shin Lin, Stanford University

value: Primary Tissue

value: Autopsy

value: polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)

value: Caucasian

value: Histone H3K27me3

value: Biorupter

value: 500 micrograms

value: magnetic anti-rabbit

value: 5 micrograms

value: Active Motif


title: Reference Epigenome: ChIP-Seq Analysis of H3K9me3 in Human Spleen Tissue; renlab.H3K9me3.STL003SX.01.01

description:
sample_term_id: UBERON_0002106
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K9me3 in Human Spleen Tissue. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: AY196
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.12235
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.11852
****************
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: GSM910588_UCSD.Spleen.H3K9me3.STL003.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K9me3.STL003SX.01.01.hg19.level.1.release.8
ANALYSIS TITLE: Mapping of Spleen H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K9me3 ChIP-Seq on Spleen, Donor STL003, 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.13440
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 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 14,340,530
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 16
FINDPEAKS_SCORE: 0.1822
FINDPEAKS_PERCENTILE: 63
HOTSPOT_SCORE: 0.3137
HOTSPOT_PERCENTILE: 69
IROC_SCORE: 0.8945
IROC_PERCENTILE: 63
POISSON_SCORE: 0.4165
POISSON_PERCENTILE: 38
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM910588_UCSD.Spleen.H3K9me3.STL003.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K9me3.STL003SX.01.01.hg19.level.2.release.8
ANALYSIS TITLE: Raw Signal Density Graphs of Spleen H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K9me3 ChIP-Seq read mappings from Spleen, Donor STL003, 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.13560
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 8
BROWSER_TRACK_NAME: Spleen H3K9me3 03 96
BROWSER_TRACK_DESCRIPTION: UCSD Spleen Histone H3K9me3 Donor STL003 Library AY196 EA Release 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 14,340,530
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 16
FINDPEAKS_SCORE: 0.1822
FINDPEAKS_PERCENTILE: 63
HOTSPOT_SCORE: 0.3137
HOTSPOT_PERCENTILE: 69
IROC_SCORE: 0.8945
IROC_PERCENTILE: 63
POISSON_SCORE: 0.4165
POISSON_PERCENTILE: 38
MAXIMUM_REPLICATE_CORRELATION: NA

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

value: Spleen

value: Male

value: Histone H3K9me3


city: San Francisco

first: UCSF-UBC

last: CENTER

address: UCSF-UBC

institute: UCSF-UBC

description:
design description: ChIP-Seq input analysis of peripheral cd8 naive from TC001 (HS2846) using Illumina Genome Analyzer IIx
library name: HS2846
EXPERIMENT_TYPE: ChIP-Seq Input
EXTRACTION_PROTOCOL: Refer to document 'REMC ChIP and Library Construction Protocol' from the Farnham Lab at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
EXTRACTION_PROTOCOL_TYPE_OF_SONICATOR: Bioruptor
EXTRACTION_PROTOCOL_SONICATION_CYCLES: 30 min
CHIP_PROTOCOL: Input
CHIP_PROTOCOL_CHROMATIN_AMOUNT: 0.2 ug
SIZE_FRACTION: 80-1880 bp
****************
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: GSM959126_UCSF-UBC.CD8_Naive_Primary_Cells.Input.TC001.HS2846.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: HS2846-1.hg19.level.1.release.8
ANALYSIS TITLE: Mapping of CD8 Naive Primary Cells Input ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Input ChIP-Seq on CD8 Naive Primary Cells, Donor TC001 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.13423
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 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 17,290,432
NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 19
FINDPEAKS_SCORE: 0.0256
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.1398
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.598
IROC_PERCENTILE: 100
POISSON_SCORE: 0.2031
POISSON_PERCENTILE: 100
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

ANALYSIS FILE NAME: GSM959126_UCSF-UBC.CD8_Naive_Primary_Cells.Input.TC001.HS2846.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: HS2846-1.hg19.level.2.release.8
ANALYSIS TITLE: Raw Signal Density Graphs of CD8 Naive Primary Cells Input ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Input ChIP-Seq read mappings from CD8 Naive Primary Cells, Donor TC001 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.13432
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 8
BROWSER_TRACK_NAME: CD8N Input 01 46
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC CD8 Naive Primary Cells ChIP-Seq Input Donor TC001 Library HS2846 EA Release 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 17,290,432
NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 19
FINDPEAKS_SCORE: 0.0256
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.1398
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.598
IROC_PERCENTILE: 100
POISSON_SCORE: 0.2031
POISSON_PERCENTILE: 100
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

extract_protocol: library construction protocol: Refer to document 'REMC ChIP and Library Construction Protocol' from the Farnham Lab at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)

tag: submitted sample id

tag: Sex

value: male

tag: body site

value: Blood

tag: histological type

value: CD8 naive cell

tag: is tumor

value: No

value: primary cell


title: Reference Epigenome: ChIP-Seq Analysis of H3K4me1 in Human Gastric Tissue; renlab.H3K4me1.STL003GA.01.01

description:
sample_term_id: UBERON_0000945
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K4me1 in Human Gastric Tissue. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: AY187
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.12241
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.12180
****************
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: GSM910574_UCSD.Gastric.H3K4me1.STL003.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K4me1.STL003GA.01.01.hg19.level.1.release.8
ANALYSIS TITLE: Mapping of Gastric H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K4me1 ChIP-Seq on Gastric, Donor STL003, 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.13520
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 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 25,227,243
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 12
FINDPEAKS_SCORE: 0.1285
FINDPEAKS_PERCENTILE: 25
HOTSPOT_SCORE: 0.2542
HOTSPOT_PERCENTILE: 25
IROC_SCORE: 0.8917
IROC_PERCENTILE: 17
POISSON_SCORE: 0.4076
POISSON_PERCENTILE: 25
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM910574_UCSD.Gastric.H3K4me1.STL003.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K4me1.STL003GA.01.01.hg19.level.2.release.8
ANALYSIS TITLE: Raw Signal Density Graphs of Gastric H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K4me1 ChIP-Seq read mappings from Gastric, Donor STL003, 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.13640
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 8
BROWSER_TRACK_NAME: Gastric H3K4me1 03 87
BROWSER_TRACK_DESCRIPTION: UCSD Gastric Histone H3K4me1 Donor STL003 Library AY187 EA Release 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 25,227,243
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 12
FINDPEAKS_SCORE: 0.1285
FINDPEAKS_PERCENTILE: 25
HOTSPOT_SCORE: 0.2542
HOTSPOT_PERCENTILE: 25
IROC_SCORE: 0.8917
IROC_PERCENTILE: 17
POISSON_SCORE: 0.4076
POISSON_PERCENTILE: 25
MAXIMUM_REPLICATE_CORRELATION: NA

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

value: Gastric

value: genomic DNA

value: Shin Lin, Stanford University

value: Primary Tissue

value: Autopsy

value: Histone H3K4me1

value: Abcam


title: Reference Epigenome: ChIP-Seq Analysis of H3K4me1 in Human Pancreas Tissue; renlab.H3K4me1.STL003PA.01.01

description:
sample_term_id: UBERON_0001264
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K4me1 in Human Pancreas Tissue. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: AK191
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.12209
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.11847
****************
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: GSM910576_UCSD.Pancreas.H3K4me1.STL003.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K4me1.STL003PA.01.01.hg19.level.1.release.8
ANALYSIS TITLE: Mapping of Pancreas H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K4me1 ChIP-Seq on Pancreas, Donor STL003, 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.13486
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 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 27,843,884
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 12
FINDPEAKS_SCORE: 0.273
FINDPEAKS_PERCENTILE: 50
HOTSPOT_SCORE: 0.3764
HOTSPOT_PERCENTILE: 50
IROC_SCORE: 0.9732
IROC_PERCENTILE: 50
POISSON_SCORE: 0.4821
POISSON_PERCENTILE: 42
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM910576_UCSD.Pancreas.H3K4me1.STL003.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K4me1.STL003PA.01.01.hg19.level.2.release.8
ANALYSIS TITLE: Raw Signal Density Graphs of Pancreas H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K4me1 ChIP-Seq read mappings from Pancreas, Donor STL003, 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.13606
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 8
BROWSER_TRACK_NAME: Pancreas H3K4me1 03 91
BROWSER_TRACK_DESCRIPTION: UCSD Pancreas Histone H3K4me1 Donor STL003 Library AK191 EA Release 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 27,843,884
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 12
FINDPEAKS_SCORE: 0.273
FINDPEAKS_PERCENTILE: 50
HOTSPOT_SCORE: 0.3764
HOTSPOT_PERCENTILE: 50
IROC_SCORE: 0.9732
IROC_PERCENTILE: 50
POISSON_SCORE: 0.4821
POISSON_PERCENTILE: 42
MAXIMUM_REPLICATE_CORRELATION: NA

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

value: Pancreas

value: polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)

value: Caucasian

value: Biorupter

value: 500 micrograms

value: magnetic anti-rabbit

value: 5 micrograms


description:
design description: ChIP-Seq input analysis of breast progenitor enriched cell from RM080 (HS2803) using Illumina Genome Analyzer IIx
library name: HS2803
EXPERIMENT_TYPE: ChIP-Seq Input
EXTRACTION_PROTOCOL: Refer to document 'Chromatin Immunoprecipitation (ChIP)' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
EXTRACTION_PROTOCOL_TYPE_OF_SONICATOR: Fisher 550 Sonic Dismembrator
EXTRACTION_PROTOCOL_SONICATION_CYCLES: 10 min
CHIP_PROTOCOL: Input
CHIP_PROTOCOL_CHROMATIN_AMOUNT: 4.3 ug
SIZE_FRACTION: 65-280 bp
****************
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: GSM959125_UCSF-UBC.Breast_Stem_Cells.Input.RM080.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: HS2803-1.hg19.level.1.release.8
ANALYSIS TITLE: Mapping of Breast Stem Cells Input ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Input ChIP-Seq on Breast Stem Cells, Donor RM080 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.13422
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 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 12,053,984
NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 19
FINDPEAKS_SCORE: 0.0073
FINDPEAKS_PERCENTILE: 63
HOTSPOT_SCORE: 0.1023
HOTSPOT_PERCENTILE: 68
IROC_SCORE: 0.4175
IROC_PERCENTILE: 20
POISSON_SCORE: 0.135
POISSON_PERCENTILE: 42
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM959125_UCSF-UBC.Breast_Stem_Cells.Input.RM080.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: HS2803-1.hg19.level.2.release.8
ANALYSIS TITLE: Raw Signal Density Graphs of Breast Stem Cells Input ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Input ChIP-Seq read mappings from Breast Stem Cells, Donor RM080 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.13431
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 8
BROWSER_TRACK_NAME: BSC Input 80 03
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Breast Stem Cells ChIP-Seq Input Donor RM080 Library HS2803 EA Release 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 12,053,984
NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 19
FINDPEAKS_SCORE: 0.0073
FINDPEAKS_PERCENTILE: 63
HOTSPOT_SCORE: 0.1023
HOTSPOT_PERCENTILE: 68
IROC_SCORE: 0.4175
IROC_PERCENTILE: 20
POISSON_SCORE: 0.135
POISSON_PERCENTILE: 42
MAXIMUM_REPLICATE_CORRELATION: NA

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

extract_protocol: library construction protocol: Refer to document 'Chromatin Immunoprecipitation (ChIP)' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)

value: female

value: Breast

value: Progenitor enriched cell

value: breast progenitor enriched cell


title: Reference Epigenome: ChIP-Seq Analysis of H3K27me3 in Human Pancreas Tissue; renlab.H3K27me3.STL003PA.01.01

description:
sample_term_id: UBERON_0001264
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K27me3 in Human Pancreas Tissue. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: AK343
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.12205
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.11847
****************
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: GSM910563_UCSD.Pancreas.H3K27me3.STL003.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K27me3.STL003PA.01.01.hg19.level.1.release.8
ANALYSIS TITLE: Mapping of Pancreas H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K27me3 ChIP-Seq on Pancreas, Donor STL003, 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.13556
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 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 12,716,997
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 19
FINDPEAKS_SCORE: 0.0106
FINDPEAKS_PERCENTILE: 21
HOTSPOT_SCORE: 0.131
HOTSPOT_PERCENTILE: 32
IROC_SCORE: NA
IROC_PERCENTILE: NA
POISSON_SCORE: 0.2073
POISSON_PERCENTILE: 16
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM910563_UCSD.Pancreas.H3K27me3.STL003.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K27me3.STL003PA.01.01.hg19.level.2.release.8
ANALYSIS TITLE: Raw Signal Density Graphs of Pancreas H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K27me3 ChIP-Seq read mappings from Pancreas, Donor STL003, 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.13676
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 8
BROWSER_TRACK_NAME: Pancreas H3K27me3 03 43
BROWSER_TRACK_DESCRIPTION: UCSD Pancreas Histone H3K27me3 Donor STL003 Library AK343 EA Release 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 12,716,997
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 19
FINDPEAKS_SCORE: 0.0106
FINDPEAKS_PERCENTILE: 21
HOTSPOT_SCORE: 0.131
HOTSPOT_PERCENTILE: 32
IROC_SCORE: NA
IROC_PERCENTILE: NA
POISSON_SCORE: 0.2073
POISSON_PERCENTILE: 16
MAXIMUM_REPLICATE_CORRELATION: NA

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

value: genomic DNA

value: Male

value: Histone H3K27me3

value: Active Motif


description:
design description: ChIP-Seq input analysis of breast luminal epithelial cell from RM080 (HS2797) using Illumina Genome Analyzer IIx
library name: HS2797
EXPERIMENT_TYPE: ChIP-Seq Input
EXTRACTION_PROTOCOL: Refer to document 'Chromatin Immunoprecipitation (ChIP)' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
EXTRACTION_PROTOCOL_TYPE_OF_SONICATOR: Fisher 550 Sonic Dismembrator
EXTRACTION_PROTOCOL_SONICATION_CYCLES: 10 min
CHIP_PROTOCOL: Input
CHIP_PROTOCOL_CHROMATIN_AMOUNT: 3.04 ug
SIZE_FRACTION: 70-315 bp
****************
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: GSM959124_UCSF-UBC.Breast_Luminal_Epithelial_Cells.Input.RM080.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: HS2797-1.hg19.level.1.release.8
ANALYSIS TITLE: Mapping of Breast Luminal Epithelial Cells Input ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Input ChIP-Seq on Breast Luminal Epithelial Cells, Donor RM080 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.13424
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 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 24,133,379
NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 19
FINDPEAKS_SCORE: 0.0068
FINDPEAKS_PERCENTILE: 47
HOTSPOT_SCORE: 0.0123
HOTSPOT_PERCENTILE: 21
IROC_SCORE: 0.9715
IROC_PERCENTILE: 93
POISSON_SCORE: 0.0352
POISSON_PERCENTILE: 5
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM959124_UCSF-UBC.Breast_Luminal_Epithelial_Cells.Input.RM080.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: HS2797-1.hg19.level.2.release.8
ANALYSIS TITLE: Raw Signal Density Graphs of Breast Luminal Epithelial Cells Input ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Input ChIP-Seq read mappings from Breast Luminal Epithelial Cells, Donor RM080 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.13433
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 8
BROWSER_TRACK_NAME: BLEC Input 80 97
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Breast Luminal Epithelial Cells ChIP-Seq Input Donor RM080 Library HS2797 EA Release 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 24,133,379
NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 19
FINDPEAKS_SCORE: 0.0068
FINDPEAKS_PERCENTILE: 47
HOTSPOT_SCORE: 0.0123
HOTSPOT_PERCENTILE: 21
IROC_SCORE: 0.9715
IROC_PERCENTILE: 93
POISSON_SCORE: 0.0352
POISSON_PERCENTILE: 5
MAXIMUM_REPLICATE_CORRELATION: NA

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

value: Luminal epithelial cell

value: No

value: primary cell

value: breast luminal epithelial cell


title: Reference Epigenome: ChIP-Seq Analysis of H3K27me3 in Human Aorta Tissue; renlab.H3K27me3.STL003AO.01.01

description:
sample_term_id: UBERON_0000947
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K27me3 in Human Aorta Tissue. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: AY129
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.12185
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.11864
****************
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: GSM910560_UCSD.Aorta.H3K27me3.STL003.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K27me3.STL003AO.01.01.hg19.level.1.release.8
ANALYSIS TITLE: Mapping of Aorta H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K27me3 ChIP-Seq on Aorta, Donor STL003, 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.13529
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 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 16,802,936
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 19
FINDPEAKS_SCORE: 0.0452
FINDPEAKS_PERCENTILE: 58
HOTSPOT_SCORE: 0.2122
HOTSPOT_PERCENTILE: 68
IROC_SCORE: 0.8134
IROC_PERCENTILE: 40
POISSON_SCORE: 0.3712
POISSON_PERCENTILE: 63
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM910560_UCSD.Aorta.H3K27me3.STL003.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K27me3.STL003AO.01.01.hg19.level.2.release.8
ANALYSIS TITLE: Raw Signal Density Graphs of Aorta H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K27me3 ChIP-Seq read mappings from Aorta, Donor STL003, 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.13649
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 8
BROWSER_TRACK_NAME: Aorta H3K27me3 03 29
BROWSER_TRACK_DESCRIPTION: UCSD Aorta Histone H3K27me3 Donor STL003 Library AY129 EA Release 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 16,802,936
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 19
FINDPEAKS_SCORE: 0.0452
FINDPEAKS_PERCENTILE: 58
HOTSPOT_SCORE: 0.2122
HOTSPOT_PERCENTILE: 68
IROC_SCORE: 0.8134
IROC_PERCENTILE: 40
POISSON_SCORE: 0.3712
POISSON_PERCENTILE: 63
MAXIMUM_REPLICATE_CORRELATION: NA

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

value: Aorta

value: Shin Lin, Stanford University

value: Primary Tissue

value: Autopsy

value: polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)

value: Caucasian


title: Reference Epigenome: ChIP-Seq Analysis of H3K27me3 in Human Gastric Tissue; renlab.H3K27me3.STL003GA.01.01

description:
sample_term_id: UBERON_0000945
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K27me3 in Human Gastric Tissue. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: AK340
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.12237
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.12180
****************
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: GSM910561_UCSD.Gastric.H3K27me3.STL003.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K27me3.STL003GA.01.01.hg19.level.1.release.8
ANALYSIS TITLE: Mapping of Gastric H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K27me3 ChIP-Seq on Gastric, Donor STL003, 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.13478
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 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 15,462,046
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 19
FINDPEAKS_SCORE: 0.0092
FINDPEAKS_PERCENTILE: 11
HOTSPOT_SCORE: 0.1127
HOTSPOT_PERCENTILE: 26
IROC_SCORE: NA
IROC_PERCENTILE: NA
POISSON_SCORE: 0.2136
POISSON_PERCENTILE: 21
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM910561_UCSD.Gastric.H3K27me3.STL003.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K27me3.STL003GA.01.01.hg19.level.2.release.8
ANALYSIS TITLE: Raw Signal Density Graphs of Gastric H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K27me3 ChIP-Seq read mappings from Gastric, Donor STL003, 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.13598
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 8
BROWSER_TRACK_NAME: Gastric H3K27me3 03 40
BROWSER_TRACK_DESCRIPTION: UCSD Gastric Histone H3K27me3 Donor STL003 Library AK340 EA Release 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 15,462,046
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 19
FINDPEAKS_SCORE: 0.0092
FINDPEAKS_PERCENTILE: 11
HOTSPOT_SCORE: 0.1127
HOTSPOT_PERCENTILE: 26
IROC_SCORE: NA
IROC_PERCENTILE: NA
POISSON_SCORE: 0.2136
POISSON_PERCENTILE: 21
MAXIMUM_REPLICATE_CORRELATION: NA

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

value: Gastric

value: Biorupter

value: 500 micrograms

value: magnetic anti-rabbit

value: 5 micrograms


title: Reference Epigenome: ChIP-Seq Analysis of H3K27ac in Human Sigmoid Colon Tissue; renlab.H3K27ac.STL001SG.01.01

description:
sample_term_id: UBERON_0001159
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K27ac in Human Sigmoid Colon Tissue. Sequencing was done on the Illumina Genome Analyzer IIx platform.
Library name: AK229
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.12266
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.12265
****************
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: GSM915331_UCSD.Sigmoid_Colon.H3K27ac.STL001.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K27ac.STL001SG.01.01.hg19.level.1.release.8
ANALYSIS TITLE: Mapping of Sigmoid Colon H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K27ac ChIP-Seq on Sigmoid Colon, Donor STL001, 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.13471
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 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 32,376,823
NUMBER_OF_H3K27ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 21
FINDPEAKS_SCORE: 0.3759
FINDPEAKS_PERCENTILE: 43
HOTSPOT_SCORE: 0.4172
HOTSPOT_PERCENTILE: 38
IROC_SCORE: 0.9973
IROC_PERCENTILE: 57
POISSON_SCORE: 0.4857
POISSON_PERCENTILE: 38
MAXIMUM_REPLICATE_CORRELATION: 0.97

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

ANALYSIS FILE NAME: GSM915331_UCSD.Sigmoid_Colon.H3K27ac.STL001.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K27ac.STL001SG.01.01.hg19.level.2.release.8
ANALYSIS TITLE: Raw Signal Density Graphs of Sigmoid Colon H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K27ac ChIP-Seq read mappings from Sigmoid Colon, Donor STL001, 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.13591
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 8
BROWSER_TRACK_NAME: SC H3K27ac 01 29
BROWSER_TRACK_DESCRIPTION: UCSD Sigmoid Colon Histone H3K27ac Donor STL001 Library AK229 EA Release 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 32,376,823
NUMBER_OF_H3K27ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 21
FINDPEAKS_SCORE: 0.3759
FINDPEAKS_PERCENTILE: 43
HOTSPOT_SCORE: 0.4172
HOTSPOT_PERCENTILE: 38
IROC_SCORE: 0.9973
IROC_PERCENTILE: 57
POISSON_SCORE: 0.4857
POISSON_PERCENTILE: 38
MAXIMUM_REPLICATE_CORRELATION: 0.97

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

source_name: Sigmoid Colon tissue; renlab.H3K27ac.STL001SG.01.01

value: Sigmoid Colon

value: genomic DNA

value: healthy, no prior medical history (NO diabetes, hypertension, coronary artery disease, cancer)

value: Male

value: Caucasian and African American

value: Histone H3K27ac


title: Reference Epigenome: ChIP-Seq Input from Human Small Bowel Tissue; renlab.Input.STL001SB.01.01

description:
sample_term_id: UBERON_0002108
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Input from Human Small Bowel Tissue. Sequencing was done on the Illumina Genome Analyzer IIx platform.
Library name: AK225
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.12263
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.12250
****************
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: GSM915337_UCSD.Small_Intestine.Input.STL001.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.Input.STL001SB.01.01.hg19.level.1.release.8
ANALYSIS TITLE: Mapping of Small Intestine Input ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Input ChIP-Seq on Small Intestine, Donor STL001, 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.13557
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 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 34,464,193
NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 19
FINDPEAKS_SCORE: 0.0071
FINDPEAKS_PERCENTILE: 58
HOTSPOT_SCORE: 0.0517
HOTSPOT_PERCENTILE: 42
IROC_SCORE: NA
IROC_PERCENTILE: NA
POISSON_SCORE: 0.1564
POISSON_PERCENTILE: 53
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM915337_UCSD.Small_Intestine.Input.STL001.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.Input.STL001SB.01.01.hg19.level.2.release.8
ANALYSIS TITLE: Raw Signal Density Graphs of Small Intestine Input ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Input ChIP-Seq read mappings from Small Intestine, Donor STL001, 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.13677
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 8
BROWSER_TRACK_NAME: SI Input 01 25
BROWSER_TRACK_DESCRIPTION: UCSD Small Intestine ChIP-Seq Input Donor STL001 Library AK225 EA Release 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 34,464,193
NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 19
FINDPEAKS_SCORE: 0.0071
FINDPEAKS_PERCENTILE: 58
HOTSPOT_SCORE: 0.0517
HOTSPOT_PERCENTILE: 42
IROC_SCORE: NA
IROC_PERCENTILE: NA
POISSON_SCORE: 0.1564
POISSON_PERCENTILE: 53
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: Small Intestine tissue; renlab.Input.STL001SB.01.01

value: Small Intestine

value: ChIP-Seq Input

value: Input


title: Reference Epigenome: ChIP-Seq Analysis of H3K27me3 in Human Left Ventricle Tissue; renlab.H3K27me3.STL003LV.01.01

description:
sample_term_id: UBERON_0002084
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K27me3 in Human Left Ventricle Tissue. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: AY134
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.12197
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.11885
****************
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: GSM910562_UCSD.Left_Ventricle.H3K27me3.STL003.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K27me3.STL003LV.01.01.hg19.level.1.release.8
ANALYSIS TITLE: Mapping of Left Ventricle H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K27me3 ChIP-Seq on Left Ventricle, Donor STL003, 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.13479
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 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 18,491,631
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 19
FINDPEAKS_SCORE: 0.0716
FINDPEAKS_PERCENTILE: 63
HOTSPOT_SCORE: 0.2044
HOTSPOT_PERCENTILE: 63
IROC_SCORE: 0.8568
IROC_PERCENTILE: 53
POISSON_SCORE: 0.3681
POISSON_PERCENTILE: 58
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

ANALYSIS FILE NAME: GSM910562_UCSD.Left_Ventricle.H3K27me3.STL003.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K27me3.STL003LV.01.01.hg19.level.2.release.8
ANALYSIS TITLE: Raw Signal Density Graphs of Left Ventricle H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K27me3 ChIP-Seq read mappings from Left Ventricle, Donor STL003, 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.13599
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 8
BROWSER_TRACK_NAME: LV H3K27me3 03 34
BROWSER_TRACK_DESCRIPTION: UCSD Left Ventricle Histone H3K27me3 Donor STL003 Library AY134 EA Release 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 18,491,631
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 19
FINDPEAKS_SCORE: 0.0716
FINDPEAKS_PERCENTILE: 63
HOTSPOT_SCORE: 0.2044
HOTSPOT_PERCENTILE: 63
IROC_SCORE: 0.8568
IROC_PERCENTILE: 53
POISSON_SCORE: 0.3681
POISSON_PERCENTILE: 58
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

source_name: Left Ventricle tissue; renlab.H3K27me3.STL003LV.01.01

value: Left Ventricle

value: Shin Lin, Stanford University

value: Primary Tissue

value: Autopsy

value: Histone H3K27me3

value: Active Motif


title: Reference Epigenome: ChIP-Seq Analysis of H3K27ac in Human Small Bowel Tissue; renlab.H3K27ac.STL001SB.01.01

description:
sample_term_id: UBERON_0002108
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K27ac in Human Small Bowel Tissue. Sequencing was done on the Illumina Genome Analyzer IIx platform.
Library name: AK223
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.12261
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.12250
****************
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: GSM915330_UCSD.Small_Intestine.H3K27ac.STL001.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K27ac.STL001SB.01.01.hg19.level.1.release.8
ANALYSIS TITLE: Mapping of Small Intestine H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K27ac ChIP-Seq on Small Intestine, Donor STL001, 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.13548
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 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 31,098,865
NUMBER_OF_H3K27ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 21
FINDPEAKS_SCORE: 0.4865
FINDPEAKS_PERCENTILE: 67
HOTSPOT_SCORE: 0.5146
HOTSPOT_PERCENTILE: 67
IROC_SCORE: 0.9973
IROC_PERCENTILE: 57
POISSON_SCORE: 0.5764
POISSON_PERCENTILE: 71
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM915330_UCSD.Small_Intestine.H3K27ac.STL001.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K27ac.STL001SB.01.01.hg19.level.2.release.8
ANALYSIS TITLE: Raw Signal Density Graphs of Small Intestine H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K27ac ChIP-Seq read mappings from Small Intestine, Donor STL001, 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.13668
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 8
BROWSER_TRACK_NAME: SI H3K27ac 01 23
BROWSER_TRACK_DESCRIPTION: UCSD Small Intestine Histone H3K27ac Donor STL001 Library AK223 EA Release 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 31,098,865
NUMBER_OF_H3K27ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 21
FINDPEAKS_SCORE: 0.4865
FINDPEAKS_PERCENTILE: 67
HOTSPOT_SCORE: 0.5146
HOTSPOT_PERCENTILE: 67
IROC_SCORE: 0.9973
IROC_PERCENTILE: 57
POISSON_SCORE: 0.5764
POISSON_PERCENTILE: 71
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: Small Intestine tissue; renlab.H3K27ac.STL001SB.01.01

value: Biorupter

value: 500 micrograms

value: magnetic anti-rabbit


title: Reference Epigenome: ChIP-Seq Analysis of H3K27ac in Human Sigmoid Colon Tissue; renlab.H3K27ac.STL003SG.01.01

description:
sample_term_id: UBERON_0001159
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K27ac in Human Sigmoid Colon Tissue. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: AY94
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.12225
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.11872
****************
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: GSM910559_UCSD.Sigmoid_Colon.H3K27ac.STL003.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K27ac.STL003SG.01.01.hg19.level.1.release.8
ANALYSIS TITLE: Mapping of Sigmoid Colon H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K27ac ChIP-Seq on Sigmoid Colon, Donor STL003, 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.13474
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 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 20,307,929
NUMBER_OF_H3K27ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 21
FINDPEAKS_SCORE: 0.5321
FINDPEAKS_PERCENTILE: 81
HOTSPOT_SCORE: 0.5599
HOTSPOT_PERCENTILE: 81
IROC_SCORE: 0.9984
IROC_PERCENTILE: 81
POISSON_SCORE: 0.5936
POISSON_PERCENTILE: 76
MAXIMUM_REPLICATE_CORRELATION: 0.97

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

ANALYSIS FILE NAME: GSM910559_UCSD.Sigmoid_Colon.H3K27ac.STL003.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K27ac.STL003SG.01.01.hg19.level.2.release.8
ANALYSIS TITLE: Raw Signal Density Graphs of Sigmoid Colon H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K27ac ChIP-Seq read mappings from Sigmoid Colon, Donor STL003, 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.13594
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 8
BROWSER_TRACK_NAME: SC H3K27ac 03 94
BROWSER_TRACK_DESCRIPTION: UCSD Sigmoid Colon Histone H3K27ac Donor STL003 Library AY94 EA Release 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 20,307,929
NUMBER_OF_H3K27ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 21
FINDPEAKS_SCORE: 0.5321
FINDPEAKS_PERCENTILE: 81
HOTSPOT_SCORE: 0.5599
HOTSPOT_PERCENTILE: 81
IROC_SCORE: 0.9984
IROC_PERCENTILE: 81
POISSON_SCORE: 0.5936
POISSON_PERCENTILE: 76
MAXIMUM_REPLICATE_CORRELATION: 0.97

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

source_name: Sigmoid Colon tissue; renlab.H3K27ac.STL003SG.01.01

value: Sigmoid Colon

value: genomic DNA

value: polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)

value: Caucasian

value: 5 micrograms


title: Reference Epigenome: ChIP-Seq Analysis of H3K27me3 in Human Psoas Muscle Tissue; renlab.H3K27me3.STL003PO.01.01

description:
sample_term_id: UBERON_0008450
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K27me3 in Human Psoas Muscle Tissue. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: AY93
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.12172
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.11875
****************
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: GSM908953_UCSD.Psoas_Muscle.H3K27me3.STL003.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K27me3.STL003PO.01.01.hg19.level.1.release.8
ANALYSIS TITLE: Mapping of Psoas Muscle H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K27me3 ChIP-Seq on Psoas Muscle, Donor STL003, 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.13485
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 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 8,863,125
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 19
FINDPEAKS_SCORE: 0.2244
FINDPEAKS_PERCENTILE: 89
HOTSPOT_SCORE: 0.373
HOTSPOT_PERCENTILE: 95
IROC_SCORE: 0.933
IROC_PERCENTILE: 73
POISSON_SCORE: 0.4973
POISSON_PERCENTILE: 100
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM908953_UCSD.Psoas_Muscle.H3K27me3.STL003.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K27me3.STL003PO.01.01.hg19.level.2.release.8
ANALYSIS TITLE: Raw Signal Density Graphs of Psoas Muscle H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K27me3 ChIP-Seq read mappings from Psoas Muscle, Donor STL003, 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.13605
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 8
BROWSER_TRACK_NAME: PM H3K27me3 03 93
BROWSER_TRACK_DESCRIPTION: UCSD Psoas Muscle Histone H3K27me3 Donor STL003 Library AY93 EA Release 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 8,863,125
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 19
FINDPEAKS_SCORE: 0.2244
FINDPEAKS_PERCENTILE: 89
HOTSPOT_SCORE: 0.373
HOTSPOT_PERCENTILE: 95
IROC_SCORE: 0.933
IROC_PERCENTILE: 73
POISSON_SCORE: 0.4973
POISSON_PERCENTILE: 100
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: Psoas Muscle tissue; renlab.H3K27me3.STL003PO.01.01

value: Psoas Muscle

value: Male


title: Reference Epigenome: ChIP-Seq Analysis of H3K27ac in Human Psoas Muscle Tissue; renlab.H3K27ac.STL003PO.01.01

description:
sample_term_id: UBERON_0008450
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K27ac in Human Psoas Muscle Tissue. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: AY92
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.12215
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.11875
****************
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: GSM910556_UCSD.Psoas_Muscle.H3K27ac.STL003.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K27ac.STL003PO.01.01.hg19.level.1.release.8
ANALYSIS TITLE: Mapping of Psoas Muscle H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K27ac ChIP-Seq on Psoas Muscle, Donor STL003, 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.13464
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 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 6,236,978
NUMBER_OF_H3K27ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 21
FINDPEAKS_SCORE: 0.673
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.6936
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.9984
IROC_PERCENTILE: 81
POISSON_SCORE: 0.7438
POISSON_PERCENTILE: 100
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM910556_UCSD.Psoas_Muscle.H3K27ac.STL003.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K27ac.STL003PO.01.01.hg19.level.2.release.8
ANALYSIS TITLE: Raw Signal Density Graphs of Psoas Muscle H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K27ac ChIP-Seq read mappings from Psoas Muscle, Donor STL003, 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.13584
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 8
BROWSER_TRACK_NAME: PM H3K27ac 03 92
BROWSER_TRACK_DESCRIPTION: UCSD Psoas Muscle Histone H3K27ac Donor STL003 Library AY92 EA Release 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 6,236,978
NUMBER_OF_H3K27ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 21
FINDPEAKS_SCORE: 0.673
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.6936
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.9984
IROC_PERCENTILE: 81
POISSON_SCORE: 0.7438
POISSON_PERCENTILE: 100
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: Psoas Muscle tissue; renlab.H3K27ac.STL003PO.01.01

value: Histone H3K27ac


title: Reference Epigenome: ChIP-Seq Input from Human Left Ventricle Tissue; renlab.Input.STL001LV.01.01

description:
sample_term_id: UBERON_0002084
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Input from Human Left Ventricle Tissue. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: AK237
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.12178
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.11835
****************
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: GSM908968_UCSD.Left_Ventricle.Input.STL001.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.Input.STL001LV.01.01.hg19.level.1.release.8
ANALYSIS TITLE: Mapping of Left Ventricle Input ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Input ChIP-Seq on Left Ventricle, Donor STL001, 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.13467
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 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 46,049,267
NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 19
FINDPEAKS_SCORE: 0.0077
FINDPEAKS_PERCENTILE: 74
HOTSPOT_SCORE: 0.0921
HOTSPOT_PERCENTILE: 58
IROC_SCORE: 0.6551
IROC_PERCENTILE: 53
POISSON_SCORE: 0.2704
POISSON_PERCENTILE: 68
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

ANALYSIS FILE NAME: GSM908968_UCSD.Left_Ventricle.Input.STL001.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.Input.STL001LV.01.01.hg19.level.2.release.8
ANALYSIS TITLE: Raw Signal Density Graphs of Left Ventricle Input ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Input ChIP-Seq read mappings from Left Ventricle, Donor STL001, 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.13587
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 8
BROWSER_TRACK_NAME: LV Input 01 37
BROWSER_TRACK_DESCRIPTION: UCSD Left Ventricle ChIP-Seq Input Donor STL001 Library AK237 EA Release 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 46,049,267
NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 19
FINDPEAKS_SCORE: 0.0077
FINDPEAKS_PERCENTILE: 74
HOTSPOT_SCORE: 0.0921
HOTSPOT_PERCENTILE: 58
IROC_SCORE: 0.6551
IROC_PERCENTILE: 53
POISSON_SCORE: 0.2704
POISSON_PERCENTILE: 68
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

source_name: Left Ventricle tissue; renlab.Input.STL001LV.01.01

value: Left Ventricle

value: healthy, no prior medical history (NO diabetes, hypertension, coronary artery disease, cancer)

value: Caucasian and African American

value: ChIP-Seq Input

value: Input


title: Reference Epigenome: ChIP-Seq Analysis of H3K27ac in Human Right Atrium Tissue; renlab.H3K27ac.STL003RA.01.01

description:
sample_term_id: UBERON_0002078
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K27ac in Human Right Atrium Tissue. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: AY52
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.12217
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.11888
****************
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: GSM910557_UCSD.Right_Atrium.H3K27ac.STL003.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K27ac.STL003RA.01.01.hg19.level.1.release.8
ANALYSIS TITLE: Mapping of Right Atrium H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K27ac ChIP-Seq on Right Atrium, Donor STL003, 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.13453
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 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 24,665,058
NUMBER_OF_H3K27ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 21
FINDPEAKS_SCORE: 0.4594
FINDPEAKS_PERCENTILE: 62
HOTSPOT_SCORE: 0.4926
HOTSPOT_PERCENTILE: 57
IROC_SCORE: 0.9979
IROC_PERCENTILE: 71
POISSON_SCORE: 0.5474
POISSON_PERCENTILE: 62
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM910557_UCSD.Right_Atrium.H3K27ac.STL003.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K27ac.STL003RA.01.01.hg19.level.2.release.8
ANALYSIS TITLE: Raw Signal Density Graphs of Right Atrium H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K27ac ChIP-Seq read mappings from Right Atrium, Donor STL003, 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.13573
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 8
BROWSER_TRACK_NAME: RA H3K27ac 03 52
BROWSER_TRACK_DESCRIPTION: UCSD Right Atrium Histone H3K27ac Donor STL003 Library AY52 EA Release 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 24,665,058
NUMBER_OF_H3K27ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 21
FINDPEAKS_SCORE: 0.4594
FINDPEAKS_PERCENTILE: 62
HOTSPOT_SCORE: 0.4926
HOTSPOT_PERCENTILE: 57
IROC_SCORE: 0.9979
IROC_PERCENTILE: 71
POISSON_SCORE: 0.5474
POISSON_PERCENTILE: 62
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: Right Atrium tissue; renlab.H3K27ac.STL003RA.01.01

value: Right Atrium

value: Shin Lin, Stanford University

value: Primary Tissue

value: Autopsy

value: Active Motif


title: Reference Epigenome: ChIP-Seq Analysis of H3K27ac in Human Gastric Tissue; renlab.H3K27ac.STL003GA.01.01

description:
sample_term_id: UBERON_0000945
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K27ac in Human Gastric Tissue. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: AK339
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.12181
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.12180
****************
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: GSM910555_UCSD.Gastric.H3K27ac.STL003.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K27ac.STL003GA.01.01.hg19.level.1.release.8
ANALYSIS TITLE: Mapping of Gastric H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K27ac ChIP-Seq on Gastric, Donor STL003, 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.13546
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 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 16,834,677
NUMBER_OF_H3K27ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 21
FINDPEAKS_SCORE: 0.2213
FINDPEAKS_PERCENTILE: 29
HOTSPOT_SCORE: 0.2992
HOTSPOT_PERCENTILE: 29
IROC_SCORE: 0.9943
IROC_PERCENTILE: 29
POISSON_SCORE: 0.338
POISSON_PERCENTILE: 24
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM910555_UCSD.Gastric.H3K27ac.STL003.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K27ac.STL003GA.01.01.hg19.level.2.release.8
ANALYSIS TITLE: Raw Signal Density Graphs of Gastric H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K27ac ChIP-Seq read mappings from Gastric, Donor STL003, 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.13666
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 8
BROWSER_TRACK_NAME: Gastric H3K27ac 03 39
BROWSER_TRACK_DESCRIPTION: UCSD Gastric Histone H3K27ac Donor STL003 Library AK339 EA Release 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 16,834,677
NUMBER_OF_H3K27ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 21
FINDPEAKS_SCORE: 0.2213
FINDPEAKS_PERCENTILE: 29
HOTSPOT_SCORE: 0.2992
HOTSPOT_PERCENTILE: 29
IROC_SCORE: 0.9943
IROC_PERCENTILE: 29
POISSON_SCORE: 0.338
POISSON_PERCENTILE: 24
MAXIMUM_REPLICATE_CORRELATION: NA

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

value: Gastric

value: genomic DNA

value: Biorupter

value: 500 micrograms

value: magnetic anti-rabbit


title: Reference Epigenome: ChIP-Seq Analysis of H3K27ac in Human Left Ventricle Tissue; renlab.H3K27ac.STL001LV.01.01

description:
sample_term_id: UBERON_0002084
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K27ac in Human Left Ventricle Tissue. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: AK235
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.12174
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.11835
****************
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: GSM908951_UCSD.Left_Ventricle.H3K27ac.STL001.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K27ac.STL001LV.01.01.hg19.level.1.release.8
ANALYSIS TITLE: Mapping of Left Ventricle H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K27ac ChIP-Seq on Left Ventricle, Donor STL001, 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.13451
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 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 22,776,160
NUMBER_OF_H3K27ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 21
FINDPEAKS_SCORE: 0.5873
FINDPEAKS_PERCENTILE: 86
HOTSPOT_SCORE: 0.5891
HOTSPOT_PERCENTILE: 86
IROC_SCORE: 0.9989
IROC_PERCENTILE: 90
POISSON_SCORE: 0.636
POISSON_PERCENTILE: 86
MAXIMUM_REPLICATE_CORRELATION: 0.89

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

ANALYSIS FILE NAME: GSM908951_UCSD.Left_Ventricle.H3K27ac.STL001.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K27ac.STL001LV.01.01.hg19.level.2.release.8
ANALYSIS TITLE: Raw Signal Density Graphs of Left Ventricle H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K27ac ChIP-Seq read mappings from Left Ventricle, Donor STL001, 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.13571
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 8
BROWSER_TRACK_NAME: LV H3K27ac 01 35
BROWSER_TRACK_DESCRIPTION: UCSD Left Ventricle Histone H3K27ac Donor STL001 Library AK235 EA Release 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 22,776,160
NUMBER_OF_H3K27ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 21
FINDPEAKS_SCORE: 0.5873
FINDPEAKS_PERCENTILE: 86
HOTSPOT_SCORE: 0.5891
HOTSPOT_PERCENTILE: 86
IROC_SCORE: 0.9989
IROC_PERCENTILE: 90
POISSON_SCORE: 0.636
POISSON_PERCENTILE: 86
MAXIMUM_REPLICATE_CORRELATION: 0.89

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

source_name: Left Ventricle tissue; renlab.H3K27ac.STL001LV.01.01

value: Male

value: 5 micrograms


title: Reference Epigenome: ChIP-Seq Input from Human Left Ventricle Tissue; renlab.Input.STL003LV.01.01

description:
sample_term_id: UBERON_0002084
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Input from Human Left Ventricle Tissue. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: AY62
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.11886
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.11885
****************
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: GSM906418_UCSD.Left_Ventricle.Input.STL003.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.Input.STL003LV.01.01.hg19.level.1.release.8
ANALYSIS TITLE: Mapping of Left Ventricle Input ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Input ChIP-Seq on Left Ventricle, Donor STL003, 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.13469
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 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 21,462,832
NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 19
FINDPEAKS_SCORE: 0.0133
FINDPEAKS_PERCENTILE: 89
HOTSPOT_SCORE: 0.1679
HOTSPOT_PERCENTILE: 95
IROC_SCORE: 0.7305
IROC_PERCENTILE: 67
POISSON_SCORE: 0.3436
POISSON_PERCENTILE: 89
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

ANALYSIS FILE NAME: GSM906418_UCSD.Left_Ventricle.Input.STL003.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.Input.STL003LV.01.01.hg19.level.2.release.8
ANALYSIS TITLE: Raw Signal Density Graphs of Left Ventricle Input ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Input ChIP-Seq read mappings from Left Ventricle, Donor STL003, 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.13589
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 8
BROWSER_TRACK_NAME: LV Input 03 62
BROWSER_TRACK_DESCRIPTION: UCSD Left Ventricle ChIP-Seq Input Donor STL003 Library AY62 EA Release 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 21,462,832
NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 19
FINDPEAKS_SCORE: 0.0133
FINDPEAKS_PERCENTILE: 89
HOTSPOT_SCORE: 0.1679
HOTSPOT_PERCENTILE: 95
IROC_SCORE: 0.7305
IROC_PERCENTILE: 67
POISSON_SCORE: 0.3436
POISSON_PERCENTILE: 89
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

source_name: Left Ventricle tissue; renlab.Input.STL003LV.01.01

value: Left Ventricle

value: polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)

value: Caucasian