title: Reference Epigenome: ChIP-Seq Analysis of H3K36me3 in Human Right Atrium Tissue; renlab.H3K36me3.STL003RA.01.01

description:
sample_term_id: UBERON_0002078
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K36me3 in Human Right Atrium Tissue. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: AY317
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.14076
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.11888
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

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

ANALYSIS FILE NAME: GSM1013144_UCSD.Right_Atrium.H3K36me3.STL003.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K36me3.STL003RA.01.01.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Right Atrium H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K36me3 ChIP-Seq on Right Atrium, Donor STL003, were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.16478
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: 7,104,970
FINDPEAKS_SCORE: 0.2209
FINDPEAKS_PERCENTILE: 41
HOTSPOT_SCORE: 0.3709
HOTSPOT_PERCENTILE: 80
IROC_SCORE: 0.9342
IROC_PERCENTILE: 31
POISSON_SCORE: 0.5106
POISSON_PERCENTILE: 59
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM1013144_UCSD.Right_Atrium.H3K36me3.STL003.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K36me3.STL003RA.01.01.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Right Atrium H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K36me3 ChIP-Seq read mappings from Right Atrium, Donor STL003, were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.16632
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: RA H3K36me3 03 17
BROWSER_TRACK_DESCRIPTION: UCSD Right Atrium Histone H3K36me3 Donor STL003 Library AY317 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 7,104,970
FINDPEAKS_SCORE: 0.2209
FINDPEAKS_PERCENTILE: 41
HOTSPOT_SCORE: 0.3709
HOTSPOT_PERCENTILE: 80
IROC_SCORE: 0.9342
IROC_PERCENTILE: 31
POISSON_SCORE: 0.5106
POISSON_PERCENTILE: 59
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: Right Atrium tissue; renlab.H3K36me3.STL003RA.01.01

value: Right Atrium

value: genomic DNA

value: Shin Lin, Stanford University

value: Male

value: magnetic anti-rabbit

value: 5 micrograms

value: Abcam


title: Reference Epigenome: ChIP-Seq Analysis of H3K27ac in Human Esophagus Tissue; renlab.H3K27ac.STL002EG.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_0001043
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K27ac in Human Esophagus Tissue. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: AY336
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.14002
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.14001
****************
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: GSM1013127_UCSD.Esophagus.H3K27ac.STL002.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K27ac.STL002EG.01.01.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Esophagus H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K27ac ChIP-Seq on Esophagus, 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.16361
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: 17,999,217
FINDPEAKS_SCORE: 0.5618
FINDPEAKS_PERCENTILE: 79
HOTSPOT_SCORE: 0.5728
HOTSPOT_PERCENTILE: 80
IROC_SCORE: 0.9977
IROC_PERCENTILE: 67
POISSON_SCORE: 0.6312
POISSON_PERCENTILE: 83
MAXIMUM_REPLICATE_CORRELATION: 0.95

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

ANALYSIS FILE NAME: GSM1013127_UCSD.Esophagus.H3K27ac.STL002.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K27ac.STL002EG.01.01.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Esophagus H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K27ac ChIP-Seq read mappings from Esophagus, 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.16515
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: Esophagus H3K27ac 02 36
BROWSER_TRACK_DESCRIPTION: UCSD Esophagus Histone H3K27ac Donor STL002 Library AY336 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 17,999,217
FINDPEAKS_SCORE: 0.5618
FINDPEAKS_PERCENTILE: 79
HOTSPOT_SCORE: 0.5728
HOTSPOT_PERCENTILE: 80
IROC_SCORE: 0.9977
IROC_PERCENTILE: 67
POISSON_SCORE: 0.6312
POISSON_PERCENTILE: 83
MAXIMUM_REPLICATE_CORRELATION: 0.95

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

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: Esophagus

tag: molecule

tag: disease

value: iron deficiency, bipolar

value: Primary Tissue

value: Autopsy

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

value: Female

value: Caucasian

value: Histone H3K27ac

value: Biorupter

value: 500 micrograms

value: Active Motif


title: Reference Epigenome: ChIP-Seq Analysis of H3K27ac in Human Pancreas Tissue; renlab.H3K27ac.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 H3K27ac in Human Pancreas Tissue. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: CY56
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.14040
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: GSM1013129_UCSD.Pancreas.H3K27ac.STL002.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K27ac.STL002PA.01.01.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Pancreas H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K27ac 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.16454
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: 12,511,533
FINDPEAKS_SCORE: 0.3404
FINDPEAKS_PERCENTILE: 37
HOTSPOT_SCORE: 0.4322
HOTSPOT_PERCENTILE: 50
IROC_SCORE: 0.9589
IROC_PERCENTILE: 9
POISSON_SCORE: 0.504
POISSON_PERCENTILE: 57
MAXIMUM_REPLICATE_CORRELATION: 0.97

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

ANALYSIS FILE NAME: GSM1013129_UCSD.Pancreas.H3K27ac.STL002.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K27ac.STL002PA.01.01.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Pancreas H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K27ac 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.16608
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 H3K27ac 02 56
BROWSER_TRACK_DESCRIPTION: UCSD Pancreas Histone H3K27ac Donor STL002 Library CY56 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 12,511,533
FINDPEAKS_SCORE: 0.3404
FINDPEAKS_PERCENTILE: 37
HOTSPOT_SCORE: 0.4322
HOTSPOT_PERCENTILE: 50
IROC_SCORE: 0.9589
IROC_PERCENTILE: 9
POISSON_SCORE: 0.504
POISSON_PERCENTILE: 57
MAXIMUM_REPLICATE_CORRELATION: 0.97

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

value: Pancreas

value: genomic DNA


title: Reference Epigenome: ChIP-Seq Analysis of H3K27ac in Human Thymus Tissue; renlab.H3K27ac.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 H3K27ac in Human Thymus Tissue. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: AY310
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.13962
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: GSM1013125_UCSD.Thymus.H3K27ac.STL001.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K27ac.STL001TH.01.01.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Thymus H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K27ac 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.16371
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: 18,035,878
FINDPEAKS_SCORE: 0.2726
FINDPEAKS_PERCENTILE: 26
HOTSPOT_SCORE: 0.3342
HOTSPOT_PERCENTILE: 29
IROC_SCORE: 0.9857
IROC_PERCENTILE: 21
POISSON_SCORE: 0.3956
POISSON_PERCENTILE: 24
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM1013125_UCSD.Thymus.H3K27ac.STL001.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K27ac.STL001TH.01.01.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Thymus H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K27ac 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.16525
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 H3K27ac 01 10
BROWSER_TRACK_DESCRIPTION: UCSD Thymus Histone H3K27ac Donor STL001 Library AY310 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 18,035,878
FINDPEAKS_SCORE: 0.2726
FINDPEAKS_PERCENTILE: 26
HOTSPOT_SCORE: 0.3342
HOTSPOT_PERCENTILE: 29
IROC_SCORE: 0.9857
IROC_PERCENTILE: 21
POISSON_SCORE: 0.3956
POISSON_PERCENTILE: 24
MAXIMUM_REPLICATE_CORRELATION: NA

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

value: Thymus

value: Shin Lin, Stanford University

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

value: Male

value: Caucasian and African American


title: Reference Epigenome: ChIP-Seq Analysis of H3K27ac in Human Adrenal Gland Tissue; renlab.H3K27ac.STL002AD.01.01

description:
sample_term_id: UBERON_0002369
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K27ac in Human Adrenal Gland Tissue. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: CY60
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.13996
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: GSM1013126_UCSD.Adrenal_Gland.H3K27ac.STL002.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K27ac.STL002AD.01.01.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Adrenal Gland H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K27ac 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.16476
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: 10,652,041
FINDPEAKS_SCORE: 0.4885
FINDPEAKS_PERCENTILE: 70
HOTSPOT_SCORE: 0.5319
HOTSPOT_PERCENTILE: 73
IROC_SCORE: 0.9893
IROC_PERCENTILE: 29
POISSON_SCORE: 0.5714
POISSON_PERCENTILE: 70
MAXIMUM_REPLICATE_CORRELATION: 0.96

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

ANALYSIS FILE NAME: GSM1013126_UCSD.Adrenal_Gland.H3K27ac.STL002.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K27ac.STL002AD.01.01.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Adrenal Gland H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K27ac 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.16630
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 H3K27ac 02 60
BROWSER_TRACK_DESCRIPTION: UCSD Adrenal Gland Histone H3K27ac Donor STL002 Library CY60 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 10,652,041
FINDPEAKS_SCORE: 0.4885
FINDPEAKS_PERCENTILE: 70
HOTSPOT_SCORE: 0.5319
HOTSPOT_PERCENTILE: 73
IROC_SCORE: 0.9893
IROC_PERCENTILE: 29
POISSON_SCORE: 0.5714
POISSON_PERCENTILE: 70
MAXIMUM_REPLICATE_CORRELATION: 0.96

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

source_name: Adrenal Gland tissue; renlab.H3K27ac.STL002AD.01.01

value: Adrenal Gland

value: iron deficiency, bipolar

value: magnetic anti-rabbit

value: 5 micrograms


title: Reference Epigenome: ChIP-Seq Analysis of H3K27ac in Human Gastric Tissue; renlab.H3K27ac.STL002GA.01.01

description:
sample_term_id: UBERON_0000945
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K27ac in Human Gastric Tissue. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: AY338
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.14005
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: GSM1013128_UCSD.Gastric.H3K27ac.STL002.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K27ac.STL002GA.01.01.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Gastric H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K27ac 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.16479
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: 21,131,017
FINDPEAKS_SCORE: 0.5062
FINDPEAKS_PERCENTILE: 71
HOTSPOT_SCORE: 0.5281
HOTSPOT_PERCENTILE: 70
IROC_SCORE: 0.9963
IROC_PERCENTILE: 57
POISSON_SCORE: 0.5821
POISSON_PERCENTILE: 73
MAXIMUM_REPLICATE_CORRELATION: 0.97

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

ANALYSIS FILE NAME: GSM1013128_UCSD.Gastric.H3K27ac.STL002.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K27ac.STL002GA.01.01.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Gastric H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K27ac 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.16633
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 H3K27ac 02 38
BROWSER_TRACK_DESCRIPTION: UCSD Gastric Histone H3K27ac Donor STL002 Library AY338 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 21,131,017
FINDPEAKS_SCORE: 0.5062
FINDPEAKS_PERCENTILE: 71
HOTSPOT_SCORE: 0.5281
HOTSPOT_PERCENTILE: 70
IROC_SCORE: 0.9963
IROC_PERCENTILE: 57
POISSON_SCORE: 0.5821
POISSON_PERCENTILE: 73
MAXIMUM_REPLICATE_CORRELATION: 0.97

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

value: Gastric

value: Primary Tissue

value: Autopsy

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

value: Female


title: Reference Epigenome: ChIP-Seq Analysis of H3K4me1 in Human Ovary Tissue; renlab.H3K4me1.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 H3K4me1 in Human Ovary Tissue. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: AY347
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.14018
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: GSM1013148_UCSD.Ovary.H3K4me1.STL002.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K4me1.STL002OV.01.01.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Ovary H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K4me1 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.16499
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: 28,551,305
FINDPEAKS_SCORE: 0.2251
FINDPEAKS_PERCENTILE: 44
HOTSPOT_SCORE: 0.2963
HOTSPOT_PERCENTILE: 40
IROC_SCORE: 0.9632
IROC_PERCENTILE: 46
POISSON_SCORE: 0.4375
POISSON_PERCENTILE: 38
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM1013148_UCSD.Ovary.H3K4me1.STL002.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K4me1.STL002OV.01.01.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Ovary H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K4me1 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.16653
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 H3K4me1 02 47
BROWSER_TRACK_DESCRIPTION: UCSD Ovary Histone H3K4me1 Donor STL002 Library AY347 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 28,551,305
FINDPEAKS_SCORE: 0.2251
FINDPEAKS_PERCENTILE: 44
HOTSPOT_SCORE: 0.2963
HOTSPOT_PERCENTILE: 40
IROC_SCORE: 0.9632
IROC_PERCENTILE: 46
POISSON_SCORE: 0.4375
POISSON_PERCENTILE: 38
MAXIMUM_REPLICATE_CORRELATION: NA

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

value: Ovary

value: Caucasian

value: Histone H3K4me1

value: Biorupter

value: 500 micrograms

value: Abcam


title: Reference Epigenome: ChIP-Seq Analysis of H3K27ac in Human Bladder Tissue; renlab.H3K27ac.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 H3K27ac in Human Bladder Tissue. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: AY334
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.14072
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: GSM1013133_UCSD.Bladder.H3K27ac.STL003.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K27ac.STL001BL.01.01.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Bladder H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K27ac 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.16408
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: 17,835,843
FINDPEAKS_SCORE: 0.1776
FINDPEAKS_PERCENTILE: 13
HOTSPOT_SCORE: 0.2522
HOTSPOT_PERCENTILE: 16
IROC_SCORE: 0.982
IROC_PERCENTILE: 19
POISSON_SCORE: 0.3082
POISSON_PERCENTILE: 10
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM1013133_UCSD.Bladder.H3K27ac.STL003.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K27ac.STL001BL.01.01.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Bladder H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K27ac 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.16562
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 H3K27ac 03 34
BROWSER_TRACK_DESCRIPTION: UCSD Bladder Histone H3K27ac Donor STL001 Library AY334 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 17,835,843
FINDPEAKS_SCORE: 0.1776
FINDPEAKS_PERCENTILE: 13
HOTSPOT_SCORE: 0.2522
HOTSPOT_PERCENTILE: 16
IROC_SCORE: 0.982
IROC_PERCENTILE: 19
POISSON_SCORE: 0.3082
POISSON_PERCENTILE: 10
MAXIMUM_REPLICATE_CORRELATION: NA

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

value: Bladder

value: genomic DNA

value: Shin Lin, Stanford University

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

value: Male

value: Histone H3K27ac

value: Active Motif


title: Reference Epigenome: ChIP-Seq Input from Human Right Ventricle Tissue; renlab.Input.STL001RV.01.01

description:
sample_term_id: UBERON_0002080
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Input from Human Right Ventricle Tissue. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: CY50
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.14089
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.14086
****************
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: GSM1013167_UCSD.Right_Ventricle.Input.STL001.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.Input.STL001RV.01.01.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Right Ventricle Input ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Input ChIP-Seq on Right Ventricle, Donor STL001, were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.16366
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: 31,690,466
FINDPEAKS_SCORE: 0.0069
FINDPEAKS_PERCENTILE: 69
HOTSPOT_SCORE: 0.148
HOTSPOT_PERCENTILE: 94
IROC_SCORE: 0.8306
IROC_PERCENTILE: 34
POISSON_SCORE: 0.3674
POISSON_PERCENTILE: 96
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

ANALYSIS FILE NAME: GSM1013167_UCSD.Right_Ventricle.Input.STL001.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.Input.STL001RV.01.01.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Right Ventricle Input ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Input ChIP-Seq read mappings from Right Ventricle, Donor STL001, were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.16520
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 Input 01 50
BROWSER_TRACK_DESCRIPTION: UCSD Right Ventricle ChIP-Seq Input Donor STL001 Library CY50 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 31,690,466
FINDPEAKS_SCORE: 0.0069
FINDPEAKS_PERCENTILE: 69
HOTSPOT_SCORE: 0.148
HOTSPOT_PERCENTILE: 94
IROC_SCORE: 0.8306
IROC_PERCENTILE: 34
POISSON_SCORE: 0.3674
POISSON_PERCENTILE: 96
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

source_name: Right Ventricle tissue; renlab.Input.STL001RV.01.01

value: Right Ventricle

value: Primary Tissue

value: Caucasian and African American

value: ChIP-Seq Input

value: Input


title: Reference Epigenome: ChIP-Seq Input from Human Ovary Tissue; renlab.Input.STL002OV.01.01

description:
sample_term_id: UBERON_0000992
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Input from Human Ovary Tissue. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: AY294
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.14030
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: GSM1013171_UCSD.Ovary.Input.STL002.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.Input.STL002OV.01.01.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Ovary Input ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Input 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.16362
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: 43,340,926
FINDPEAKS_SCORE: 0.088
FINDPEAKS_PERCENTILE: 98
HOTSPOT_SCORE: 0.139
HOTSPOT_PERCENTILE: 93
IROC_SCORE: 0.9872
IROC_PERCENTILE: 70
POISSON_SCORE: 0.2442
POISSON_PERCENTILE: 85
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM1013171_UCSD.Ovary.Input.STL002.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.Input.STL002OV.01.01.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Ovary Input ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Input 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.16516
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 Input 02 94
BROWSER_TRACK_DESCRIPTION: UCSD Ovary ChIP-Seq Input Donor STL002 Library AY294 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 43,340,926
FINDPEAKS_SCORE: 0.088
FINDPEAKS_PERCENTILE: 98
HOTSPOT_SCORE: 0.139
HOTSPOT_PERCENTILE: 93
IROC_SCORE: 0.9872
IROC_PERCENTILE: 70
POISSON_SCORE: 0.2442
POISSON_PERCENTILE: 85
MAXIMUM_REPLICATE_CORRELATION: NA

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

value: Ovary

value: iron deficiency, bipolar

value: Autopsy

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 Psoas Muscle Tissue; renlab.H3K27ac.STL002PO.01.01

description:
sample_term_id: UBERON_0008450
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K27ac in Human Psoas Muscle Tissue. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: AY340
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.14051
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: GSM1013130_UCSD.Psoas_Muscle.H3K27ac.STL002.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K27ac.STL002PO.01.01.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Psoas Muscle H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K27ac 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.16370
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: 11,012,099
FINDPEAKS_SCORE: 0.5158
FINDPEAKS_PERCENTILE: 74
HOTSPOT_SCORE: 0.5383
HOTSPOT_PERCENTILE: 74
IROC_SCORE: 0.9961
IROC_PERCENTILE: 54
POISSON_SCORE: 0.5759
POISSON_PERCENTILE: 71
MAXIMUM_REPLICATE_CORRELATION: 0.95

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

ANALYSIS FILE NAME: GSM1013130_UCSD.Psoas_Muscle.H3K27ac.STL002.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K27ac.STL002PO.01.01.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Psoas Muscle H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K27ac ChIP-Seq read mappings from Psoas Muscle, Donor 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.16524
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 H3K27ac 02 40
BROWSER_TRACK_DESCRIPTION: UCSD Psoas Muscle Histone H3K27ac Donor STL002 Library AY340 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 11,012,099
FINDPEAKS_SCORE: 0.5158
FINDPEAKS_PERCENTILE: 74
HOTSPOT_SCORE: 0.5383
HOTSPOT_PERCENTILE: 74
IROC_SCORE: 0.9961
IROC_PERCENTILE: 54
POISSON_SCORE: 0.5759
POISSON_PERCENTILE: 71
MAXIMUM_REPLICATE_CORRELATION: 0.95

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

source_name: Psoas Muscle tissue; renlab.H3K27ac.STL002PO.01.01

value: Psoas Muscle

value: genomic DNA

value: Biorupter

value: 500 micrograms

value: magnetic anti-rabbit

value: 5 micrograms


title: Reference Epigenome: ChIP-Seq Analysis of H3K27ac in Human Right Ventricle Tissue; renlab.H3K27ac.STL001RV.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 H3K27ac in Human Right Ventricle Tissue. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: CY54
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.14087
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.14086
****************
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: GSM1013124_UCSD.Right_Ventricle.H3K27ac.STL001.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K27ac.STL001RV.01.01.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Right Ventricle H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K27ac ChIP-Seq on Right Ventricle, Donor STL001, were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.16397
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: 11,040,740
FINDPEAKS_SCORE: 0.5678
FINDPEAKS_PERCENTILE: 81
HOTSPOT_SCORE: 0.59
HOTSPOT_PERCENTILE: 81
IROC_SCORE: 0.9949
IROC_PERCENTILE: 46
POISSON_SCORE: 0.6261
POISSON_PERCENTILE: 80
MAXIMUM_REPLICATE_CORRELATION: 0.94

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

ANALYSIS FILE NAME: GSM1013124_UCSD.Right_Ventricle.H3K27ac.STL001.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K27ac.STL001RV.01.01.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Right Ventricle H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K27ac ChIP-Seq read mappings from Right Ventricle, Donor STL001, were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.16551
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 H3K27ac 01 54
BROWSER_TRACK_DESCRIPTION: UCSD Right Ventricle Histone H3K27ac Donor STL001 Library CY54 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 11,040,740
FINDPEAKS_SCORE: 0.5678
FINDPEAKS_PERCENTILE: 81
HOTSPOT_SCORE: 0.59
HOTSPOT_PERCENTILE: 81
IROC_SCORE: 0.9949
IROC_PERCENTILE: 46
POISSON_SCORE: 0.6261
POISSON_PERCENTILE: 80
MAXIMUM_REPLICATE_CORRELATION: 0.94

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

source_name: Right Ventricle tissue; renlab.H3K27ac.STL001RV.01.01

value: Right Ventricle

value: Shin Lin, Stanford University

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

value: Male

value: Histone H3K27ac

value: Active Motif


title: RNA-Seq analysis of cDNA_Lib 13 derived from human CD56+ ectoderm cells; cDNA_Lib 13

city: Cambridge

first: BROAD

last: INSTITUTE

state: MA

institute: Broad Institute

description:
sample_term_id: CL_0000221
assay_term_id: OBI_0001271
nucleic_acid_term_id: SO_0000871
Design description: mRNA-Seq for REMC on Illumina
Library name: cDNA_Lib 13
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.15788
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.15412
****************
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: transcriptomic

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

ANALYSIS FILE NAME: GSM1112846_BI.hESC_Derived_CD56+_Ectoderm_Cultured_Cells.mRNA-Seq.cDNA_Lib_13.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: cDNA_Lib 13.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of hESC Derived CD56+ Ectoderm Cultured Cells mRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by mRNA-Seq on the hESC Derived CD56+ Ectoderm Cultured Cells, Library cDNA_Lib 13 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.16657
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: mRNA-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: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 87,695,601
PERCENT_READS_MAPPING_TO_UCSC_GENES: 87.98
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 18
MAXIMUM_REPLICATE_CORRELATION: 0.68

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

ANALYSIS FILE NAME: GSM1112846_BI.hESC_Derived_CD56+_Ectoderm_Cultured_Cells.mRNA-Seq.cDNA_Lib_13.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: cDNA_Lib 13.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of hESC Derived CD56+ Ectoderm Cultured Cells mRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina mRNA-Seq read mappings from the hESC Derived CD56+ Ectoderm Cultured Cells, Library cDNA_Lib 13 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.16666
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: mRNA-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: hDCEcto mRNA 13
BROWSER_TRACK_DESCRIPTION: BI hESC Derived CD56+ Ectoderm Cultured Cells mRNA-Seq Library cDNA_Lib 13 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 87,695,601
PERCENT_READS_MAPPING_TO_UCSC_GENES: 87.98
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 18
MAXIMUM_REPLICATE_CORRELATION: 0.68

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

molecule: total RNA

source_name: CD56+ ectodermal germ layer cells derived in vitro from embrionic stem cells by culture in the presence of inhibitors of the BMP, TGFbeta, and WNT signaling pathways.; cDNA_Lib 13

extract_protocol: Library construction protocol: Direct RNA-seq method based on RNA 3' linker ligation, unpublished

value: BioSam 1247

tag: lineage

value: ectoderm

tag: medium

value: CD56 ectoderm - Days 0-5:DMEM F12, 15% KSR, Dorsomorphin (2um), A83-01 (2um), PNU 74654 (2um)

value: presumed normal

tag: passage

tag: line

value: CD56+ ectoderm

value: adherence

tag: batch

value: BioSAli 1890

value: Cell Line

value: intermediate

tag: Sex

value: Harvard

value: 3' cDNA ligation

value: Our protocol using T4 RNA ligase from NEB

value: ILLUMINA A1+B1, C1+D1, E1+F1, G1+H1

value: around 10ng

value: 3x RLT + 15/20 ul of Silane + 0.4x EtOn, eluted in 100ul, recleaned using 0.95X SPRI

value: yes

value: OligodT - Dynabeads mRNA purification kit (Invitrogen)

value: 98C 30 sec, 8 cycles of: 98C for 10 sec, 67C for 20 sec, 72C for 20 min, then 72C for 30 seconds, hold 4C

value: Qiagen AllPrep DNA/RNA/Protein Mini Kit

value: Adapter ligated cDNA made by reverse transcription of RNA

value: Phusion High Fidelity

value: 12 pmoles of each/50 ul of reaction

value: 70C for 4 min in Ambion Fragmentation Buffer

value: NO

value: mRNA-Seq

value: We synthesized first-strand cDNA using affinity-script reverse transcriptase


title: Reference Epigenome: ChIP-Seq Analysis of H3K27ac in Human Gastric Tissue; renlab.H3K27ac.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 H3K27ac in Human Gastric Tissue. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: CY58
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.13945
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: GSM1013122_UCSD.Gastric.H3K27ac.STL001.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K27ac.STL001GA.01.01.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Gastric H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K27ac 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.16475
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: 10,352,743
FINDPEAKS_SCORE: 0.4451
FINDPEAKS_PERCENTILE: 61
HOTSPOT_SCORE: 0.5006
HOTSPOT_PERCENTILE: 66
IROC_SCORE: 0.9783
IROC_PERCENTILE: 14
POISSON_SCORE: 0.5498
POISSON_PERCENTILE: 67
MAXIMUM_REPLICATE_CORRELATION: 0.97

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

ANALYSIS FILE NAME: GSM1013122_UCSD.Gastric.H3K27ac.STL001.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K27ac.STL001GA.01.01.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Gastric H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K27ac 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.16629
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 H3K27ac 01 58
BROWSER_TRACK_DESCRIPTION: UCSD Gastric Histone H3K27ac Donor STL001 Library CY58 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 10,352,743
FINDPEAKS_SCORE: 0.4451
FINDPEAKS_PERCENTILE: 61
HOTSPOT_SCORE: 0.5006
HOTSPOT_PERCENTILE: 66
IROC_SCORE: 0.9783
IROC_PERCENTILE: 14
POISSON_SCORE: 0.5498
POISSON_PERCENTILE: 67
MAXIMUM_REPLICATE_CORRELATION: 0.97

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

value: Gastric

value: genomic DNA

value: Shin Lin, Stanford University

value: Primary Tissue

value: Autopsy

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

value: Male

value: Caucasian and African American

value: Histone H3K27ac

value: Biorupter

value: 500 micrograms

value: magnetic anti-rabbit

value: 5 micrograms

value: Active Motif


title: Reference Epigenome: ChIP-Seq Analysis of H3K4me1 in Human Right Ventricle Tissue; renlab.H3K4me1.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 H3K4me1 in Human Right Ventricle Tissue. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: AY277
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.13338
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: GSM956022_UCSD.Right_Ventricle.H3K4me1.STL003.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K4me1.STL003RV.01.01.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Right Ventricle H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K4me1 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.16354
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: 18,151,296
FINDPEAKS_SCORE: 0.2063
FINDPEAKS_PERCENTILE: 40
HOTSPOT_SCORE: 0.3205
HOTSPOT_PERCENTILE: 46
IROC_SCORE: 0.9423
IROC_PERCENTILE: 33
POISSON_SCORE: 0.4499
POISSON_PERCENTILE: 46
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

ANALYSIS FILE NAME: GSM956022_UCSD.Right_Ventricle.H3K4me1.STL003.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K4me1.STL003RV.01.01.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Right Ventricle H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K4me1 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.16508
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 H3K4me1 03 77
BROWSER_TRACK_DESCRIPTION: UCSD Right Ventricle Histone H3K4me1 Donor STL003 Library AY277 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 18,151,296
FINDPEAKS_SCORE: 0.2063
FINDPEAKS_PERCENTILE: 40
HOTSPOT_SCORE: 0.3205
HOTSPOT_PERCENTILE: 46
IROC_SCORE: 0.9423
IROC_PERCENTILE: 33
POISSON_SCORE: 0.4499
POISSON_PERCENTILE: 46
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

source_name: Right Ventricle tissue; renlab.H3K4me1.STL003RV.01.01

value: Right Ventricle

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

value: Caucasian

value: Histone H3K4me1

value: Abcam


title: Reference Epigenome: ChIP-Seq Analysis of H3K9me3 in Human Sigmoid Colon Tissue; renlab.H3K9me3.STL003SG.01.01

description:
sample_term_id: UBERON_0001159
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K9me3 in Human Sigmoid Colon Tissue. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: AY281
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.13365
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.11872
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

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

ANALYSIS FILE NAME: GSM956027_UCSD.Sigmoid_Colon.H3K9me3.STL003.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K9me3.STL003SG.01.01.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Sigmoid Colon H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K9me3 ChIP-Seq on Sigmoid Colon, Donor STL003, were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.16444
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: 15,676,332
FINDPEAKS_SCORE: 0.0865
FINDPEAKS_PERCENTILE: 69
HOTSPOT_SCORE: 0.1993
HOTSPOT_PERCENTILE: 72
IROC_SCORE: 0.812
IROC_PERCENTILE: 56
POISSON_SCORE: 0.3018
POISSON_PERCENTILE: 56
MAXIMUM_REPLICATE_CORRELATION: 0.97

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

ANALYSIS FILE NAME: GSM956027_UCSD.Sigmoid_Colon.H3K9me3.STL003.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K9me3.STL003SG.01.01.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Sigmoid Colon H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K9me3 ChIP-Seq read mappings from Sigmoid Colon, Donor STL003, were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.16598
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: SC H3K9me3 03 81
BROWSER_TRACK_DESCRIPTION: UCSD Sigmoid Colon Histone H3K9me3 Donor STL003 Library AY281 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 15,676,332
FINDPEAKS_SCORE: 0.0865
FINDPEAKS_PERCENTILE: 69
HOTSPOT_SCORE: 0.1993
HOTSPOT_PERCENTILE: 72
IROC_SCORE: 0.812
IROC_PERCENTILE: 56
POISSON_SCORE: 0.3018
POISSON_PERCENTILE: 56
MAXIMUM_REPLICATE_CORRELATION: 0.97

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

source_name: Sigmoid Colon tissue; renlab.H3K9me3.STL003SG.01.01

value: Sigmoid Colon

value: genomic DNA

value: Shin Lin, Stanford University

value: Histone H3K9me3


title: Reference Epigenome: ChIP-Seq Analysis of H3K4me1 in Human Psoas Muscle Tissue; renlab.H3K4me1.STL003PO.01.01

description:
sample_term_id: UBERON_0008450
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K4me1 in Human Psoas Muscle Tissue. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: A292
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.13348
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.11875
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

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

ANALYSIS FILE NAME: GSM956021_UCSD.Psoas_Muscle.H3K4me1.STL003.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K4me1.STL003PO.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 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.16466
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: 15,984,133
FINDPEAKS_SCORE: 0.321
FINDPEAKS_PERCENTILE: 58
HOTSPOT_SCORE: 0.4251
HOTSPOT_PERCENTILE: 71
IROC_SCORE: 0.974
IROC_PERCENTILE: 50
POISSON_SCORE: 0.5137
POISSON_PERCENTILE: 58
MAXIMUM_REPLICATE_CORRELATION: 0.97

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

ANALYSIS FILE NAME: GSM956021_UCSD.Psoas_Muscle.H3K4me1.STL003.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K4me1.STL003PO.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 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.16620
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 03 92
BROWSER_TRACK_DESCRIPTION: UCSD Psoas Muscle Histone H3K4me1 Donor STL003 Library A292 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 15,984,133
FINDPEAKS_SCORE: 0.321
FINDPEAKS_PERCENTILE: 58
HOTSPOT_SCORE: 0.4251
HOTSPOT_PERCENTILE: 71
IROC_SCORE: 0.974
IROC_PERCENTILE: 50
POISSON_SCORE: 0.5137
POISSON_PERCENTILE: 58
MAXIMUM_REPLICATE_CORRELATION: 0.97

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

source_name: Psoas Muscle tissue; renlab.H3K4me1.STL003PO.01.01

value: Psoas Muscle

value: Primary Tissue

value: Autopsy

value: Male


title: Reference Epigenome: ChIP-Seq Analysis of H3K4me1 in Human Sigmoid Colon Tissue; renlab.H3K4me1.STL003SG.01.01

description:
sample_term_id: UBERON_0001159
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K4me1 in Human Sigmoid Colon Tissue. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: AY280
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.13344
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.11872
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

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

ANALYSIS FILE NAME: GSM956023_UCSD.Sigmoid_Colon.H3K4me1.STL003.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K4me1.STL003SG.01.01.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Sigmoid Colon H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K4me1 ChIP-Seq on Sigmoid Colon, Donor STL003, were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.16471
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: 21,346,134
FINDPEAKS_SCORE: 0.216
FINDPEAKS_PERCENTILE: 42
HOTSPOT_SCORE: 0.3102
HOTSPOT_PERCENTILE: 44
IROC_SCORE: 0.9552
IROC_PERCENTILE: 44
POISSON_SCORE: 0.4379
POISSON_PERCENTILE: 40
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

ANALYSIS FILE NAME: GSM956023_UCSD.Sigmoid_Colon.H3K4me1.STL003.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K4me1.STL003SG.01.01.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Sigmoid Colon H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K4me1 ChIP-Seq read mappings from Sigmoid Colon, Donor STL003, were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.16625
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: SC H3K4me1 03 80
BROWSER_TRACK_DESCRIPTION: UCSD Sigmoid Colon Histone H3K4me1 Donor STL003 Library AY280 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 21,346,134
FINDPEAKS_SCORE: 0.216
FINDPEAKS_PERCENTILE: 42
HOTSPOT_SCORE: 0.3102
HOTSPOT_PERCENTILE: 44
IROC_SCORE: 0.9552
IROC_PERCENTILE: 44
POISSON_SCORE: 0.4379
POISSON_PERCENTILE: 40
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

source_name: Sigmoid Colon tissue; renlab.H3K4me1.STL003SG.01.01

value: Biorupter

value: 500 micrograms


title: E2_1

status: Public on Jun 21 2013

city: Chicago

first: Thien

last: Le

state: IL

institute: University of Chicago

description: GROseq - Global run-on followed by sequencing

data_processing:
Alignment: Short-reads were aligned to the human reference genome (hg18, NCBI36), including autosomes, X-chromosome, and one complete copy of an rDNA repeat (GenBank ID: U13369.1). The SOAP2 software package was used to align reads with the following options: (1) all non-unique mappings were removed (-r 0), (2) three mismatches were allowed in each mapped read (-v 3), (3) low-quality reads with more than 10 ambiguous bases were removed (-N 10), and (4) for reads failing to align over the entire length of the read, the first 32 bp was used (-l 32). SOAP2 output was processed using custom Perl scripts, and imported into R for most the analysis.  In order to identify E2-regulated genes, we focused on RefSeq-annotated genes, counting reads in a fixed window between +1 kb and +13 kb relative to the transcription start site of each gene, so as to avoid possible complications introduced by paused polymerases, and to allow easy side-by-side comparison among samples. The normalized expression value of 1e-5 (normalized against the sample total read counts) was used as the threshold to select genes for further analyses. Comparing E2 treated samples versus vehicle treated samples, genes with FC>1.2 were considered upregulated; those with FC<0.8 were considered downregulated.
Genome_build: hg18
Supplementary_files_format_and_content: txt: read locations, count reads

source_name: Immortalized human breast cancer cells

extract_protocol:
After 1 hour of E2 or Vehicle treatment, nuclei from C4-12/Flag-ERβ cells were extracted and processed with nuclear run-on assay.
Run-on RNA was ligated with adapters and reverse transcribed to generate cDNA library.

tag: treatment

value: 10nM E2

tag: replicate


title: Reference Epigenome: ChIP-Seq Analysis of H3K4me1 in Human Sigmoid Colon Tissue; renlab.H3K4me1.STL001SG.01.01

description:
sample_term_id: UBERON_0001159
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K4me1 in Human Sigmoid Colon Tissue. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: AK332
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.13123
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.12265
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

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

ANALYSIS FILE NAME: GSM956020_UCSD.Sigmoid_Colon.H3K4me1.STL001.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K4me1.STL001SG.01.01.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Sigmoid Colon H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K4me1 ChIP-Seq on Sigmoid Colon, Donor STL001, were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.16463
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: 31,703,694
FINDPEAKS_SCORE: 0.0099
FINDPEAKS_PERCENTILE: 2
HOTSPOT_SCORE: 0.1302
HOTSPOT_PERCENTILE: 4
IROC_SCORE: 0.7521
IROC_PERCENTILE: 6
POISSON_SCORE: 0.2918
POISSON_PERCENTILE: 4
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

ANALYSIS FILE NAME: GSM956020_UCSD.Sigmoid_Colon.H3K4me1.STL001.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K4me1.STL001SG.01.01.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Sigmoid Colon H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K4me1 ChIP-Seq read mappings from Sigmoid Colon, Donor STL001, were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.16617
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: SC H3K4me1 01 32
BROWSER_TRACK_DESCRIPTION: UCSD Sigmoid Colon Histone H3K4me1 Donor STL001 Library AK332 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 31,703,694
FINDPEAKS_SCORE: 0.0099
FINDPEAKS_PERCENTILE: 2
HOTSPOT_SCORE: 0.1302
HOTSPOT_PERCENTILE: 4
IROC_SCORE: 0.7521
IROC_PERCENTILE: 6
POISSON_SCORE: 0.2918
POISSON_PERCENTILE: 4
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

source_name: Sigmoid Colon tissue; renlab.H3K4me1.STL001SG.01.01

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

value: Caucasian and African American

value: magnetic anti-rabbit

value: 5 micrograms


title: Veh_1

value: Vehicle


title: Reference Epigenome: ChIP-Seq Analysis of H3K36me3 in Human Sigmoid Colon Tissue; renlab.H3K36me3.STL001SG.01.01

description:
sample_term_id: UBERON_0001159
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K36me3 in Human Sigmoid Colon Tissue. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: AK331
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.13119
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.12265
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

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

ANALYSIS FILE NAME: GSM956013_UCSD.Sigmoid_Colon.H3K36me3.STL001.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K36me3.STL001SG.01.01.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Sigmoid Colon H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K36me3 ChIP-Seq on Sigmoid Colon, Donor STL001, were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.16426
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: 13,223,608
FINDPEAKS_SCORE: 0.1876
FINDPEAKS_PERCENTILE: 33
HOTSPOT_SCORE: 0.2756
HOTSPOT_PERCENTILE: 39
IROC_SCORE: 0.9267
IROC_PERCENTILE: 27
POISSON_SCORE: 0.4049
POISSON_PERCENTILE: 24
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

ANALYSIS FILE NAME: GSM956013_UCSD.Sigmoid_Colon.H3K36me3.STL001.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K36me3.STL001SG.01.01.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Sigmoid Colon H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K36me3 ChIP-Seq read mappings from Sigmoid Colon, Donor STL001, were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.16580
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: SC H3K36me3 01 31
BROWSER_TRACK_DESCRIPTION: UCSD Sigmoid Colon Histone H3K36me3 Donor STL001 Library AK331 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 13,223,608
FINDPEAKS_SCORE: 0.1876
FINDPEAKS_PERCENTILE: 33
HOTSPOT_SCORE: 0.2756
HOTSPOT_PERCENTILE: 39
IROC_SCORE: 0.9267
IROC_PERCENTILE: 27
POISSON_SCORE: 0.4049
POISSON_PERCENTILE: 24
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

source_name: Sigmoid Colon tissue; renlab.H3K36me3.STL001SG.01.01

value: Histone H3K36me3

value: Abcam


title: Reference Epigenome: ChIP-Seq Input from Human Gastric Tissue; renlab.Input.STL003GA.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: AK341
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.13107
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.12180
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

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

ANALYSIS FILE NAME: GSM956032_UCSD.Gastric.Input.STL003.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.Input.STL003GA.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 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.16485
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: 66,891,283
FINDPEAKS_SCORE: 0.0038
FINDPEAKS_PERCENTILE: 20
HOTSPOT_SCORE: 0.003
HOTSPOT_PERCENTILE: 11
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.046
POISSON_PERCENTILE: 41
MAXIMUM_REPLICATE_CORRELATION: 0.96

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

ANALYSIS FILE NAME: GSM956032_UCSD.Gastric.Input.STL003.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.Input.STL003GA.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 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.16639
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 03 41
BROWSER_TRACK_DESCRIPTION: UCSD Gastric ChIP-Seq Input Donor STL003 Library AK341 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 66,891,283
FINDPEAKS_SCORE: 0.0038
FINDPEAKS_PERCENTILE: 20
HOTSPOT_SCORE: 0.003
HOTSPOT_PERCENTILE: 11
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.046
POISSON_PERCENTILE: 41
MAXIMUM_REPLICATE_CORRELATION: 0.96

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

value: Gastric

value: genomic DNA

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

value: Caucasian

value: ChIP-Seq Input

value: Input


title: Celeg-1-FED-RPF

city: Stanford

first: Michael

last: Stadler

address: 300 Pasteur Dr.

department: Pathology

institute: Stanford University

data_processing:
Library strategy: RPF
Basecalls performed standard Illumina software
Reads that map multiply to the genome were removed
Remaining reads were mapped to the CDS sequences + 18 nucleotides of genomic flanking regions using Bowtie v0.12.7
Raw counts for each experiment were determined from mappings
Normalization, fold-change, and significance calculations performed using DESeq (Anders and Huber 2010) software package in R.
Genome_build: WS234
Supplementary_files_format_and_content: Matrix of normalized counts, fold change, and statistical output for genes listed by their associated protein name.

organism: Caenorhabditis elegans

source_name: population-whole animal

growth_protocol: 36 million embryos were grown in S-complete liquid media at 20 C. Animals were starved for 24 hours and either harvested by freezing in liquid nitrogen (diapause animals) or fed for three hours with E. coli HB101 at 15 mg/mL.

extract_protocol:
Total mRNA was isolated using Ambion's micro-poly(A) purist kit, fragmented by alkali and heat, followed by library preparation. Ribosome profiling was carried out as described in Ingolia et al (2009) with modifications as Stadler and Fire (2011).
Libraries were constructed using the circligase protocol as described in Ingolia et al. (2009) with modifications described in Stadler and Fire (2013).

tag: developmental stage

value: L1 fed 3 hours

tag: strain

tag: rna subtype

value: ribosome protected fragments


title: Celeg-3-FED-RPF


title: Input2

description: Additional input sample was required to identify FDR

data_processing:
Peak-calling software: QuEST
Genome_build: hg18
Supplementary_files_format_and_content: BED file

source_name: Genomic DNA

extract_protocol:
On 15-cm plates, C4-12/Flag.ERβ cells were treated with 10nM E2 for 1 hour then crosslinked with 1% formaldehyde. Cells were lysed with 1mL of ChIP-lysis buffer (50mM Tris pH 7.4, 100mM NaCl, 0.1% SDS, 1% Triton-X, 0.5% NP40, PICIII) and sonicated for 10 cycles, each of which was 10 seconds. The lysate was collected and incubated with 30uL Protein G Plus-Agarose (Santa Cruz) preimmuned with 10ug anti-Flag M2 antibodies (Sigma) to capture protein-DNA complex overnight in ChIP-lysis buffer. The Protein G beads were washed once with ChIP-wash buffer I (20mM Tris pH 8.1, 150mM NaCl, 0.1% SDS, 1% Triton X, 2mM EDTA), once with ChIP-wash buffer II (20mM Tris pH 8.1, 500mM NaCl, 0.1% SDS, 1% Triton X, 2mM EDTA), once with ChIP-wash buffer III (10mM Tris pH 8.1, 250mM LiCl, 1% NP40, 1% deoxycholate, 1mM EDTA), and twice with TE buffer. The protein-DNA complexes were eluted with ChIP-elution buffer (100mM NaHCO3, 1% SDS). The crosslinking was reversed by incubating samples at 65oC overnight. After treatment of RNase A and Proteinase K, the inputs and immunoprecipitated samples were extracted once with phenol/chloroform, once with chloroform, and precipitated in ethanol. The genomic DNA precipitate was suspended in 20uL nuclease-free water.
Illumina ChIP-seq kit

tag: ChIP

value: input

tag: cell line


title: Input1


title: Reference Epigenome: ChIP-Seq Input from Human Thymus Tissue; renlab.Input.STL001TH.01.01

description:
sample_term_id: UBERON_0002370
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Input from Human Thymus Tissue. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: AY295
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.13370
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: GSM956030_UCSD.Thymus.Input.STL001.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.Input.STL001TH.01.01.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Thymus Input ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Input 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.16411
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: 13,636,668
FINDPEAKS_SCORE: 0.0071
FINDPEAKS_PERCENTILE: 74
HOTSPOT_SCORE: 0.0829
HOTSPOT_PERCENTILE: 83
IROC_SCORE: 0.2395
IROC_PERCENTILE: 23
POISSON_SCORE: 0.1319
POISSON_PERCENTILE: 78
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM956030_UCSD.Thymus.Input.STL001.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.Input.STL001TH.01.01.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Thymus Input ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Input 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.16565
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 Input 01 95
BROWSER_TRACK_DESCRIPTION: UCSD Thymus ChIP-Seq Input Donor STL001 Library AY295 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 13,636,668
FINDPEAKS_SCORE: 0.0071
FINDPEAKS_PERCENTILE: 74
HOTSPOT_SCORE: 0.0829
HOTSPOT_PERCENTILE: 83
IROC_SCORE: 0.2395
IROC_PERCENTILE: 23
POISSON_SCORE: 0.1319
POISSON_PERCENTILE: 78
MAXIMUM_REPLICATE_CORRELATION: NA

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

tag: sample alias

value: Thymus

value: Shin Lin, Stanford University

value: Primary Tissue

value: Autopsy

value: Male

value: Biorupter

value: 500 micrograms


title: Celeg-2-ST-RPF

value: L1 diapause