title: Reference Epigenome: ChIP-Seq Input from Human Spleen Tissue; renlab.Input.STL003SX.01.01

description:
sample_term_id: UBERON_0002106
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Input from Human Spleen Tissue. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: AK350
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.11853
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: GSM906423_UCSD.Spleen.Input.STL003.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.Input.STL003SX.01.01.hg19.level.1.release.8
ANALYSIS TITLE: Mapping of Spleen Input ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Input 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.13503
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: 28,903,692
NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 19
FINDPEAKS_SCORE: 0.0062
FINDPEAKS_PERCENTILE: 26
HOTSPOT_SCORE: 0.0096
HOTSPOT_PERCENTILE: 11
IROC_SCORE: 0.0
IROC_PERCENTILE: 13
POISSON_SCORE: 0.0512
POISSON_PERCENTILE: 11
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM906423_UCSD.Spleen.Input.STL003.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.Input.STL003SX.01.01.hg19.level.2.release.8
ANALYSIS TITLE: Raw Signal Density Graphs of Spleen Input ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Input 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.13623
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 Input 03 50
BROWSER_TRACK_DESCRIPTION: UCSD Spleen ChIP-Seq Input Donor STL003 Library AK350 EA Release 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 28,903,692
NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 19
FINDPEAKS_SCORE: 0.0062
FINDPEAKS_PERCENTILE: 26
HOTSPOT_SCORE: 0.0096
HOTSPOT_PERCENTILE: 11
IROC_SCORE: 0.0
IROC_PERCENTILE: 13
POISSON_SCORE: 0.0512
POISSON_PERCENTILE: 11
MAXIMUM_REPLICATE_CORRELATION: NA

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

value: Spleen

value: ChIP-Seq Input


title: Reference Epigenome: ChIP-Seq Input from Human Adipose Tissue; renlab.Input.STL003FT.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_0001013
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Input from Human Adipose Tissue. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: AK347
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.11862
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.11859
****************
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: GSM906416_UCSD.Adipose_Tissue.Input.STL003.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.Input.STL003FT.01.01.hg19.level.1.release.8
ANALYSIS TITLE: Mapping of Adipose Tissue Input ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Input ChIP-Seq on Adipose Tissue, 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.13442
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: 34,405,736
NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 19
FINDPEAKS_SCORE: 0.0062
FINDPEAKS_PERCENTILE: 26
HOTSPOT_SCORE: 0.0124
HOTSPOT_PERCENTILE: 26
IROC_SCORE: 0.9612
IROC_PERCENTILE: 87
POISSON_SCORE: 0.1013
POISSON_PERCENTILE: 32
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM906416_UCSD.Adipose_Tissue.Input.STL003.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.Input.STL003FT.01.01.hg19.level.2.release.8
ANALYSIS TITLE: Raw Signal Density Graphs of Adipose Tissue Input ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Input ChIP-Seq read mappings from Adipose Tissue, 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.13562
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: AT Input 03 47
BROWSER_TRACK_DESCRIPTION: UCSD Adipose Tissue ChIP-Seq Input Donor STL003 Library AK347 EA Release 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 34,405,736
NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 19
FINDPEAKS_SCORE: 0.0062
FINDPEAKS_PERCENTILE: 26
HOTSPOT_SCORE: 0.0124
HOTSPOT_PERCENTILE: 26
IROC_SCORE: 0.9612
IROC_PERCENTILE: 87
POISSON_SCORE: 0.1013
POISSON_PERCENTILE: 32
MAXIMUM_REPLICATE_CORRELATION: NA

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

molecule: genomic DNA

organism: Homo sapiens

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

tag: sample alias

tag: sample common name

value: Adipose Tissue

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: Male

value: Caucasian

value: Biorupter

value: Input

value: 500 micrograms


title: Reference Epigenome: ChIP-Seq Input from Human Right Atrium Tissue; renlab.Input.STL003RA.01.01

description:
sample_term_id: UBERON_0002078
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Input from Human Right Atrium Tissue. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: AY63
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.11889
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: GSM906421_UCSD.Right_Atrium.Input.STL003.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.Input.STL003RA.01.01.hg19.level.1.release.8
ANALYSIS TITLE: Mapping of Right Atrium Input ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Input 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.13468
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: 21,727,932
NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 19
FINDPEAKS_SCORE: 0.0237
FINDPEAKS_PERCENTILE: 95
HOTSPOT_SCORE: 0.153
HOTSPOT_PERCENTILE: 89
IROC_SCORE: 0.7582
IROC_PERCENTILE: 73
POISSON_SCORE: 0.2834
POISSON_PERCENTILE: 74
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM906421_UCSD.Right_Atrium.Input.STL003.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.Input.STL003RA.01.01.hg19.level.2.release.8
ANALYSIS TITLE: Raw Signal Density Graphs of Right Atrium Input ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Input 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.13588
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 Input 03 63
BROWSER_TRACK_DESCRIPTION: UCSD Right Atrium ChIP-Seq Input Donor STL003 Library AY63 EA Release 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 21,727,932
NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 19
FINDPEAKS_SCORE: 0.0237
FINDPEAKS_PERCENTILE: 95
HOTSPOT_SCORE: 0.153
HOTSPOT_PERCENTILE: 89
IROC_SCORE: 0.7582
IROC_PERCENTILE: 73
POISSON_SCORE: 0.2834
POISSON_PERCENTILE: 74
MAXIMUM_REPLICATE_CORRELATION: NA

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

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

value: Right Atrium


title: Reference Epigenome: ChIP-Seq Input from Human Psoas Muscle Tissue; renlab.Input.STL003PO.01.01

description:
sample_term_id: UBERON_0008450
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Input from Human Psoas Muscle Tissue. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: AY57
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.11876
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: GSM906420_UCSD.Psoas_Muscle.Input.STL003.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.Input.STL003PO.01.01.hg19.level.1.release.8
ANALYSIS TITLE: Mapping of Psoas Muscle Input ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Input 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.13488
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: 35,915,869
NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 19
FINDPEAKS_SCORE: 0.007
FINDPEAKS_PERCENTILE: 53
HOTSPOT_SCORE: 0.1169
HOTSPOT_PERCENTILE: 79
IROC_SCORE: 0.6018
IROC_PERCENTILE: 47
POISSON_SCORE: 0.3406
POISSON_PERCENTILE: 84
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM906420_UCSD.Psoas_Muscle.Input.STL003.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.Input.STL003PO.01.01.hg19.level.2.release.8
ANALYSIS TITLE: Raw Signal Density Graphs of Psoas Muscle Input ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Input 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.13608
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 Input 03 57
BROWSER_TRACK_DESCRIPTION: UCSD Psoas Muscle ChIP-Seq Input Donor STL003 Library AY57 EA Release 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 35,915,869
NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 19
FINDPEAKS_SCORE: 0.007
FINDPEAKS_PERCENTILE: 53
HOTSPOT_SCORE: 0.1169
HOTSPOT_PERCENTILE: 79
IROC_SCORE: 0.6018
IROC_PERCENTILE: 47
POISSON_SCORE: 0.3406
POISSON_PERCENTILE: 84
MAXIMUM_REPLICATE_CORRELATION: NA

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

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

value: Psoas Muscle


title: Reference Epigenome: ChIP-Seq Input from Human Sigmoid Colon Tissue; renlab.Input.STL003SG.01.01

description:
sample_term_id: UBERON_0001159
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Input from Human Sigmoid Colon Tissue. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: AY58
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.11873
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: GSM906422_UCSD.Sigmoid_Colon.Input.STL003.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.Input.STL003SG.01.01.hg19.level.1.release.8
ANALYSIS TITLE: Mapping of Sigmoid Colon Input ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Input 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.13538
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: 18,674,192
NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 19
FINDPEAKS_SCORE: 0.0075
FINDPEAKS_PERCENTILE: 68
HOTSPOT_SCORE: 0.1021
HOTSPOT_PERCENTILE: 63
IROC_SCORE: 0.4595
IROC_PERCENTILE: 27
POISSON_SCORE: 0.2071
POISSON_PERCENTILE: 63
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM906422_UCSD.Sigmoid_Colon.Input.STL003.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.Input.STL003SG.01.01.hg19.level.2.release.8
ANALYSIS TITLE: Raw Signal Density Graphs of Sigmoid Colon Input ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Input 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.13658
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 Input 03 58
BROWSER_TRACK_DESCRIPTION: UCSD Sigmoid Colon ChIP-Seq Input Donor STL003 Library AY58 EA Release 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 18,674,192
NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 19
FINDPEAKS_SCORE: 0.0075
FINDPEAKS_PERCENTILE: 68
HOTSPOT_SCORE: 0.1021
HOTSPOT_PERCENTILE: 63
IROC_SCORE: 0.4595
IROC_PERCENTILE: 27
POISSON_SCORE: 0.2071
POISSON_PERCENTILE: 63
MAXIMUM_REPLICATE_CORRELATION: NA

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

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

value: Sigmoid Colon


title: Reference Epigenome: ChIP-Seq Input from Human Esophagus Tissue; renlab.Input.STL003EG.01.01

description:
sample_term_id: UBERON_0001043
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Input from Human Esophagus Tissue. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: AK326
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.11831
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.11826
****************
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: GSM906415_UCSD.Esophagus.Input.STL003.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.Input.STL003EG.01.01.hg19.level.1.release.8
ANALYSIS TITLE: Mapping of Esophagus Input ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Input ChIP-Seq on Esophagus, 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.13497
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: 34,772,278
NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 19
FINDPEAKS_SCORE: 0.0063
FINDPEAKS_PERCENTILE: 37
HOTSPOT_SCORE: 0.0219
HOTSPOT_PERCENTILE: 32
IROC_SCORE: 0.5476
IROC_PERCENTILE: 33
POISSON_SCORE: 0.1267
POISSON_PERCENTILE: 37
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM906415_UCSD.Esophagus.Input.STL003.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.Input.STL003EG.01.01.hg19.level.2.release.8
ANALYSIS TITLE: Raw Signal Density Graphs of Esophagus Input ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Input ChIP-Seq read mappings from Esophagus, 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.13617
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: Esophagus Input 03 26
BROWSER_TRACK_DESCRIPTION: UCSD Esophagus ChIP-Seq Input Donor STL003 Library AK326 EA Release 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 34,772,278
NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 19
FINDPEAKS_SCORE: 0.0063
FINDPEAKS_PERCENTILE: 37
HOTSPOT_SCORE: 0.0219
HOTSPOT_PERCENTILE: 32
IROC_SCORE: 0.5476
IROC_PERCENTILE: 33
POISSON_SCORE: 0.1267
POISSON_PERCENTILE: 37
MAXIMUM_REPLICATE_CORRELATION: NA

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

value: Esophagus


title: Reference Epigenome: ChIP-Seq Input from Human Bladder Tissue; renlab.Input.STL001BL.01.01

description:
sample_term_id: UBERON_0001255
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Input from Human Bladder Tissue. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: AY59
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.11881
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.11880
****************
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: GSM906414_UCSD.Bladder.Input.STL003.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.Input.STL001BL.01.01.hg19.level.1.release.8
ANALYSIS TITLE: Mapping of Bladder Input ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Input ChIP-Seq on Bladder, 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.13447
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: 36,588,069
NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 19
FINDPEAKS_SCORE: 0.0063
FINDPEAKS_PERCENTILE: 37
HOTSPOT_SCORE: 0.1072
HOTSPOT_PERCENTILE: 74
IROC_SCORE: 0.5693
IROC_PERCENTILE: 40
POISSON_SCORE: 0.378
POISSON_PERCENTILE: 95
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM906414_UCSD.Bladder.Input.STL003.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.Input.STL001BL.01.01.hg19.level.2.release.8
ANALYSIS TITLE: Raw Signal Density Graphs of Bladder Input ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Input ChIP-Seq read mappings from Bladder, 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.13567
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: Bladder Input 03 59
BROWSER_TRACK_DESCRIPTION: UCSD Bladder ChIP-Seq Input Donor STL001 Library AY59 EA Release 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 36,588,069
NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 19
FINDPEAKS_SCORE: 0.0063
FINDPEAKS_PERCENTILE: 37
HOTSPOT_SCORE: 0.1072
HOTSPOT_PERCENTILE: 74
IROC_SCORE: 0.5693
IROC_PERCENTILE: 40
POISSON_SCORE: 0.378
POISSON_PERCENTILE: 95
MAXIMUM_REPLICATE_CORRELATION: NA

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

value: Bladder

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

value: Caucasian and African American


title: Reference Epigenome: ChIP-Seq Input from Human Aorta Tissue; renlab.Input.STL003AO.01.01

description:
sample_term_id: UBERON_0000947
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Input from Human Aorta Tissue. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: AY60
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.11895
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: GSM906413_UCSD.Aorta.Input.STL003.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.Input.STL003AO.01.01.hg19.level.1.release.8
ANALYSIS TITLE: Mapping of Aorta Input ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Input 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.13552
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: 16,683,788
NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 19
FINDPEAKS_SCORE: 0.1089
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.2656
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.8937
IROC_PERCENTILE: 80
POISSON_SCORE: 0.4255
POISSON_PERCENTILE: 100
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM906413_UCSD.Aorta.Input.STL003.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.Input.STL003AO.01.01.hg19.level.2.release.8
ANALYSIS TITLE: Raw Signal Density Graphs of Aorta Input ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Input 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.13672
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 Input 03 60
BROWSER_TRACK_DESCRIPTION: UCSD Aorta ChIP-Seq Input Donor STL003 Library AY60 EA Release 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 16,683,788
NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 19
FINDPEAKS_SCORE: 0.1089
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.2656
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.8937
IROC_PERCENTILE: 80
POISSON_SCORE: 0.4255
POISSON_PERCENTILE: 100
MAXIMUM_REPLICATE_CORRELATION: NA

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

value: Aorta

value: genomic DNA

value: ChIP-Seq Input


title: Reference Epigenome: ChIP-Seq Analysis of H3K9me3 in Human Left Ventricle Tissue; renlab.H3K9me3.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 H3K9me3 in Human Left Ventricle Tissue. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: AY51
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.11893
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: GSM906412_UCSD.Left_Ventricle.H3K9me3.STL003.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K9me3.STL003LV.01.01.hg19.level.1.release.8
ANALYSIS TITLE: Mapping of Left Ventricle H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K9me3 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.13516
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: 6,697,027
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 16
FINDPEAKS_SCORE: 0.2466
FINDPEAKS_PERCENTILE: 81
HOTSPOT_SCORE: 0.4113
HOTSPOT_PERCENTILE: 94
IROC_SCORE: 0.9131
IROC_PERCENTILE: 69
POISSON_SCORE: 0.4632
POISSON_PERCENTILE: 75
MAXIMUM_REPLICATE_CORRELATION: 0.96

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

ANALYSIS FILE NAME: GSM906412_UCSD.Left_Ventricle.H3K9me3.STL003.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K9me3.STL003LV.01.01.hg19.level.2.release.8
ANALYSIS TITLE: Raw Signal Density Graphs of Left Ventricle H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K9me3 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.13636
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 H3K9me3 03 51
BROWSER_TRACK_DESCRIPTION: UCSD Left Ventricle Histone H3K9me3 Donor STL003 Library AY51 EA Release 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 6,697,027
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 16
FINDPEAKS_SCORE: 0.2466
FINDPEAKS_PERCENTILE: 81
HOTSPOT_SCORE: 0.4113
HOTSPOT_PERCENTILE: 94
IROC_SCORE: 0.9131
IROC_PERCENTILE: 69
POISSON_SCORE: 0.4632
POISSON_PERCENTILE: 75
MAXIMUM_REPLICATE_CORRELATION: 0.96

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

source_name: Left Ventricle tissue; renlab.H3K9me3.STL003LV.01.01

value: Left Ventricle

value: Shin Lin, Stanford University

value: Primary Tissue

value: Autopsy

value: Histone H3K9me3

value: magnetic anti-rabbit

value: 5 micrograms

value: Abcam


title: Reference Epigenome: ChIP-Seq Analysis of H3K9me3 in Human Left Ventricle Tissue; renlab.H3K9me3.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 H3K9me3 in Human Left Ventricle Tissue. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: AK338
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.11842
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: GSM906409_UCSD.Left_Ventricle.H3K9me3.STL001.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K9me3.STL001LV.01.01.hg19.level.1.release.8
ANALYSIS TITLE: Mapping of Left Ventricle H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K9me3 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.13510
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: 11,594,305
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 16
FINDPEAKS_SCORE: 0.0494
FINDPEAKS_PERCENTILE: 13
HOTSPOT_SCORE: 0.211
HOTSPOT_PERCENTILE: 25
IROC_SCORE: 0.7538
IROC_PERCENTILE: 19
POISSON_SCORE: 0.3127
POISSON_PERCENTILE: 19
MAXIMUM_REPLICATE_CORRELATION: 0.96

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

ANALYSIS FILE NAME: GSM906409_UCSD.Left_Ventricle.H3K9me3.STL001.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K9me3.STL001LV.01.01.hg19.level.2.release.8
ANALYSIS TITLE: Raw Signal Density Graphs of Left Ventricle H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K9me3 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.13630
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 H3K9me3 01 38
BROWSER_TRACK_DESCRIPTION: UCSD Left Ventricle Histone H3K9me3 Donor STL001 Library AK338 EA Release 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 11,594,305
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 16
FINDPEAKS_SCORE: 0.0494
FINDPEAKS_PERCENTILE: 13
HOTSPOT_SCORE: 0.211
HOTSPOT_PERCENTILE: 25
IROC_SCORE: 0.7538
IROC_PERCENTILE: 19
POISSON_SCORE: 0.3127
POISSON_PERCENTILE: 19
MAXIMUM_REPLICATE_CORRELATION: 0.96

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

source_name: Left Ventricle tissue; renlab.H3K9me3.STL001LV.01.01

value: Male

value: Biorupter

value: 500 micrograms


title: Reference Epigenome: ChIP-Seq Analysis of H3K9me3 in Human Lung Tissue; renlab.H3K9me3.STL002LG.01.01

description:
sample_term_id: UBERON_0002048
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K9me3 in Human Lung Tissue. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: AY49
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.11878
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.11869
****************
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: GSM906411_UCSD.Lung.H3K9me3.STL002.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K9me3.STL002LG.01.01.hg19.level.1.release.8
ANALYSIS TITLE: Mapping of Lung H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K9me3 ChIP-Seq on Lung, Donor STL002, 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.13555
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: 26,134,290
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 16
FINDPEAKS_SCORE: 0.1985
FINDPEAKS_PERCENTILE: 69
HOTSPOT_SCORE: 0.3585
HOTSPOT_PERCENTILE: 88
IROC_SCORE: 0.8917
IROC_PERCENTILE: 56
POISSON_SCORE: 0.5046
POISSON_PERCENTILE: 88
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM906411_UCSD.Lung.H3K9me3.STL002.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K9me3.STL002LG.01.01.hg19.level.2.release.8
ANALYSIS TITLE: Raw Signal Density Graphs of Lung H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K9me3 ChIP-Seq read mappings from Lung, Donor STL002, 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.13675
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: Lung H3K9me3 02 49
BROWSER_TRACK_DESCRIPTION: UCSD Lung Histone H3K9me3 Donor STL002 Library AY49 EA Release 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 26,134,290
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 16
FINDPEAKS_SCORE: 0.1985
FINDPEAKS_PERCENTILE: 69
HOTSPOT_SCORE: 0.3585
HOTSPOT_PERCENTILE: 88
IROC_SCORE: 0.8917
IROC_PERCENTILE: 56
POISSON_SCORE: 0.5046
POISSON_PERCENTILE: 88
MAXIMUM_REPLICATE_CORRELATION: NA

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

value: Lung

value: iron deficiency, bipolar

value: iron deficiency, bipolar disease (NO diabetes, hypertension, coronary artery disease, cancer)

value: Female

value: Caucasian


title: Reference Epigenome: ChIP-Seq Analysis of H3K9me3 in Human Aorta Tissue; renlab.H3K9me3.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 H3K9me3 in Human Aorta Tissue. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: AY47
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.11867
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: GSM906410_UCSD.Aorta.H3K9me3.STL003.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K9me3.STL003AO.01.01.hg19.level.1.release.8
ANALYSIS TITLE: Mapping of Aorta H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K9me3 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.13459
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: 27,557,850
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 16
FINDPEAKS_SCORE: 0.1234
FINDPEAKS_PERCENTILE: 38
HOTSPOT_SCORE: 0.2678
HOTSPOT_PERCENTILE: 44
IROC_SCORE: 0.864
IROC_PERCENTILE: 50
POISSON_SCORE: 0.4167
POISSON_PERCENTILE: 44
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM906410_UCSD.Aorta.H3K9me3.STL003.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K9me3.STL003AO.01.01.hg19.level.2.release.8
ANALYSIS TITLE: Raw Signal Density Graphs of Aorta H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K9me3 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.13579
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 H3K9me3 03 47
BROWSER_TRACK_DESCRIPTION: UCSD Aorta Histone H3K9me3 Donor STL003 Library AY47 EA Release 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 27,557,850
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 16
FINDPEAKS_SCORE: 0.1234
FINDPEAKS_PERCENTILE: 38
HOTSPOT_SCORE: 0.2678
HOTSPOT_PERCENTILE: 44
IROC_SCORE: 0.864
IROC_PERCENTILE: 50
POISSON_SCORE: 0.4167
POISSON_PERCENTILE: 44
MAXIMUM_REPLICATE_CORRELATION: NA

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

value: Aorta

value: genomic DNA

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


title: Reference Epigenome: ChIP-Seq Analysis of H3K4me3 in Human Small Bowel Tissue; renlab.H3K4me3.STL003SB.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 H3K4me3 in Human Small Bowel Tissue. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: AK329
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.11845
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.11844
****************
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: GSM906407_UCSD.Small_Intestine.H3K4me3.STL003.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K4me3.STL003SB.01.01.hg19.level.1.release.8
ANALYSIS TITLE: Mapping of Small Intestine H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K4me3 ChIP-Seq on Small Intestine, 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.13476
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: 10,626,577
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 14
FINDPEAKS_SCORE: 0.1669
FINDPEAKS_PERCENTILE: 21
HOTSPOT_SCORE: 0.268
HOTSPOT_PERCENTILE: 29
IROC_SCORE: 0.9979
IROC_PERCENTILE: 25
POISSON_SCORE: 0.3048
POISSON_PERCENTILE: 21
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM906407_UCSD.Small_Intestine.H3K4me3.STL003.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K4me3.STL003SB.01.01.hg19.level.2.release.8
ANALYSIS TITLE: Raw Signal Density Graphs of Small Intestine H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K4me3 ChIP-Seq read mappings from Small Intestine, 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.13596
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 H3K4me3 03 29
BROWSER_TRACK_DESCRIPTION: UCSD Small Intestine Histone H3K4me3 Donor STL003 Library AK329 EA Release 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 10,626,577
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 14
FINDPEAKS_SCORE: 0.1669
FINDPEAKS_PERCENTILE: 21
HOTSPOT_SCORE: 0.268
HOTSPOT_PERCENTILE: 29
IROC_SCORE: 0.9979
IROC_PERCENTILE: 25
POISSON_SCORE: 0.3048
POISSON_PERCENTILE: 21
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: Small Intestine tissue; renlab.H3K4me3.STL003SB.01.01

value: Small Intestine

value: Shin Lin, Stanford University

value: Primary Tissue

value: Histone H3K4me3

value: Active Motif


title: Reference Epigenome: ChIP-Seq Analysis of H3K36me3 in Human Left Ventricle Tissue; renlab.H3K36me3.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 H3K36me3 in Human Left Ventricle Tissue. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: AK335
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.11836
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: GSM906402_UCSD.Left_Ventricle.H3K36me3.STL001.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K36me3.STL001LV.01.01.hg19.level.1.release.8
ANALYSIS TITLE: Mapping of Left Ventricle H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K36me3 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.13456
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: 15,810,069
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 12
FINDPEAKS_SCORE: 0.1301
FINDPEAKS_PERCENTILE: 8
HOTSPOT_SCORE: 0.2406
HOTSPOT_PERCENTILE: 17
IROC_SCORE: 0.9062
IROC_PERCENTILE: 8
POISSON_SCORE: 0.3626
POISSON_PERCENTILE: 8
MAXIMUM_REPLICATE_CORRELATION: 0.97

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

ANALYSIS FILE NAME: GSM906402_UCSD.Left_Ventricle.H3K36me3.STL001.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K36me3.STL001LV.01.01.hg19.level.2.release.8
ANALYSIS TITLE: Raw Signal Density Graphs of Left Ventricle H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K36me3 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.13576
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 H3K36me3 01 35
BROWSER_TRACK_DESCRIPTION: UCSD Left Ventricle Histone H3K36me3 Donor STL001 Library AK335 EA Release 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 15,810,069
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 12
FINDPEAKS_SCORE: 0.1301
FINDPEAKS_PERCENTILE: 8
HOTSPOT_SCORE: 0.2406
HOTSPOT_PERCENTILE: 17
IROC_SCORE: 0.9062
IROC_PERCENTILE: 8
POISSON_SCORE: 0.3626
POISSON_PERCENTILE: 8
MAXIMUM_REPLICATE_CORRELATION: 0.97

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

source_name: Left Ventricle tissue; renlab.H3K36me3.STL001LV.01.01

value: Left Ventricle

value: Autopsy

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

value: Caucasian and African American

value: Histone H3K36me3

value: magnetic anti-rabbit

value: 5 micrograms

value: Abcam


title: Reference Epigenome: ChIP-Seq Analysis of H3K27me3 in Human Esophagus Tissue; renlab.H3K27me3.STL003EG.01.01

description:
sample_term_id: UBERON_0001043
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K27me3 in Human Esophagus Tissue. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: AK325
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.11829
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.11826
****************
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: GSM906399_UCSD.Esophagus.H3K27me3.STL003.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K27me3.STL003EG.01.01.hg19.level.1.release.8
ANALYSIS TITLE: Mapping of Esophagus H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K27me3 ChIP-Seq on Esophagus, 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.13534
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: 24,649,364
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 19
FINDPEAKS_SCORE: 0.0145
FINDPEAKS_PERCENTILE: 32
HOTSPOT_SCORE: 0.1075
HOTSPOT_PERCENTILE: 16
IROC_SCORE: NA
IROC_PERCENTILE: NA
POISSON_SCORE: 0.2445
POISSON_PERCENTILE: 32
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM906399_UCSD.Esophagus.H3K27me3.STL003.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K27me3.STL003EG.01.01.hg19.level.2.release.8
ANALYSIS TITLE: Raw Signal Density Graphs of Esophagus H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K27me3 ChIP-Seq read mappings from Esophagus, 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.13654
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: Esophagus H3K27me3 03 25
BROWSER_TRACK_DESCRIPTION: UCSD Esophagus Histone H3K27me3 Donor STL003 Library AK325 EA Release 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 24,649,364
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 19
FINDPEAKS_SCORE: 0.0145
FINDPEAKS_PERCENTILE: 32
HOTSPOT_SCORE: 0.1075
HOTSPOT_PERCENTILE: 16
IROC_SCORE: NA
IROC_PERCENTILE: NA
POISSON_SCORE: 0.2445
POISSON_PERCENTILE: 32
MAXIMUM_REPLICATE_CORRELATION: NA

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

value: Esophagus

value: Male

value: Caucasian

value: Histone H3K27me3

value: Biorupter

value: 500 micrograms


title: Reference Epigenome: ChIP-Seq Analysis of H3K4me1 in Human Left Ventricle Tissue; renlab.H3K4me1.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 H3K4me1 in Human Left Ventricle Tissue. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: AK336
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.11838
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: GSM906404_UCSD.Left_Ventricle.H3K4me1.STL001.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K4me1.STL001LV.01.01.hg19.level.1.release.8
ANALYSIS TITLE: Mapping of Left Ventricle H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K4me1 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.13525
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: 24,872,864
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 12
FINDPEAKS_SCORE: 0.1011
FINDPEAKS_PERCENTILE: 17
HOTSPOT_SCORE: 0.2408
HOTSPOT_PERCENTILE: 17
IROC_SCORE: 0.906
IROC_PERCENTILE: 25
POISSON_SCORE: 0.3944
POISSON_PERCENTILE: 17
MAXIMUM_REPLICATE_CORRELATION: 0.96

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

ANALYSIS FILE NAME: GSM906404_UCSD.Left_Ventricle.H3K4me1.STL001.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K4me1.STL001LV.01.01.hg19.level.2.release.8
ANALYSIS TITLE: Raw Signal Density Graphs of Left Ventricle H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K4me1 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.13645
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 H3K4me1 01 36
BROWSER_TRACK_DESCRIPTION: UCSD Left Ventricle Histone H3K4me1 Donor STL001 Library AK336 EA Release 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 24,872,864
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 12
FINDPEAKS_SCORE: 0.1011
FINDPEAKS_PERCENTILE: 17
HOTSPOT_SCORE: 0.2408
HOTSPOT_PERCENTILE: 17
IROC_SCORE: 0.906
IROC_PERCENTILE: 25
POISSON_SCORE: 0.3944
POISSON_PERCENTILE: 17
MAXIMUM_REPLICATE_CORRELATION: 0.96

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

source_name: Left Ventricle tissue; renlab.H3K4me1.STL001LV.01.01

value: genomic DNA

value: Shin Lin, Stanford University

value: Primary Tissue

value: Histone H3K4me1


title: Reference Epigenome: ChIP-Seq Analysis of H3K27me3 in Human Spleen Tissue; renlab.H3K27me3.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 H3K27me3 in Human Spleen Tissue. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: AK349
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.11857
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: GSM906400_UCSD.Spleen.H3K27me3.STL003.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K27me3.STL003SX.01.01.hg19.level.1.release.8
ANALYSIS TITLE: Mapping of Spleen H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K27me3 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.13527
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: 15,494,871
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 19
FINDPEAKS_SCORE: 0.0097
FINDPEAKS_PERCENTILE: 16
HOTSPOT_SCORE: 0.1097
HOTSPOT_PERCENTILE: 21
IROC_SCORE: NA
IROC_PERCENTILE: NA
POISSON_SCORE: 0.1784
POISSON_PERCENTILE: 11
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM906400_UCSD.Spleen.H3K27me3.STL003.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K27me3.STL003SX.01.01.hg19.level.2.release.8
ANALYSIS TITLE: Raw Signal Density Graphs of Spleen H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K27me3 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.13647
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 H3K27me3 03 49
BROWSER_TRACK_DESCRIPTION: UCSD Spleen Histone H3K27me3 Donor STL003 Library AK349 EA Release 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 15,494,871
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 19
FINDPEAKS_SCORE: 0.0097
FINDPEAKS_PERCENTILE: 16
HOTSPOT_SCORE: 0.1097
HOTSPOT_PERCENTILE: 21
IROC_SCORE: NA
IROC_PERCENTILE: NA
POISSON_SCORE: 0.1784
POISSON_PERCENTILE: 11
MAXIMUM_REPLICATE_CORRELATION: NA

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

value: Spleen

value: Autopsy

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

value: Active Motif


title: Reference Epigenome: ChIP-Seq Analysis of H3K27ac in Human Spleen Tissue; renlab.H3K27ac.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 H3K27ac in Human Spleen Tissue. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: AK348
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.11855
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: GSM906398_UCSD.Spleen.H3K27ac.STL003.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K27ac.STL003SX.01.01.hg19.level.1.release.8
ANALYSIS TITLE: Mapping of Spleen H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K27ac 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.13522
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: 16,942,570
NUMBER_OF_H3K27ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 21
FINDPEAKS_SCORE: 0.4984
FINDPEAKS_PERCENTILE: 71
HOTSPOT_SCORE: 0.5255
HOTSPOT_PERCENTILE: 71
IROC_SCORE: 0.9975
IROC_PERCENTILE: 62
POISSON_SCORE: 0.5608
POISSON_PERCENTILE: 67
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM906398_UCSD.Spleen.H3K27ac.STL003.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K27ac.STL003SX.01.01.hg19.level.2.release.8
ANALYSIS TITLE: Raw Signal Density Graphs of Spleen H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K27ac 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.13642
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 H3K27ac 03 48
BROWSER_TRACK_DESCRIPTION: UCSD Spleen Histone H3K27ac Donor STL003 Library AK348 EA Release 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 16,942,570
NUMBER_OF_H3K27ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 21
FINDPEAKS_SCORE: 0.4984
FINDPEAKS_PERCENTILE: 71
HOTSPOT_SCORE: 0.5255
HOTSPOT_PERCENTILE: 71
IROC_SCORE: 0.9975
IROC_PERCENTILE: 62
POISSON_SCORE: 0.5608
POISSON_PERCENTILE: 67
MAXIMUM_REPLICATE_CORRELATION: NA

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

value: Histone H3K27ac

value: magnetic anti-rabbit


title: Reference Epigenome: ChIP-Seq Analysis of H3K27ac in Human Lung Tissue; renlab.H3K27ac.STL002LG.01.01

description:
sample_term_id: UBERON_0002048
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K27ac in Human Lung Tissue. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: AY48
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.11870
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.11869
****************
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: GSM906395_UCSD.Lung.H3K27ac.STL002.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K27ac.STL002LG.01.01.hg19.level.1.release.8
ANALYSIS TITLE: Mapping of Lung H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K27ac ChIP-Seq on Lung, Donor STL002, 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.13507
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: 29,556,736
NUMBER_OF_H3K27ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 21
FINDPEAKS_SCORE: 0.3754
FINDPEAKS_PERCENTILE: 38
HOTSPOT_SCORE: 0.433
HOTSPOT_PERCENTILE: 43
IROC_SCORE: 0.9951
IROC_PERCENTILE: 33
POISSON_SCORE: 0.5162
POISSON_PERCENTILE: 43
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM906395_UCSD.Lung.H3K27ac.STL002.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K27ac.STL002LG.01.01.hg19.level.2.release.8
ANALYSIS TITLE: Raw Signal Density Graphs of Lung H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K27ac ChIP-Seq read mappings from Lung, Donor STL002, 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.13627
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: Lung H3K27ac 02 48
BROWSER_TRACK_DESCRIPTION: UCSD Lung Histone H3K27ac Donor STL002 Library AY48 EA Release 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 29,556,736
NUMBER_OF_H3K27ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 21
FINDPEAKS_SCORE: 0.3754
FINDPEAKS_PERCENTILE: 38
HOTSPOT_SCORE: 0.433
HOTSPOT_PERCENTILE: 43
IROC_SCORE: 0.9951
IROC_PERCENTILE: 33
POISSON_SCORE: 0.5162
POISSON_PERCENTILE: 43
MAXIMUM_REPLICATE_CORRELATION: NA

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

value: Lung

value: iron deficiency, bipolar

value: iron deficiency, bipolar disease (NO diabetes, hypertension, coronary artery disease, cancer)

value: Female

value: 5 micrograms


title: Reference Epigenome: ChIP-Seq Input from Human Pancreas Tissue; renlab.Input.STL003PA.01.01

description:
sample_term_id: UBERON_0001264
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Input from Human Pancreas Tissue. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: AK344
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.11850
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: GSM906419_UCSD.Pancreas.Input.STL003.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.Input.STL003PA.01.01.hg19.level.1.release.8
ANALYSIS TITLE: Mapping of Pancreas Input ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Input 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.13543
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: 43,943,140
NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 19
FINDPEAKS_SCORE: 0.0049
FINDPEAKS_PERCENTILE: 16
HOTSPOT_SCORE: 0.0102
HOTSPOT_PERCENTILE: 16
IROC_SCORE: 0.0
IROC_PERCENTILE: 13
POISSON_SCORE: 0.0988
POISSON_PERCENTILE: 26
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM906419_UCSD.Pancreas.Input.STL003.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.Input.STL003PA.01.01.hg19.level.2.release.8
ANALYSIS TITLE: Raw Signal Density Graphs of Pancreas Input ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Input 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.13663
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 Input 03 44
BROWSER_TRACK_DESCRIPTION: UCSD Pancreas ChIP-Seq Input Donor STL003 Library AK344 EA Release 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 43,943,140
NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 19
FINDPEAKS_SCORE: 0.0049
FINDPEAKS_PERCENTILE: 16
HOTSPOT_SCORE: 0.0102
HOTSPOT_PERCENTILE: 16
IROC_SCORE: 0.0
IROC_PERCENTILE: 13
POISSON_SCORE: 0.0988
POISSON_PERCENTILE: 26
MAXIMUM_REPLICATE_CORRELATION: NA

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

value: Pancreas

value: Male

value: Caucasian

value: ChIP-Seq Input

value: Biorupter

value: Input


title: Reference Epigenome: ChIP-Seq Analysis of H3K27ac in Human Esophagus Tissue; renlab.H3K27ac.STL003EG.01.01

description:
sample_term_id: UBERON_0001043
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K27ac in Human Esophagus Tissue. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: AK324
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.11827
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.11826
****************
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: GSM906393_UCSD.Esophagus.H3K27ac.STL003.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K27ac.STL003EG.01.01.hg19.level.1.release.8
ANALYSIS TITLE: Mapping of Esophagus H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K27ac ChIP-Seq on Esophagus, 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.13455
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: 19,719,725
NUMBER_OF_H3K27ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 21
FINDPEAKS_SCORE: 0.4493
FINDPEAKS_PERCENTILE: 52
HOTSPOT_SCORE: 0.4804
HOTSPOT_PERCENTILE: 52
IROC_SCORE: 0.9972
IROC_PERCENTILE: 48
POISSON_SCORE: 0.5389
POISSON_PERCENTILE: 52
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM906393_UCSD.Esophagus.H3K27ac.STL003.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K27ac.STL003EG.01.01.hg19.level.2.release.8
ANALYSIS TITLE: Raw Signal Density Graphs of Esophagus H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K27ac ChIP-Seq read mappings from Esophagus, 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.13575
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: Esophagus H3K27ac 03 24
BROWSER_TRACK_DESCRIPTION: UCSD Esophagus Histone H3K27ac Donor STL003 Library AK324 EA Release 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 19,719,725
NUMBER_OF_H3K27ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 21
FINDPEAKS_SCORE: 0.4493
FINDPEAKS_PERCENTILE: 52
HOTSPOT_SCORE: 0.4804
HOTSPOT_PERCENTILE: 52
IROC_SCORE: 0.9972
IROC_PERCENTILE: 48
POISSON_SCORE: 0.5389
POISSON_PERCENTILE: 52
MAXIMUM_REPLICATE_CORRELATION: NA

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

value: Esophagus

value: genomic DNA

value: Shin Lin, Stanford University

value: Primary Tissue

value: 500 micrograms


title: Reference Epigenome: ChIP-Seq Analysis of H3K27ac in Human Adipose Tissue; renlab.H3K27ac.STL003FT.01.01

description:
sample_term_id: UBERON_0001013
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K27ac in Human Adipose Tissue. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: AK345
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.11860
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.11859
****************
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: GSM906394_UCSD.Adipose_Tissue.H3K27ac.STL003.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K27ac.STL003FT.01.01.hg19.level.1.release.8
ANALYSIS TITLE: Mapping of Adipose Tissue H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K27ac ChIP-Seq on Adipose Tissue, 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.13490
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: 16,468,705
NUMBER_OF_H3K27ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 21
FINDPEAKS_SCORE: 0.0602
FINDPEAKS_PERCENTILE: 14
HOTSPOT_SCORE: 0.1745
HOTSPOT_PERCENTILE: 14
IROC_SCORE: 0.8695
IROC_PERCENTILE: 10
POISSON_SCORE: 0.2736
POISSON_PERCENTILE: 14
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM906394_UCSD.Adipose_Tissue.H3K27ac.STL003.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K27ac.STL003FT.01.01.hg19.level.2.release.8
ANALYSIS TITLE: Raw Signal Density Graphs of Adipose Tissue H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K27ac ChIP-Seq read mappings from Adipose Tissue, 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.13610
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: AT H3K27ac 03 45
BROWSER_TRACK_DESCRIPTION: UCSD Adipose Tissue Histone H3K27ac Donor STL003 Library AK345 EA Release 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 16,468,705
NUMBER_OF_H3K27ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 21
FINDPEAKS_SCORE: 0.0602
FINDPEAKS_PERCENTILE: 14
HOTSPOT_SCORE: 0.1745
HOTSPOT_PERCENTILE: 14
IROC_SCORE: 0.8695
IROC_PERCENTILE: 10
POISSON_SCORE: 0.2736
POISSON_PERCENTILE: 14
MAXIMUM_REPLICATE_CORRELATION: NA

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

value: Adipose Tissue

value: Autopsy

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

value: Histone H3K27ac

value: magnetic anti-rabbit

value: Active Motif


title: Reference Epigenome: ChIP-Seq Input from Human Lung Tissue; renlab.Input.STL002LG.01.01

description:
sample_term_id: UBERON_0002048
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Input from Human Lung Tissue. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: AY61
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.11883
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.11869
****************
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: GSM906417_UCSD.Lung.Input.STL002.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.Input.STL002LG.01.01.hg19.level.1.release.8
ANALYSIS TITLE: Mapping of Lung Input ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Input ChIP-Seq on Lung, Donor STL002, 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.13545
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: 18,548,742
NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 19
FINDPEAKS_SCORE: 0.0101
FINDPEAKS_PERCENTILE: 84
HOTSPOT_SCORE: 0.1459
HOTSPOT_PERCENTILE: 84
IROC_SCORE: 0.708
IROC_PERCENTILE: 60
POISSON_SCORE: 0.3017
POISSON_PERCENTILE: 79
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM906417_UCSD.Lung.Input.STL002.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.Input.STL002LG.01.01.hg19.level.2.release.8
ANALYSIS TITLE: Raw Signal Density Graphs of Lung Input ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Input ChIP-Seq read mappings from Lung, Donor STL002, 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.13665
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: Lung Input 02 61
BROWSER_TRACK_DESCRIPTION: UCSD Lung ChIP-Seq Input Donor STL002 Library AY61 EA Release 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 18,548,742
NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 19
FINDPEAKS_SCORE: 0.0101
FINDPEAKS_PERCENTILE: 84
HOTSPOT_SCORE: 0.1459
HOTSPOT_PERCENTILE: 84
IROC_SCORE: 0.708
IROC_PERCENTILE: 60
POISSON_SCORE: 0.3017
POISSON_PERCENTILE: 79
MAXIMUM_REPLICATE_CORRELATION: NA

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

value: Lung

value: iron deficiency, bipolar

value: iron deficiency, bipolar disease (NO diabetes, hypertension, coronary artery disease, cancer)

value: Female