title: Reference Epigenome: ChIP-Seq Input from Human Spleen Tissue; renlab.Input.STL002SX.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: AY333
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.14065
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.14062
****************
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: GSM1013174_UCSD.Spleen.Input.STL002.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.Input.STL002SX.01.01.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Spleen Input ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Input ChIP-Seq on Spleen, 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.16407
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 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 20,495,589
FINDPEAKS_SCORE: 0.0063
FINDPEAKS_PERCENTILE: 63
HOTSPOT_SCORE: 0.0585
HOTSPOT_PERCENTILE: 72
IROC_SCORE: 0.0
IROC_PERCENTILE: 21
POISSON_SCORE: 0.0921
POISSON_PERCENTILE: 65
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

ANALYSIS FILE NAME: GSM1013174_UCSD.Spleen.Input.STL002.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.Input.STL002SX.01.01.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Spleen Input ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Input ChIP-Seq read mappings from Spleen, 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.16561
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 9
BROWSER_TRACK_NAME: Spleen Input 02 33
BROWSER_TRACK_DESCRIPTION: UCSD Spleen ChIP-Seq Input Donor STL002 Library AY333 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 20,495,589
FINDPEAKS_SCORE: 0.0063
FINDPEAKS_PERCENTILE: 63
HOTSPOT_SCORE: 0.0585
HOTSPOT_PERCENTILE: 72
IROC_SCORE: 0.0
IROC_PERCENTILE: 21
POISSON_SCORE: 0.0921
POISSON_PERCENTILE: 65
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

value: Spleen

value: iron deficiency, bipolar

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

value: Female

value: Caucasian

value: ChIP-Seq Input

value: Input


title: Reference Epigenome: ChIP-Seq Input from Human Pancreas Tissue; renlab.Input.STL002PA.01.01

status: Public on Jun 22 2013

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_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: CY45
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.14048
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.14039
****************
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: GSM1013172_UCSD.Pancreas.Input.STL002.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.Input.STL002PA.01.01.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Pancreas Input ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Input ChIP-Seq on Pancreas, 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.16473
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 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 28,314,654
FINDPEAKS_SCORE: 0.0066
FINDPEAKS_PERCENTILE: 67
HOTSPOT_SCORE: 0.0497
HOTSPOT_PERCENTILE: 70
IROC_SCORE: 0.9638
IROC_PERCENTILE: 55
POISSON_SCORE: 0.127
POISSON_PERCENTILE: 76
MAXIMUM_REPLICATE_CORRELATION: 0.97

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

ANALYSIS FILE NAME: GSM1013172_UCSD.Pancreas.Input.STL002.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.Input.STL002PA.01.01.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Pancreas Input ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Input ChIP-Seq read mappings from Pancreas, 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.16627
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 9
BROWSER_TRACK_NAME: Pancreas Input 02 45
BROWSER_TRACK_DESCRIPTION: UCSD Pancreas ChIP-Seq Input Donor STL002 Library CY45 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 28,314,654
FINDPEAKS_SCORE: 0.0066
FINDPEAKS_PERCENTILE: 67
HOTSPOT_SCORE: 0.0497
HOTSPOT_PERCENTILE: 70
IROC_SCORE: 0.9638
IROC_PERCENTILE: 55
POISSON_SCORE: 0.127
POISSON_PERCENTILE: 76
MAXIMUM_REPLICATE_CORRELATION: 0.97

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

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: Pancreas

tag: molecule

value: genomic DNA

tag: disease

value: Shin Lin, Stanford University

value: Primary Tissue

value: Autopsy

value: Biorupter

value: 500 micrograms


title: Reference Epigenome: ChIP-Seq Input from Human Psoas Muscle Tissue; renlab.Input.STL002PO.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: AY332
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.14053
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.14050
****************
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: GSM1013173_UCSD.Psoas_Muscle.Input.STL002.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.Input.STL002PO.01.01.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Psoas Muscle Input ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Input ChIP-Seq on Psoas Muscle, 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.16394
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 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 33,826,158
FINDPEAKS_SCORE: 0.1954
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.3338
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.944
IROC_PERCENTILE: 42
POISSON_SCORE: 0.5402
POISSON_PERCENTILE: 100
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

ANALYSIS FILE NAME: GSM1013173_UCSD.Psoas_Muscle.Input.STL002.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.Input.STL002PO.01.01.hg19.level.2.release.9
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 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.16548
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 9
BROWSER_TRACK_NAME: PM Input 02 32
BROWSER_TRACK_DESCRIPTION: UCSD Psoas Muscle ChIP-Seq Input Donor STL002 Library AY332 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 33,826,158
FINDPEAKS_SCORE: 0.1954
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.3338
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.944
IROC_PERCENTILE: 42
POISSON_SCORE: 0.5402
POISSON_PERCENTILE: 100
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

source_name: Psoas Muscle tissue; renlab.Input.STL002PO.01.01

value: Psoas Muscle


title: Reference Epigenome: ChIP-Seq Input from Human Gastric Tissue; renlab.Input.STL002GA.01.01

description:
sample_term_id: UBERON_0000945
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Input from Human Gastric Tissue. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: AY331
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.14014
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.14004
****************
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: GSM1013170_UCSD.Gastric.Input.STL002.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.Input.STL002GA.01.01.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Gastric Input ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Input ChIP-Seq on Gastric, 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.16484
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 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 23,783,078
FINDPEAKS_SCORE: 0.0071
FINDPEAKS_PERCENTILE: 74
HOTSPOT_SCORE: 0.1327
HOTSPOT_PERCENTILE: 91
IROC_SCORE: 0.7462
IROC_PERCENTILE: 30
POISSON_SCORE: 0.2973
POISSON_PERCENTILE: 91
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

ANALYSIS FILE NAME: GSM1013170_UCSD.Gastric.Input.STL002.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.Input.STL002GA.01.01.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Gastric Input ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Input ChIP-Seq read mappings from Gastric, 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.16638
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 9
BROWSER_TRACK_NAME: Gastric Input 02 31
BROWSER_TRACK_DESCRIPTION: UCSD Gastric ChIP-Seq Input Donor STL002 Library AY331 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 23,783,078
FINDPEAKS_SCORE: 0.0071
FINDPEAKS_PERCENTILE: 74
HOTSPOT_SCORE: 0.1327
HOTSPOT_PERCENTILE: 91
IROC_SCORE: 0.7462
IROC_PERCENTILE: 30
POISSON_SCORE: 0.2973
POISSON_PERCENTILE: 91
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

value: Gastric


title: Reference Epigenome: ChIP-Seq Input from Human Aorta Tissue; renlab.Input.STL002AO.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: AY357
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.14008
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.14007
****************
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: GSM1013169_UCSD.Aorta.Input.STL002.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.Input.STL002AO.01.01.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Aorta Input ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Input ChIP-Seq on Aorta, 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.16487
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 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 29,273,404
FINDPEAKS_SCORE: 0.0122
FINDPEAKS_PERCENTILE: 94
HOTSPOT_SCORE: 0.1736
HOTSPOT_PERCENTILE: 96
IROC_SCORE: 0.8753
IROC_PERCENTILE: 40
POISSON_SCORE: 0.4104
POISSON_PERCENTILE: 98
MAXIMUM_REPLICATE_CORRELATION: 0.97

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

ANALYSIS FILE NAME: GSM1013169_UCSD.Aorta.Input.STL002.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.Input.STL002AO.01.01.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Aorta Input ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Input ChIP-Seq read mappings from Aorta, 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.16641
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 9
BROWSER_TRACK_NAME: Aorta Input 02 57
BROWSER_TRACK_DESCRIPTION: UCSD Aorta ChIP-Seq Input Donor STL002 Library AY357 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 29,273,404
FINDPEAKS_SCORE: 0.0122
FINDPEAKS_PERCENTILE: 94
HOTSPOT_SCORE: 0.1736
HOTSPOT_PERCENTILE: 96
IROC_SCORE: 0.8753
IROC_PERCENTILE: 40
POISSON_SCORE: 0.4104
POISSON_PERCENTILE: 98
MAXIMUM_REPLICATE_CORRELATION: 0.97

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

value: Aorta


title: Reference Epigenome: ChIP-Seq Input from Human Adrenal Gland Tissue; renlab.Input.STL002AD.01.01

description:
sample_term_id: UBERON_0002369
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Input from Human Adrenal Gland Tissue. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: CY48
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.14037
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.13995
****************
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: GSM1013168_UCSD.Adrenal_Gland.Input.STL002.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.Input.STL002AD.01.01.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Adrenal Gland Input ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Input ChIP-Seq on Adrenal Gland, 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.16445
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 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 31,759,933
FINDPEAKS_SCORE: 0.0066
FINDPEAKS_PERCENTILE: 67
HOTSPOT_SCORE: 0.0994
HOTSPOT_PERCENTILE: 87
IROC_SCORE: 0.6779
IROC_PERCENTILE: 26
POISSON_SCORE: 0.2853
POISSON_PERCENTILE: 87
MAXIMUM_REPLICATE_CORRELATION: 0.97

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

ANALYSIS FILE NAME: GSM1013168_UCSD.Adrenal_Gland.Input.STL002.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.Input.STL002AD.01.01.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Adrenal Gland Input ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Input ChIP-Seq read mappings from Adrenal Gland, 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.16599
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 9
BROWSER_TRACK_NAME: AG Input 02 48
BROWSER_TRACK_DESCRIPTION: UCSD Adrenal Gland ChIP-Seq Input Donor STL002 Library CY48 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 31,759,933
FINDPEAKS_SCORE: 0.0066
FINDPEAKS_PERCENTILE: 67
HOTSPOT_SCORE: 0.0994
HOTSPOT_PERCENTILE: 87
IROC_SCORE: 0.6779
IROC_PERCENTILE: 26
POISSON_SCORE: 0.2853
POISSON_PERCENTILE: 87
MAXIMUM_REPLICATE_CORRELATION: 0.97

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

source_name: Adrenal Gland tissue; renlab.Input.STL002AD.01.01

value: Adrenal Gland


title: Reference Epigenome: ChIP-Seq Analysis of H3K4me1 in Human Psoas Muscle Tissue; renlab.H3K4me1.STL001PO.01.01

description:
sample_term_id: UBERON_0008450
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K4me1 in Human Psoas Muscle Tissue. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: CY105
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.15094
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.14034
****************
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: GSM1059444_UCSD.Psoas_Muscle.H3K4me1.STL001.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K4me1.STL001PO.01.01.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Psoas Muscle H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K4me1 ChIP-Seq on Psoas Muscle, 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.16462
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 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 11,555,445
FINDPEAKS_SCORE: 0.11
FINDPEAKS_PERCENTILE: 17
HOTSPOT_SCORE: 0.25
HOTSPOT_PERCENTILE: 25
IROC_SCORE: 0.8664
IROC_PERCENTILE: 15
POISSON_SCORE: 0.39
POISSON_PERCENTILE: 25
MAXIMUM_REPLICATE_CORRELATION: 0.97

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

ANALYSIS FILE NAME: GSM1059444_UCSD.Psoas_Muscle.H3K4me1.STL001.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K4me1.STL001PO.01.01.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Psoas Muscle H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K4me1 ChIP-Seq read mappings from Psoas Muscle, 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.16616
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 9
BROWSER_TRACK_NAME: PM H3K4me1 01 05
BROWSER_TRACK_DESCRIPTION: UCSD Psoas Muscle Histone H3K4me1 Donor STL001 Library CY105 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 11,555,445
FINDPEAKS_SCORE: 0.11
FINDPEAKS_PERCENTILE: 17
HOTSPOT_SCORE: 0.25
HOTSPOT_PERCENTILE: 25
IROC_SCORE: 0.8664
IROC_PERCENTILE: 15
POISSON_SCORE: 0.39
POISSON_PERCENTILE: 25
MAXIMUM_REPLICATE_CORRELATION: 0.97

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

source_name: Psoas Muscle tissue; renlab.H3K4me1.STL001PO.01.01

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

value: Male

value: Caucasian and African American

value: Histone H3K4me1

value: magnetic anti-rabbit

value: 5 micrograms

value: Abcam


title: Reference Epigenome: ChIP-Seq Input from Human Psoas Muscle Tissue; renlab.Input.STL001PO.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: CY51
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.14035
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.14034
****************
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: GSM1013166_UCSD.Psoas_Muscle.Input.STL001.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.Input.STL001PO.01.01.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Psoas Muscle Input ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Input ChIP-Seq on Psoas Muscle, 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.16392
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 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 49,898,109
FINDPEAKS_SCORE: 0.0057
FINDPEAKS_PERCENTILE: 44
HOTSPOT_SCORE: 0.1264
HOTSPOT_PERCENTILE: 89
IROC_SCORE: 0.8437
IROC_PERCENTILE: 38
POISSON_SCORE: 0.3545
POISSON_PERCENTILE: 94
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

ANALYSIS FILE NAME: GSM1013166_UCSD.Psoas_Muscle.Input.STL001.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.Input.STL001PO.01.01.hg19.level.2.release.9
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 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.16546
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 9
BROWSER_TRACK_NAME: PM Input 01 51
BROWSER_TRACK_DESCRIPTION: UCSD Psoas Muscle ChIP-Seq Input Donor STL001 Library CY51 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 49,898,109
FINDPEAKS_SCORE: 0.0057
FINDPEAKS_PERCENTILE: 44
HOTSPOT_SCORE: 0.1264
HOTSPOT_PERCENTILE: 89
IROC_SCORE: 0.8437
IROC_PERCENTILE: 38
POISSON_SCORE: 0.3545
POISSON_PERCENTILE: 94
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

source_name: Psoas Muscle tissue; renlab.Input.STL001PO.01.01

value: genomic DNA

value: ChIP-Seq Input

value: Input


title: Reference Epigenome: ChIP-Seq Analysis of H3K9me3 in Human Thymus Tissue; renlab.H3K9me3.STL001TH.01.01

description:
sample_term_id: UBERON_0002370
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K9me3 in Human Thymus Tissue. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: AY352
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.13993
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.13369
****************
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: GSM1013161_UCSD.Thymus.H3K9me3.STL001.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K9me3.STL001TH.01.01.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Thymus H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K9me3 ChIP-Seq on Thymus, 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.16440
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 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 28,828,275
FINDPEAKS_SCORE: 0.024
FINDPEAKS_PERCENTILE: 31
HOTSPOT_SCORE: 0.0924
HOTSPOT_PERCENTILE: 28
IROC_SCORE: 0.6747
IROC_PERCENTILE: 28
POISSON_SCORE: 0.2287
POISSON_PERCENTILE: 31
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM1013161_UCSD.Thymus.H3K9me3.STL001.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K9me3.STL001TH.01.01.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Thymus H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K9me3 ChIP-Seq read mappings from Thymus, 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.16594
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 9
BROWSER_TRACK_NAME: Thymus H3K9me3 01 52
BROWSER_TRACK_DESCRIPTION: UCSD Thymus Histone H3K9me3 Donor STL001 Library AY352 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 28,828,275
FINDPEAKS_SCORE: 0.024
FINDPEAKS_PERCENTILE: 31
HOTSPOT_SCORE: 0.0924
HOTSPOT_PERCENTILE: 28
IROC_SCORE: 0.6747
IROC_PERCENTILE: 28
POISSON_SCORE: 0.2287
POISSON_PERCENTILE: 31
MAXIMUM_REPLICATE_CORRELATION: NA

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

value: Thymus

value: Shin Lin, Stanford University

value: Primary Tissue

value: Autopsy

value: Histone H3K9me3


title: Reference Epigenome: ChIP-Seq Input from Human Lung Tissue; renlab.Input.STL001LG.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: AY353
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.13958
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.13947
****************
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: GSM1013165_UCSD.Lung.Input.STL001.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.Input.STL001LG.01.01.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Lung Input ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Input ChIP-Seq on Lung, 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.16474
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 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 32,884,892
FINDPEAKS_SCORE: 0.0063
FINDPEAKS_PERCENTILE: 63
HOTSPOT_SCORE: 0.0937
HOTSPOT_PERCENTILE: 85
IROC_SCORE: 0.6597
IROC_PERCENTILE: 25
POISSON_SCORE: 0.289
POISSON_PERCENTILE: 89
MAXIMUM_REPLICATE_CORRELATION: 0.97

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

ANALYSIS FILE NAME: GSM1013165_UCSD.Lung.Input.STL001.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.Input.STL001LG.01.01.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Lung Input ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Input ChIP-Seq read mappings from Lung, 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.16628
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 9
BROWSER_TRACK_NAME: Lung Input 01 53
BROWSER_TRACK_DESCRIPTION: UCSD Lung ChIP-Seq Input Donor STL001 Library AY353 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 32,884,892
FINDPEAKS_SCORE: 0.0063
FINDPEAKS_PERCENTILE: 63
HOTSPOT_SCORE: 0.0937
HOTSPOT_PERCENTILE: 85
IROC_SCORE: 0.6597
IROC_PERCENTILE: 25
POISSON_SCORE: 0.289
POISSON_PERCENTILE: 89
MAXIMUM_REPLICATE_CORRELATION: 0.97

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

value: Lung

value: Biorupter

value: 500 micrograms


title: Reference Epigenome: ChIP-Seq Analysis of H3K4me1 in Human Aorta Tissue; renlab.H3K4me1.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 H3K4me1 in Human Aorta Tissue. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: AY372
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.14067
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: GSM1013150_UCSD.Aorta.H3K4me1.STL003.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K4me1.STL003AO.01.01.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Aorta H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K4me1 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.16403
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 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 16,271,558
FINDPEAKS_SCORE: 0.1381
FINDPEAKS_PERCENTILE: 23
HOTSPOT_SCORE: 0.2625
HOTSPOT_PERCENTILE: 27
IROC_SCORE: 0.8961
IROC_PERCENTILE: 21
POISSON_SCORE: 0.3832
POISSON_PERCENTILE: 23
MAXIMUM_REPLICATE_CORRELATION: 0.96

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

ANALYSIS FILE NAME: GSM1013150_UCSD.Aorta.H3K4me1.STL003.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K4me1.STL003AO.01.01.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Aorta H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K4me1 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.16557
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 9
BROWSER_TRACK_NAME: Aorta H3K4me1 03 72
BROWSER_TRACK_DESCRIPTION: UCSD Aorta Histone H3K4me1 Donor STL003 Library AY372 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 16,271,558
FINDPEAKS_SCORE: 0.1381
FINDPEAKS_PERCENTILE: 23
HOTSPOT_SCORE: 0.2625
HOTSPOT_PERCENTILE: 27
IROC_SCORE: 0.8961
IROC_PERCENTILE: 21
POISSON_SCORE: 0.3832
POISSON_PERCENTILE: 23
MAXIMUM_REPLICATE_CORRELATION: 0.96

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

value: Aorta

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

value: Male

value: Caucasian


title: Reference Epigenome: ChIP-Seq Analysis of H3K9me3 in Human Pancreas Tissue; renlab.H3K9me3.STL002PA.01.01

description:
sample_term_id: UBERON_0001264
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K9me3 in Human Pancreas Tissue. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: CY79
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.14046
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.14039
****************
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: GSM1013163_UCSD.Pancreas.H3K9me3.STL002.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K9me3.STL002PA.01.01.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Pancreas H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K9me3 ChIP-Seq on Pancreas, 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.16358
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 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 22,363,667
FINDPEAKS_SCORE: 0.079
FINDPEAKS_PERCENTILE: 67
HOTSPOT_SCORE: 0.2182
HOTSPOT_PERCENTILE: 79
IROC_SCORE: 0.7891
IROC_PERCENTILE: 49
POISSON_SCORE: 0.3416
POISSON_PERCENTILE: 67
MAXIMUM_REPLICATE_CORRELATION: 0.96

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

ANALYSIS FILE NAME: GSM1013163_UCSD.Pancreas.H3K9me3.STL002.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K9me3.STL002PA.01.01.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Pancreas H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K9me3 ChIP-Seq read mappings from Pancreas, 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.16512
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 9
BROWSER_TRACK_NAME: Pancreas H3K9me3 02 79
BROWSER_TRACK_DESCRIPTION: UCSD Pancreas Histone H3K9me3 Donor STL002 Library CY79 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 22,363,667
FINDPEAKS_SCORE: 0.079
FINDPEAKS_PERCENTILE: 67
HOTSPOT_SCORE: 0.2182
HOTSPOT_PERCENTILE: 79
IROC_SCORE: 0.7891
IROC_PERCENTILE: 49
POISSON_SCORE: 0.3416
POISSON_PERCENTILE: 67
MAXIMUM_REPLICATE_CORRELATION: 0.96

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

value: Pancreas

value: iron deficiency, bipolar

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

value: Female

value: magnetic anti-rabbit

value: 5 micrograms


title: Reference Epigenome: ChIP-Seq Analysis of H3K4me1 in Human Pancreas Tissue; renlab.H3K4me1.STL002PA.01.01

description:
sample_term_id: UBERON_0001264
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K4me1 in Human Pancreas Tissue. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: CY78
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.14042
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.14039
****************
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: GSM1013149_UCSD.Pancreas.H3K4me1.STL002.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K4me1.STL002PA.01.01.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Pancreas H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K4me1 ChIP-Seq on Pancreas, 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.16390
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 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 29,060,561
FINDPEAKS_SCORE: 0.1805
FINDPEAKS_PERCENTILE: 35
HOTSPOT_SCORE: 0.279
HOTSPOT_PERCENTILE: 33
IROC_SCORE: 0.9422
IROC_PERCENTILE: 31
POISSON_SCORE: 0.4224
POISSON_PERCENTILE: 29
MAXIMUM_REPLICATE_CORRELATION: 0.96

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

ANALYSIS FILE NAME: GSM1013149_UCSD.Pancreas.H3K4me1.STL002.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K4me1.STL002PA.01.01.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Pancreas H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K4me1 ChIP-Seq read mappings from Pancreas, 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.16544
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 9
BROWSER_TRACK_NAME: Pancreas H3K4me1 02 78
BROWSER_TRACK_DESCRIPTION: UCSD Pancreas Histone H3K4me1 Donor STL002 Library CY78 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 29,060,561
FINDPEAKS_SCORE: 0.1805
FINDPEAKS_PERCENTILE: 35
HOTSPOT_SCORE: 0.279
HOTSPOT_PERCENTILE: 33
IROC_SCORE: 0.9422
IROC_PERCENTILE: 31
POISSON_SCORE: 0.4224
POISSON_PERCENTILE: 29
MAXIMUM_REPLICATE_CORRELATION: 0.96

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

value: genomic DNA

value: Shin Lin, Stanford University

value: Histone H3K4me1

value: Abcam


title: Reference Epigenome: ChIP-Seq Analysis of H3K9me3 in Human Ovary Tissue; renlab.H3K9me3.STL002OV.01.01

description:
sample_term_id: UBERON_0000992
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K9me3 in Human Ovary Tissue. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: AY348
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.14028
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.13360
****************
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: GSM1013162_UCSD.Ovary.H3K9me3.STL002.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K9me3.STL002OV.01.01.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Ovary H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K9me3 ChIP-Seq on Ovary, 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.16353
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 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 28,261,999
FINDPEAKS_SCORE: 0.0172
FINDPEAKS_PERCENTILE: 13
HOTSPOT_SCORE: 0.0768
HOTSPOT_PERCENTILE: 21
IROC_SCORE: 0.747
IROC_PERCENTILE: 36
POISSON_SCORE: 0.1842
POISSON_PERCENTILE: 15
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM1013162_UCSD.Ovary.H3K9me3.STL002.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K9me3.STL002OV.01.01.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Ovary H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K9me3 ChIP-Seq read mappings from Ovary, 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.16507
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 9
BROWSER_TRACK_NAME: Ovary H3K9me3 02 48
BROWSER_TRACK_DESCRIPTION: UCSD Ovary Histone H3K9me3 Donor STL002 Library AY348 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 28,261,999
FINDPEAKS_SCORE: 0.0172
FINDPEAKS_PERCENTILE: 13
HOTSPOT_SCORE: 0.0768
HOTSPOT_PERCENTILE: 21
IROC_SCORE: 0.747
IROC_PERCENTILE: 36
POISSON_SCORE: 0.1842
POISSON_PERCENTILE: 15
MAXIMUM_REPLICATE_CORRELATION: NA

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

value: Ovary

value: Primary Tissue

value: Autopsy

value: Histone H3K9me3


title: Reference Epigenome: ChIP-Seq Analysis of H3K4me1 in Human Bladder Tissue; renlab.H3K4me1.STL001BL.01.01

description:
sample_term_id: UBERON_0001255
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K4me1 in Human Bladder Tissue. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: CY124
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.15131
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: GSM1059450_UCSD.Bladder.H3K4me1.STL003.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K4me1.STL001BL.01.01.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Bladder H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K4me1 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.16357
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 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 12,202,799
FINDPEAKS_SCORE: 0.05
FINDPEAKS_PERCENTILE: 13
HOTSPOT_SCORE: 0.22
HOTSPOT_PERCENTILE: 17
IROC_SCORE: 0.8149
IROC_PERCENTILE: 10
POISSON_SCORE: 0.33
POISSON_PERCENTILE: 13
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM1059450_UCSD.Bladder.H3K4me1.STL003.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K4me1.STL001BL.01.01.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Bladder H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K4me1 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.16511
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 9
BROWSER_TRACK_NAME: Bladder H3K4me1 03 24
BROWSER_TRACK_DESCRIPTION: UCSD Bladder Histone H3K4me1 Donor STL001 Library CY124 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 12,202,799
FINDPEAKS_SCORE: 0.05
FINDPEAKS_PERCENTILE: 13
HOTSPOT_SCORE: 0.22
HOTSPOT_PERCENTILE: 17
IROC_SCORE: 0.8149
IROC_PERCENTILE: 10
POISSON_SCORE: 0.33
POISSON_PERCENTILE: 13
MAXIMUM_REPLICATE_CORRELATION: NA

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

value: Bladder

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

value: Caucasian and African American

value: Biorupter

value: 500 micrograms


title: Reference Epigenome: ChIP-Seq Analysis of H3K36me3 in Human Thymus Tissue; renlab.H3K36me3.STL001TH.01.01

description:
sample_term_id: UBERON_0002370
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K36me3 in Human Thymus Tissue. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: AY349
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.13989
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.13369
****************
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: GSM1013142_UCSD.Thymus.H3K36me3.STL001.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K36me3.STL001TH.01.01.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Thymus H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K36me3 ChIP-Seq on Thymus, 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.16469
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 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 28,621,720
FINDPEAKS_SCORE: 0.2773
FINDPEAKS_PERCENTILE: 53
HOTSPOT_SCORE: 0.286
HOTSPOT_PERCENTILE: 43
IROC_SCORE: 0.9859
IROC_PERCENTILE: 65
POISSON_SCORE: 0.4574
POISSON_PERCENTILE: 41
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM1013142_UCSD.Thymus.H3K36me3.STL001.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K36me3.STL001TH.01.01.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Thymus H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K36me3 ChIP-Seq read mappings from Thymus, 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.16623
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 9
BROWSER_TRACK_NAME: Thymus H3K36me3 01 49
BROWSER_TRACK_DESCRIPTION: UCSD Thymus Histone H3K36me3 Donor STL001 Library AY349 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 28,621,720
FINDPEAKS_SCORE: 0.2773
FINDPEAKS_PERCENTILE: 53
HOTSPOT_SCORE: 0.286
HOTSPOT_PERCENTILE: 43
IROC_SCORE: 0.9859
IROC_PERCENTILE: 65
POISSON_SCORE: 0.4574
POISSON_PERCENTILE: 41
MAXIMUM_REPLICATE_CORRELATION: NA

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

value: Thymus

value: Male

value: Histone H3K36me3


title: Reference Epigenome: ChIP-Seq Analysis of H3K9me3 in Human Gastric Tissue; renlab.H3K9me3.STL001GA.01.01

description:
sample_term_id: UBERON_0000945
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K9me3 in Human Gastric Tissue. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: CY83
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.14024
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.13944
****************
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: GSM1013159_UCSD.Gastric.H3K9me3.STL001.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K9me3.STL001GA.01.01.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Gastric H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K9me3 ChIP-Seq on Gastric, 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.16379
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 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 9,822,990
FINDPEAKS_SCORE: 0.3424
FINDPEAKS_PERCENTILE: 97
HOTSPOT_SCORE: 0.4449
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.9366
IROC_PERCENTILE: 90
POISSON_SCORE: 0.4919
POISSON_PERCENTILE: 92
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

ANALYSIS FILE NAME: GSM1013159_UCSD.Gastric.H3K9me3.STL001.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K9me3.STL001GA.01.01.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Gastric H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K9me3 ChIP-Seq read mappings from Gastric, 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.16533
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 9
BROWSER_TRACK_NAME: Gastric H3K9me3 01 83
BROWSER_TRACK_DESCRIPTION: UCSD Gastric Histone H3K9me3 Donor STL001 Library CY83 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 9,822,990
FINDPEAKS_SCORE: 0.3424
FINDPEAKS_PERCENTILE: 97
HOTSPOT_SCORE: 0.4449
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.9366
IROC_PERCENTILE: 90
POISSON_SCORE: 0.4919
POISSON_PERCENTILE: 92
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

value: Gastric

value: magnetic anti-rabbit

value: 5 micrograms


title: Reference Epigenome: ChIP-Seq Analysis of H3K36me3 in Human Ovary Tissue; renlab.H3K36me3.STL002OV.01.01

description:
sample_term_id: UBERON_0000992
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K36me3 in Human Ovary Tissue. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: AY345
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.14016
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.13360
****************
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: GSM1013143_UCSD.Ovary.H3K36me3.STL002.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K36me3.STL002OV.01.01.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Ovary H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K36me3 ChIP-Seq on Ovary, 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.16482
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 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 27,630,057
FINDPEAKS_SCORE: 0.2144
FINDPEAKS_PERCENTILE: 37
HOTSPOT_SCORE: 0.2646
HOTSPOT_PERCENTILE: 33
IROC_SCORE: 0.9647
IROC_PERCENTILE: 41
POISSON_SCORE: 0.431
POISSON_PERCENTILE: 33
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM1013143_UCSD.Ovary.H3K36me3.STL002.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K36me3.STL002OV.01.01.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Ovary H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K36me3 ChIP-Seq read mappings from Ovary, 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.16636
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 9
BROWSER_TRACK_NAME: Ovary H3K36me3 02 45
BROWSER_TRACK_DESCRIPTION: UCSD Ovary Histone H3K36me3 Donor STL002 Library AY345 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 27,630,057
FINDPEAKS_SCORE: 0.2144
FINDPEAKS_PERCENTILE: 37
HOTSPOT_SCORE: 0.2646
HOTSPOT_PERCENTILE: 33
IROC_SCORE: 0.9647
IROC_PERCENTILE: 41
POISSON_SCORE: 0.431
POISSON_PERCENTILE: 33
MAXIMUM_REPLICATE_CORRELATION: NA

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

value: genomic DNA

value: iron deficiency, bipolar

value: Shin Lin, Stanford University

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

value: Female

value: Caucasian


title: Reference Epigenome: ChIP-Seq Analysis of H3K27ac in Human Spleen Tissue; renlab.H3K27ac.STL002SX.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: AY342
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.14063
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.14062
****************
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: GSM1013132_UCSD.Spleen.H3K27ac.STL002.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K27ac.STL002SX.01.01.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Spleen H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K27ac ChIP-Seq on Spleen, 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.16424
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 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 11,743,850
FINDPEAKS_SCORE: 0.7383
FINDPEAKS_PERCENTILE: 97
HOTSPOT_SCORE: 0.719
HOTSPOT_PERCENTILE: 97
IROC_SCORE: 0.9985
IROC_PERCENTILE: 77
POISSON_SCORE: 0.7552
POISSON_PERCENTILE: 97
MAXIMUM_REPLICATE_CORRELATION: 0.96

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

ANALYSIS FILE NAME: GSM1013132_UCSD.Spleen.H3K27ac.STL002.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K27ac.STL002SX.01.01.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Spleen H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K27ac ChIP-Seq read mappings from Spleen, 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.16578
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 9
BROWSER_TRACK_NAME: Spleen H3K27ac 02 42
BROWSER_TRACK_DESCRIPTION: UCSD Spleen Histone H3K27ac Donor STL002 Library AY342 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 11,743,850
FINDPEAKS_SCORE: 0.7383
FINDPEAKS_PERCENTILE: 97
HOTSPOT_SCORE: 0.719
HOTSPOT_PERCENTILE: 97
IROC_SCORE: 0.9985
IROC_PERCENTILE: 77
POISSON_SCORE: 0.7552
POISSON_PERCENTILE: 97
MAXIMUM_REPLICATE_CORRELATION: 0.96

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

value: Spleen

value: Primary Tissue

value: Autopsy

value: Histone H3K27ac

value: Active Motif


title: Reference Epigenome: ChIP-Seq Analysis of H3K9me3 in Human Small Bowel Tissue; renlab.H3K9me3.STL001SB.01.01

description:
sample_term_id: UBERON_0002108
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K9me3 in Human Small Bowel Tissue. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: AK330
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.13960
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.12250
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

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

ANALYSIS FILE NAME: GSM1013160_UCSD.Small_Intestine.H3K9me3.STL001.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K9me3.STL001SB.01.01.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Small Intestine H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K9me3 ChIP-Seq on Small Intestine, Donor STL001, were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.16382
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 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 8,983,737
FINDPEAKS_SCORE: 0.0928
FINDPEAKS_PERCENTILE: 72
HOTSPOT_SCORE: 0.2161
HOTSPOT_PERCENTILE: 77
IROC_SCORE: 0.7768
IROC_PERCENTILE: 44
POISSON_SCORE: 0.3313
POISSON_PERCENTILE: 64
MAXIMUM_REPLICATE_CORRELATION: 0.97

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

ANALYSIS FILE NAME: GSM1013160_UCSD.Small_Intestine.H3K9me3.STL001.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K9me3.STL001SB.01.01.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Small Intestine H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K9me3 ChIP-Seq read mappings from Small Intestine, Donor STL001, were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.16536
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 9
BROWSER_TRACK_NAME: SI H3K9me3 01 30
BROWSER_TRACK_DESCRIPTION: UCSD Small Intestine Histone H3K9me3 Donor STL001 Library AK330 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 8,983,737
FINDPEAKS_SCORE: 0.0928
FINDPEAKS_PERCENTILE: 72
HOTSPOT_SCORE: 0.2161
HOTSPOT_PERCENTILE: 77
IROC_SCORE: 0.7768
IROC_PERCENTILE: 44
POISSON_SCORE: 0.3313
POISSON_PERCENTILE: 64
MAXIMUM_REPLICATE_CORRELATION: 0.97

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

source_name: Small Intestine tissue; renlab.H3K9me3.STL001SB.01.01

value: Small Intestine

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

value: Caucasian and African American

value: Histone H3K9me3

value: Biorupter

value: 500 micrograms

value: Abcam


title: Reference Epigenome: ChIP-Seq Analysis of H3K4me1 in Human Gastric Tissue; renlab.H3K4me1.STL001GA.01.01

description:
sample_term_id: UBERON_0000945
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K4me1 in Human Gastric Tissue. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: CY82
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.14026
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.13944
****************
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: GSM1013147_UCSD.Gastric.H3K4me1.STL001.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K4me1.STL001GA.01.01.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Gastric H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K4me1 ChIP-Seq on Gastric, 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.16418
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 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 13,649,967
FINDPEAKS_SCORE: 0.4439
FINDPEAKS_PERCENTILE: 83
HOTSPOT_SCORE: 0.4926
HOTSPOT_PERCENTILE: 83
IROC_SCORE: 0.9817
IROC_PERCENTILE: 58
POISSON_SCORE: 0.5868
POISSON_PERCENTILE: 85
MAXIMUM_REPLICATE_CORRELATION: 0.97

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

ANALYSIS FILE NAME: GSM1013147_UCSD.Gastric.H3K4me1.STL001.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K4me1.STL001GA.01.01.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Gastric H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K4me1 ChIP-Seq read mappings from Gastric, 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.16572
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 9
BROWSER_TRACK_NAME: Gastric H3K4me1 01 82
BROWSER_TRACK_DESCRIPTION: UCSD Gastric Histone H3K4me1 Donor STL001 Library CY82 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 13,649,967
FINDPEAKS_SCORE: 0.4439
FINDPEAKS_PERCENTILE: 83
HOTSPOT_SCORE: 0.4926
HOTSPOT_PERCENTILE: 83
IROC_SCORE: 0.9817
IROC_PERCENTILE: 58
POISSON_SCORE: 0.5868
POISSON_PERCENTILE: 85
MAXIMUM_REPLICATE_CORRELATION: 0.97

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

value: Gastric

value: genomic DNA

value: Male

value: Histone H3K4me1

value: magnetic anti-rabbit

value: 5 micrograms


title: Reference Epigenome: ChIP-Seq Input from Human Gastric Tissue; renlab.Input.STL001GA.01.01

description:
sample_term_id: UBERON_0000945
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Input from Human Gastric Tissue. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: CY47
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.14032
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.13944
****************
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: GSM1013164_UCSD.Gastric.Input.STL001.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.Input.STL001GA.01.01.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Gastric Input ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Input ChIP-Seq on Gastric, 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.16481
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 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 38,569,429
FINDPEAKS_SCORE: 0.0053
FINDPEAKS_PERCENTILE: 31
HOTSPOT_SCORE: 0.0163
HOTSPOT_PERCENTILE: 54
IROC_SCORE: 0.9646
IROC_PERCENTILE: 57
POISSON_SCORE: 0.0868
POISSON_PERCENTILE: 59
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

ANALYSIS FILE NAME: GSM1013164_UCSD.Gastric.Input.STL001.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.Input.STL001GA.01.01.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Gastric Input ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Input ChIP-Seq read mappings from Gastric, 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.16635
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 9
BROWSER_TRACK_NAME: Gastric Input 01 47
BROWSER_TRACK_DESCRIPTION: UCSD Gastric ChIP-Seq Input Donor STL001 Library CY47 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 38,569,429
FINDPEAKS_SCORE: 0.0053
FINDPEAKS_PERCENTILE: 31
HOTSPOT_SCORE: 0.0163
HOTSPOT_PERCENTILE: 54
IROC_SCORE: 0.9646
IROC_PERCENTILE: 57
POISSON_SCORE: 0.0868
POISSON_PERCENTILE: 59
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

value: Shin Lin, Stanford University

value: Primary Tissue

value: ChIP-Seq Input

value: Input


title: Reference Epigenome: ChIP-Seq Analysis of H3K36me3 in Human Right Ventricle Tissue; renlab.H3K36me3.STL003RV.01.01

description:
sample_term_id: UBERON_0002080
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K36me3 in Human Right Ventricle Tissue. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: AK276
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.14080
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.12222
****************
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: GSM1013145_UCSD.Right_Ventricle.H3K36me3.STL003.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K36me3.STL003RV.01.01.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Right Ventricle H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K36me3 ChIP-Seq on Right 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.16393
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 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 10,771,814
FINDPEAKS_SCORE: 0.2462
FINDPEAKS_PERCENTILE: 43
HOTSPOT_SCORE: 0.3526
HOTSPOT_PERCENTILE: 69
IROC_SCORE: 0.9637
IROC_PERCENTILE: 39
POISSON_SCORE: 0.4422
POISSON_PERCENTILE: 37
MAXIMUM_REPLICATE_CORRELATION: 0.97

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

ANALYSIS FILE NAME: GSM1013145_UCSD.Right_Ventricle.H3K36me3.STL003.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K36me3.STL003RV.01.01.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Right Ventricle H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K36me3 ChIP-Seq read mappings from Right 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.16547
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 9
BROWSER_TRACK_NAME: RV H3K36me3 03 76
BROWSER_TRACK_DESCRIPTION: UCSD Right Ventricle Histone H3K36me3 Donor STL003 Library AK276 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 10,771,814
FINDPEAKS_SCORE: 0.2462
FINDPEAKS_PERCENTILE: 43
HOTSPOT_SCORE: 0.3526
HOTSPOT_PERCENTILE: 69
IROC_SCORE: 0.9637
IROC_PERCENTILE: 39
POISSON_SCORE: 0.4422
POISSON_PERCENTILE: 37
MAXIMUM_REPLICATE_CORRELATION: 0.97

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

source_name: Right Ventricle tissue; renlab.H3K36me3.STL003RV.01.01

value: Right Ventricle

value: Autopsy

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

value: Caucasian

value: Histone H3K36me3


title: Reference Epigenome: ChIP-Seq Analysis of H3K27ac in Human Small Intestine Tissue; renlab.H3K27ac.STL002SB.01.01

description:
sample_term_id: UBERON_0002108
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K27ac in Human Small Intestine Tissue. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: AY365
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.14056
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.14055
****************
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: GSM1013131_UCSD.Small_Intestine.H3K27ac.STL002.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K27ac.STL002SB.01.01.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Small Intestine H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K27ac ChIP-Seq on Small Intestine, 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.16480
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 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 15,360,674
FINDPEAKS_SCORE: 0.3016
FINDPEAKS_PERCENTILE: 31
HOTSPOT_SCORE: 0.3579
HOTSPOT_PERCENTILE: 36
IROC_SCORE: 0.996
IROC_PERCENTILE: 53
POISSON_SCORE: 0.3951
POISSON_PERCENTILE: 23
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

ANALYSIS FILE NAME: GSM1013131_UCSD.Small_Intestine.H3K27ac.STL002.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K27ac.STL002SB.01.01.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Small Intestine H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K27ac ChIP-Seq read mappings from Small Intestine, Donor 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.16634
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 9
BROWSER_TRACK_NAME: SI H3K27ac 02 65
BROWSER_TRACK_DESCRIPTION: UCSD Small Intestine Histone H3K27ac Donor STL002 Library AY365 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 15,360,674
FINDPEAKS_SCORE: 0.3016
FINDPEAKS_PERCENTILE: 31
HOTSPOT_SCORE: 0.3579
HOTSPOT_PERCENTILE: 36
IROC_SCORE: 0.996
IROC_PERCENTILE: 53
POISSON_SCORE: 0.3951
POISSON_PERCENTILE: 23
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

source_name: Small Intestine tissue; renlab.H3K27ac.STL002SB.01.01

value: Small Intestine

value: iron deficiency, bipolar

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

value: Female

value: Histone H3K27ac

value: Biorupter

value: 500 micrograms

value: Active Motif