title: Reference Epigenome: ChIP-Seq Analysis of H3K36me3 in Human Pancreas Tissue; renlab.H3K36me3.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 H3K36me3 in Human Pancreas Tissue. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: CY76
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.16019
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: GSM1127182_UCSD.Pancreas.H3K36me3.STL002.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K36me3.STL002PA.01.01.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Pancreas H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K36me3 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.16453
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: 15,498,801
FINDPEAKS_SCORE: 0.13
FINDPEAKS_PERCENTILE: 20
HOTSPOT_SCORE: 0.24
HOTSPOT_PERCENTILE: 18
IROC_SCORE: 0.91
IROC_PERCENTILE: 18
POISSON_SCORE: 0.35
POISSON_PERCENTILE: 14
MAXIMUM_REPLICATE_CORRELATION: 0.96

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

ANALYSIS FILE NAME: GSM1127182_UCSD.Pancreas.H3K36me3.STL002.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K36me3.STL002PA.01.01.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Pancreas H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K36me3 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.16607
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 H3K36me3 02 76
BROWSER_TRACK_DESCRIPTION: UCSD Pancreas Histone H3K36me3 Donor STL002 Library CY76 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 15,498,801
FINDPEAKS_SCORE: 0.13
FINDPEAKS_PERCENTILE: 20
HOTSPOT_SCORE: 0.24
HOTSPOT_PERCENTILE: 18
IROC_SCORE: 0.91
IROC_PERCENTILE: 18
POISSON_SCORE: 0.35
POISSON_PERCENTILE: 14
MAXIMUM_REPLICATE_CORRELATION: 0.96

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

value: Pancreas

tag: sra sample accession

value: iron deficiency, bipolar

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

value: Caucasian

value: Histone H3K36me3

value: magnetic anti-rabbit

value: 5 micrograms

value: Abcam


title: Reference Epigenome: ChIP-Seq Analysis of H3K36me3 in Human Psoas Muscle Tissue; renlab.H3K36me3.STL001PO.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_0008450
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K36me3 in Human Psoas Muscle Tissue. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: CY103
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.16016
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.14034
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

library_source: genomic

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

ANALYSIS FILE NAME: GSM1127181_UCSD.Psoas_Muscle.H3K36me3.STL001.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K36me3.STL001PO.01.01-renlab.H3K36me3.STL001PO.01.01.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Psoas Muscle H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K36me3 ChIP-Seq on Psoas Muscle, Donor STL001, were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.16389
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 20,388,181
FINDPEAKS_SCORE: 0.06
FINDPEAKS_PERCENTILE: 10
HOTSPOT_SCORE: 0.17
HOTSPOT_PERCENTILE: 8
IROC_SCORE: 0.87
IROC_PERCENTILE: 12
POISSON_SCORE: 0.31
POISSON_PERCENTILE: 10
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM1127181_UCSD.Psoas_Muscle.H3K36me3.STL001.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K36me3.STL001PO.01.01-renlab.H3K36me3.STL001PO.01.01.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Psoas Muscle H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K36me3 ChIP-Seq read mappings from Psoas Muscle, Donor STL001, were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.16543
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 H3K36me3 01 03
BROWSER_TRACK_DESCRIPTION: UCSD Psoas Muscle Histone H3K36me3 Donor STL001 Library CY103 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 20,388,181
FINDPEAKS_SCORE: 0.06
FINDPEAKS_PERCENTILE: 10
HOTSPOT_SCORE: 0.17
HOTSPOT_PERCENTILE: 8
IROC_SCORE: 0.87
IROC_PERCENTILE: 12
POISSON_SCORE: 0.31
POISSON_PERCENTILE: 10
MAXIMUM_REPLICATE_CORRELATION: NA

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

molecule: genomic DNA

organism: Homo sapiens

source_name: Psoas Muscle tissue; renlab.H3K36me3.STL001PO.01.01

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

tag: sample common name

value: Psoas Muscle

tag: disease

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: Biorupter

value: 500 micrograms


title: Reference Epigenome: ChIP-Seq Analysis of H3K27ac in Human Small Bowel Tissue; renlab.H3K27ac.STL003SB.01.01

description:
sample_term_id: UBERON_0002108
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K27ac in Human Small Bowel Tissue. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: CY62
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.16005
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.11844
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

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

ANALYSIS FILE NAME: GSM1127172_UCSD.Small_Intestine.H3K27ac.STL003.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K27ac.STL003SB.01.01-renlab.H3K27ac.STL003SB.01.01-renlab.H3K27ac.STL003SB.01.01.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Small Intestine H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K27ac ChIP-Seq on Small Intestine, Donor 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.16483
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: 18,884,593
FINDPEAKS_SCORE: 0.23
FINDPEAKS_PERCENTILE: 19
HOTSPOT_SCORE: 0.34
HOTSPOT_PERCENTILE: 30
IROC_SCORE: 0.92
IROC_PERCENTILE: 3
POISSON_SCORE: 0.45
POISSON_PERCENTILE: 37
MAXIMUM_REPLICATE_CORRELATION: 0.96

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

ANALYSIS FILE NAME: GSM1127172_UCSD.Small_Intestine.H3K27ac.STL003.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K27ac.STL003SB.01.01-renlab.H3K27ac.STL003SB.01.01-renlab.H3K27ac.STL003SB.01.01.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Small Intestine H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K27ac ChIP-Seq read mappings from Small Intestine, Donor 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.16637
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: SI H3K27ac 03 62
BROWSER_TRACK_DESCRIPTION: UCSD Small Intestine Histone H3K27ac Donor STL003 Library CY62 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 18,884,593
FINDPEAKS_SCORE: 0.23
FINDPEAKS_PERCENTILE: 19
HOTSPOT_SCORE: 0.34
HOTSPOT_PERCENTILE: 30
IROC_SCORE: 0.92
IROC_PERCENTILE: 3
POISSON_SCORE: 0.45
POISSON_PERCENTILE: 37
MAXIMUM_REPLICATE_CORRELATION: 0.96

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

source_name: Small Intestine tissue; renlab.H3K27ac.STL003SB.01.01

value: Small Intestine

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

value: Histone H3K27ac

value: Active Motif


title: Reference Epigenome: ChIP-Seq Analysis of H3K27ac in Human Left Ventricle Tissue; renlab.H3K27ac.STL011LV.01.01

description:
sample_term_id: UBERON_0002084
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K27ac in Human Left Ventricle Tissue. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: AY369
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.15929
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.15917
****************
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: GSM1127173_UCSD.Left_Ventricle.H3K27ac.STL011.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K27ac.STL011LV.01.01-renlab.H3K27ac.STL011LV.01.01.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Left Ventricle H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K27ac ChIP-Seq on Left Ventricle, Donor STL011, 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.16410
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 23,245,242
FINDPEAKS_SCORE: 0.41
FINDPEAKS_PERCENTILE: 56
HOTSPOT_SCORE: 0.43
HOTSPOT_PERCENTILE: 49
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.5
POISSON_PERCENTILE: 53
MAXIMUM_REPLICATE_CORRELATION: 0.9

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

ANALYSIS FILE NAME: GSM1127173_UCSD.Left_Ventricle.H3K27ac.STL011.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K27ac.STL011LV.01.01-renlab.H3K27ac.STL011LV.01.01.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Left Ventricle H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K27ac ChIP-Seq read mappings from Left Ventricle, Donor STL011, 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.16564
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: LV H3K27ac 11 69
BROWSER_TRACK_DESCRIPTION: UCSD Left Ventricle Histone H3K27ac Donor STL011 Library AY369 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 23,245,242
FINDPEAKS_SCORE: 0.41
FINDPEAKS_PERCENTILE: 56
HOTSPOT_SCORE: 0.43
HOTSPOT_PERCENTILE: 49
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.5
POISSON_PERCENTILE: 53
MAXIMUM_REPLICATE_CORRELATION: 0.9

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

source_name: Left Ventricle tissue; renlab.H3K27ac.STL011LV.01.01

tag: sample alias

value: Left Ventricle

value: coronary artery disease

value: coronary artery disease. No history of hypertension or diabetes.

value: Caucasian


title: Histone H3K9me3 ChIP-Seq of Fetal Muscle, Leg; Histone.DS23305

city: Seattle

first: Northwest

last: REMC

state: WA

institute: University of Washington

description:
sample_term_id: UBERON_0001383
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Histone H3K9me3 ChIP-Seq
Library name: Histone.DS23305
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.16309
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.14904
****************
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: GSM1160202_UW.Fetal_Muscle_Leg.H3K9me3.H-24644.Histone.DS23305.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Histone.DS23305-Histone.DS23305.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Fetal Muscle Leg H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K9me3 ChIP-Seq on Fetal Muscle Leg, Donor H-24644, 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.16861
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: 21,469,611
FINDPEAKS_SCORE: 0.1086
FINDPEAKS_PERCENTILE: 72
HOTSPOT_SCORE: 0.1732
HOTSPOT_PERCENTILE: 62
IROC_SCORE: 0.8778
IROC_PERCENTILE: 74
POISSON_SCORE: 0.3961
POISSON_PERCENTILE: 86
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

ANALYSIS FILE NAME: GSM1160202_UW.Fetal_Muscle_Leg.H3K9me3.H-24644.Histone.DS23305.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Histone.DS23305-Histone.DS23305.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Muscle Leg H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K9me3 ChIP-Seq read mappings from Fetal Muscle Leg, Donor H-24644, 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.16957
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: FML H3K9me3 44 05
BROWSER_TRACK_DESCRIPTION: UW Fetal Muscle Leg Histone H3K9me3 Donor H-24644 Library Histone.DS23305 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 21,469,611
FINDPEAKS_SCORE: 0.1086
FINDPEAKS_PERCENTILE: 72
HOTSPOT_SCORE: 0.1732
HOTSPOT_PERCENTILE: 62
IROC_SCORE: 0.8778
IROC_PERCENTILE: 74
POISSON_SCORE: 0.3961
POISSON_PERCENTILE: 86
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

source_name: Fetal Muscle, Leg primary tissue, day 110; Histone.DS23305

extract_protocol: Library construction protocol: Single read - Illumina

value: University of Washington, Congenital Defects Lab. Ian Glass

value: Fetal Muscle, Leg

value: UW

value: fetal

value: day 110

value: Female

value: Histone H3K9me3

value: Diagenode Bioruptor

value: 20-40 cycles of 0.5 minute on and 0.5 minute off

value: Millipore A/G agarose beads

value: 30ul A/G bead slurry


city: San Francisco

first: UCSF-UBC

last: CENTER

address: UCSF-UBC

institute: UCSF-UBC

description:
design description: ChIP-Seq input analysis of peripheral mononuclear cell from TC015 (A21632) using Illumina HiSeq 2000
library name: A21632
EXPERIMENT_TYPE: ChIP-Seq Input
EXTRACTION_PROTOCOL: Refer to document 'Chromatin Immunoprecipitation (ChIP)' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
EXTRACTION_PROTOCOL_TYPE_OF_SONICATOR: Fisher 550 Sonic Dismembrator
EXTRACTION_PROTOCOL_SONICATION_CYCLES: 10 min
CHIP_PROTOCOL: Input
CHIP_PROTOCOL_CHROMATIN_AMOUNT: 0.1 ug
SIZE_FRACTION: 94-294 bp
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

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

ANALYSIS FILE NAME: GSM1127151_UCSF-UBC.Peripheral_Blood_Mononuclear_Primary_Cells.Input.TC015.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A21632-1.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Peripheral Blood Mononuclear Primary Cells Input ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Input ChIP-Seq on Peripheral Blood Mononuclear Primary Cells, Donor TC015, Library A21632 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.17036
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: 24,367,081
FINDPEAKS_SCORE: 0.0064
FINDPEAKS_PERCENTILE: 69
HOTSPOT_SCORE: 0.0075
HOTSPOT_PERCENTILE: 40
IROC_SCORE: 0.9733
IROC_PERCENTILE: 68
POISSON_SCORE: 0.0305
POISSON_PERCENTILE: 28
MAXIMUM_REPLICATE_CORRELATION: 0.99

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

ANALYSIS FILE NAME: GSM1127151_UCSF-UBC.Peripheral_Blood_Mononuclear_Primary_Cells.Input.TC015.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A21632-1.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Peripheral Blood Mononuclear Primary Cells Input ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Input ChIP-Seq read mappings from Peripheral Blood Mononuclear Primary Cells, Donor TC015, Library A21632 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.17095
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: PBM Input 15 32
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Peripheral Blood Mononuclear Primary Cells ChIP-Seq Input Donor TC015 Library A21632 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 24,367,081
FINDPEAKS_SCORE: 0.0064
FINDPEAKS_PERCENTILE: 69
HOTSPOT_SCORE: 0.0075
HOTSPOT_PERCENTILE: 40
IROC_SCORE: 0.9733
IROC_PERCENTILE: 68
POISSON_SCORE: 0.0305
POISSON_PERCENTILE: 28
MAXIMUM_REPLICATE_CORRELATION: 0.99

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

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

tag: submitted sample id

tag: Sex

value: male

tag: body site

value: Blood

tag: histological type

value: Peripheral blood mononuclear cell

tag: is tumor

value: No

value: primary cell


title: Reference Epigenome: ChIP-Seq Analysis of H3K27ac in Human Psoas Muscle Tissue; renlab.H3K27ac.STL001PO.01.01

description:
sample_term_id: UBERON_0008450
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K27ac in Human Psoas Muscle Tissue. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: CY52
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.15938
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.14034
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

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

ANALYSIS FILE NAME: GSM1127171_UCSD.Psoas_Muscle.H3K27ac.STL001.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K27ac.STL001PO.01.01-renlab.H3K27ac.STL001PO.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 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.16369
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: 10,351,698
FINDPEAKS_SCORE: 0.43
FINDPEAKS_PERCENTILE: 60
HOTSPOT_SCORE: 0.49
HOTSPOT_PERCENTILE: 63
IROC_SCORE: 0.98
IROC_PERCENTILE: 16
POISSON_SCORE: 0.53
POISSON_PERCENTILE: 64
MAXIMUM_REPLICATE_CORRELATION: 0.75

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

ANALYSIS FILE NAME: GSM1127171_UCSD.Psoas_Muscle.H3K27ac.STL001.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K27ac.STL001PO.01.01-renlab.H3K27ac.STL001PO.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 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.16523
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 01 52
BROWSER_TRACK_DESCRIPTION: UCSD Psoas Muscle Histone H3K27ac Donor STL001 Library CY52 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 10,351,698
FINDPEAKS_SCORE: 0.43
FINDPEAKS_PERCENTILE: 60
HOTSPOT_SCORE: 0.49
HOTSPOT_PERCENTILE: 63
IROC_SCORE: 0.98
IROC_PERCENTILE: 16
POISSON_SCORE: 0.53
POISSON_PERCENTILE: 64
MAXIMUM_REPLICATE_CORRELATION: 0.75

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

source_name: Psoas Muscle tissue; renlab.H3K27ac.STL001PO.01.01

value: Psoas Muscle

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


description:
design description: ChIP-Seq input analysis of peripheral mononuclear cell from TC016 (A21639) using Illumina HiSeq 2000
library name: A21639
EXPERIMENT_TYPE: ChIP-Seq Input
EXTRACTION_PROTOCOL: Refer to document 'Chromatin Immunoprecipitation (ChIP)' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
EXTRACTION_PROTOCOL_TYPE_OF_SONICATOR: Fisher 550 Sonic Dismembrator
EXTRACTION_PROTOCOL_SONICATION_CYCLES: 10 min
CHIP_PROTOCOL: Input
CHIP_PROTOCOL_CHROMATIN_AMOUNT: 0.1 ug
SIZE_FRACTION: 94-294 bp
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

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

ANALYSIS FILE NAME: GSM1127149_UCSF-UBC.Peripheral_Blood_Mononuclear_Primary_Cells.Input.TC016.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A21639-1.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Peripheral Blood Mononuclear Primary Cells Input ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Input ChIP-Seq on Peripheral Blood Mononuclear Primary Cells, Donor TC016, Library A21639 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.17058
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 38,037,164
FINDPEAKS_SCORE: 0.0053
FINDPEAKS_PERCENTILE: 34
HOTSPOT_SCORE: 0.0039
HOTSPOT_PERCENTILE: 22
IROC_SCORE: 0.0
IROC_PERCENTILE: 25
POISSON_SCORE: 0.017
POISSON_PERCENTILE: 5
MAXIMUM_REPLICATE_CORRELATION: 0.99

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

ANALYSIS FILE NAME: GSM1127149_UCSF-UBC.Peripheral_Blood_Mononuclear_Primary_Cells.Input.TC016.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A21639-1.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Peripheral Blood Mononuclear Primary Cells Input ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Input ChIP-Seq read mappings from Peripheral Blood Mononuclear Primary Cells, Donor TC016, Library A21639 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.17117
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: PBM Input 16 39
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Peripheral Blood Mononuclear Primary Cells ChIP-Seq Input Donor TC016 Library A21639 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 38,037,164
FINDPEAKS_SCORE: 0.0053
FINDPEAKS_PERCENTILE: 34
HOTSPOT_SCORE: 0.0039
HOTSPOT_PERCENTILE: 22
IROC_SCORE: 0.0
IROC_PERCENTILE: 25
POISSON_SCORE: 0.017
POISSON_PERCENTILE: 5
MAXIMUM_REPLICATE_CORRELATION: 0.99

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

value: female

value: Blood


description:
design description: ChIP-Seq input analysis of placenta (smooth chorionic membrane) tissue from CTL02 (A21716) using Illumina HiSeq 2000
library name: A21716
EXPERIMENT_TYPE: ChIP-Seq Input
EXTRACTION_PROTOCOL: Refer to document 'Chromatin Immunoprecipitation (ChIP)' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
EXTRACTION_PROTOCOL_TYPE_OF_SONICATOR: Fisher 550 Sonic Dismembrator
EXTRACTION_PROTOCOL_SONICATION_CYCLES: 10 min
CHIP_PROTOCOL: Input
CHIP_PROTOCOL_CHROMATIN_AMOUNT: 0.1 ug
SIZE_FRACTION: 158-460 bp
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

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

ANALYSIS FILE NAME: GSM1127148_UCSF-UBC.Placenta_Chorion_Smooth.Input.CTL02.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A21716-1.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Placenta Chorion Smooth Input ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Input ChIP-Seq on Placenta Chorion Smooth, Donor CTL02 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.17073
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: 26,343,297
FINDPEAKS_SCORE: 0.006
FINDPEAKS_PERCENTILE: 60
HOTSPOT_SCORE: 0.0057
HOTSPOT_PERCENTILE: 34
IROC_SCORE: 0.0
IROC_PERCENTILE: 25
POISSON_SCORE: 0.0246
POISSON_PERCENTILE: 12
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM1127148_UCSF-UBC.Placenta_Chorion_Smooth.Input.CTL02.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A21716-1.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Placenta Chorion Smooth Input ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Input ChIP-Seq read mappings from Placenta Chorion Smooth, Donor CTL02 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.17132
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: PCS Input 02 16
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Placenta Chorion Smooth ChIP-Seq Input Donor CTL02 Library A21716 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 26,343,297
FINDPEAKS_SCORE: 0.006
FINDPEAKS_PERCENTILE: 60
HOTSPOT_SCORE: 0.0057
HOTSPOT_PERCENTILE: 34
IROC_SCORE: 0.0
IROC_PERCENTILE: 25
POISSON_SCORE: 0.0246
POISSON_PERCENTILE: 12
MAXIMUM_REPLICATE_CORRELATION: NA

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

value: male

value: Placenta

value: Chorion smooth tissue

value: No

value: primary tissue


title: Histone H3K4me3 ChIP-Seq of Fetal Adrenal Gland; Histone.DS23063

description:
sample_term_id: UBERON_0002369
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Histone H3K4me3 ChIP-Seq
Library name: Histone.DS23063
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.16264
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.15682
****************
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: GSM1160198_UW.Fetal_Adrenal_Gland.H3K4me3.H-24800.Histone.DS23063.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Histone.DS23063-Histone.DS23063.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Fetal Adrenal Gland H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K4me3 ChIP-Seq on Fetal Adrenal Gland, Donor H-24800, 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.16837
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: 42,828,119
FINDPEAKS_SCORE: 0.4172
FINDPEAKS_PERCENTILE: 59
HOTSPOT_SCORE: 0.4171
HOTSPOT_PERCENTILE: 52
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.4156
POISSON_PERCENTILE: 50
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM1160198_UW.Fetal_Adrenal_Gland.H3K4me3.H-24800.Histone.DS23063.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Histone.DS23063-Histone.DS23063.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Adrenal Gland H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K4me3 ChIP-Seq read mappings from Fetal Adrenal Gland, Donor H-24800, 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.16933
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: FAG H3K4me3 00 63
BROWSER_TRACK_DESCRIPTION: UW Fetal Adrenal Gland Histone H3K4me3 Donor H-24800 Library Histone.DS23063 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 42,828,119
FINDPEAKS_SCORE: 0.4172
FINDPEAKS_PERCENTILE: 59
HOTSPOT_SCORE: 0.4171
HOTSPOT_PERCENTILE: 52
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.4156
POISSON_PERCENTILE: 50
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: Fetal Adrenal Gland primary tissue, day 97; Histone.DS23063

value: University of Washington, Congenital Defects Lab. Ian Glass

value: Primary Tissue

value: Fetal Adrenal Gland

value: UW

value: fetal

value: day 97

value: Histone H3K4me3

value: Diagenode Bioruptor

value: 20-40 cycles of 0.5 minute on and 0.5 minute off

value: Invitrogen Dynabeads

value: Cell Signaling

value: lot 2


description:
design description: ChIP-Seq input analysis of placenta (amniotic membrane) tissue from CTL02 (A21723) using Illumina HiSeq 2000
library name: A21723
EXPERIMENT_TYPE: ChIP-Seq Input
EXTRACTION_PROTOCOL: Refer to document 'Chromatin Immunoprecipitation (ChIP)' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
EXTRACTION_PROTOCOL_TYPE_OF_SONICATOR: Fisher 550 Sonic Dismembrator
EXTRACTION_PROTOCOL_SONICATION_CYCLES: 15 min
CHIP_PROTOCOL: Input
CHIP_PROTOCOL_CHROMATIN_AMOUNT: 0.1 ug
SIZE_FRACTION: 131-474 bp
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

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

ANALYSIS FILE NAME: GSM1127150_UCSF-UBC.Placenta_Amnion.Input.CTL02.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A21723-1.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Placenta Amnion Input ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Input ChIP-Seq on Placenta Amnion, Donor CTL02 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.17061
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 27,713,946
FINDPEAKS_SCORE: 0.006
FINDPEAKS_PERCENTILE: 60
HOTSPOT_SCORE: 0.0054
HOTSPOT_PERCENTILE: 32
IROC_SCORE: 0.0
IROC_PERCENTILE: 25
POISSON_SCORE: 0.0232
POISSON_PERCENTILE: 11
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM1127150_UCSF-UBC.Placenta_Amnion.Input.CTL02.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A21723-1.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Placenta Amnion Input ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Input ChIP-Seq read mappings from Placenta Amnion, Donor CTL02 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.17120
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: PA Input 02 23
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Placenta Amnion ChIP-Seq Input Donor CTL02 Library A21723 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 27,713,946
FINDPEAKS_SCORE: 0.006
FINDPEAKS_PERCENTILE: 60
HOTSPOT_SCORE: 0.0054
HOTSPOT_PERCENTILE: 32
IROC_SCORE: 0.0
IROC_PERCENTILE: 25
POISSON_SCORE: 0.0232
POISSON_PERCENTILE: 11
MAXIMUM_REPLICATE_CORRELATION: NA

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

value: male

value: Amnion tissue

value: placenta (amniotic membrane) tissue


description:
design description: H3K27ac ChIP-Seq analysis of peripheral mononuclear cell from TC015 (A21631) using Illumina HiSeq 2000
library name: A21631
EXPERIMENT_TYPE: Histone H3K27ac
EXTRACTION_PROTOCOL: Refer to document 'Chromatin Immunoprecipitation (ChIP)' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
EXTRACTION_PROTOCOL_TYPE_OF_SONICATOR: Fisher 550 Sonic Dismembrator
EXTRACTION_PROTOCOL_SONICATION_CYCLES: 10 min
CHIP_PROTOCOL: Refer to document 'Chromatin Immunoprecipitation (ChIP)' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
CHIP_PROTOCOL_CHROMATIN_AMOUNT: 5 ug
SIZE_FRACTION: 94-294 bp
CHIP_PROTOCOL_BEAD_TYPE: Sepharose A/G Bead Mix
CHIP_PROTOCOL_BEAD_AMOUNT: 20 ul
CHIP_PROTOCOL_ANTIBODY_AMOUNT: 2.5 ug
CHIP_ANTIBODY: H3K27ac
CHIP_ANTIBODY_PROVIDER: Abcam
CHIP_ANTIBODY_CATALOG: ab4729
CHIP_ANTIBODY_LOT: GR28147-1
****************
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: GSM1127145_UCSF-UBC.Peripheral_Blood_Mononuclear_Primary_Cells.H3K27ac.TC015.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A21631-1.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Peripheral Blood Mononuclear Primary Cells H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K27ac ChIP-Seq on Peripheral Blood Mononuclear Primary Cells, Donor TC015, Library A21631 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.17060
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 22,059,262
FINDPEAKS_SCORE: 0.0616
FINDPEAKS_PERCENTILE: 5
HOTSPOT_SCORE: 0.1149
HOTSPOT_PERCENTILE: 9
IROC_SCORE: 0.9725
IROC_PERCENTILE: 14
POISSON_SCORE: 0.1741
POISSON_PERCENTILE: 2
MAXIMUM_REPLICATE_CORRELATION: 0.96

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

ANALYSIS FILE NAME: GSM1127145_UCSF-UBC.Peripheral_Blood_Mononuclear_Primary_Cells.H3K27ac.TC015.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A21631-1.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Peripheral Blood Mononuclear Primary Cells H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K27ac ChIP-Seq read mappings from Peripheral Blood Mononuclear Primary Cells, Donor TC015, Library A21631 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.17119
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: PBM H3K27ac 15 31
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Peripheral Blood Mononuclear Primary Cells Histone H3K27ac Donor TC015 Library A21631 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 22,059,262
FINDPEAKS_SCORE: 0.0616
FINDPEAKS_PERCENTILE: 5
HOTSPOT_SCORE: 0.1149
HOTSPOT_PERCENTILE: 9
IROC_SCORE: 0.9725
IROC_PERCENTILE: 14
POISSON_SCORE: 0.1741
POISSON_PERCENTILE: 2
MAXIMUM_REPLICATE_CORRELATION: 0.96

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

value: Blood

value: Peripheral blood mononuclear cell

value: No

value: primary cell


description:
design description: H3K27me3 ChIP-Seq analysis of placenta (smooth chorionic membrane) tissue from CTL02 (A21713) using Illumina HiSeq 2000
library name: A21713
EXPERIMENT_TYPE: Histone H3K27me3
EXTRACTION_PROTOCOL: Refer to document 'Chromatin Immunoprecipitation (ChIP)' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
EXTRACTION_PROTOCOL_TYPE_OF_SONICATOR: Fisher 550 Sonic Dismembrator
EXTRACTION_PROTOCOL_SONICATION_CYCLES: 10 min
CHIP_PROTOCOL: Refer to document 'Chromatin Immunoprecipitation (ChIP)' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
CHIP_PROTOCOL_CHROMATIN_AMOUNT: 4.5 ug
SIZE_FRACTION: 159-451 bp
CHIP_PROTOCOL_BEAD_TYPE: Sepharose A/G Bead Mix
CHIP_PROTOCOL_BEAD_AMOUNT: 20 ul
CHIP_PROTOCOL_ANTIBODY_AMOUNT: 5 ug
CHIP_ANTIBODY: H3K27me3
CHIP_ANTIBODY_PROVIDER: Diagenode
CHIP_ANTIBODY_CATALOG: pAb-069-050
CHIP_ANTIBODY_LOT: A1456-004P
****************
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: GSM1127146_UCSF-UBC.Placenta_Chorion_Smooth.H3K27me3.CTL02.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A21713-1.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Placenta Chorion Smooth H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K27me3 ChIP-Seq on Placenta Chorion Smooth, Donor CTL02 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.17042
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 27,053,313
FINDPEAKS_SCORE: 0.0057
FINDPEAKS_PERCENTILE: 2
HOTSPOT_SCORE: 0.0525
HOTSPOT_PERCENTILE: 4
IROC_SCORE: 0.4094
IROC_PERCENTILE: 2
POISSON_SCORE: 0.2242
POISSON_PERCENTILE: 18
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM1127146_UCSF-UBC.Placenta_Chorion_Smooth.H3K27me3.CTL02.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A21713-1.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Placenta Chorion Smooth H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K27me3 ChIP-Seq read mappings from Placenta Chorion Smooth, Donor CTL02 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.17101
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: PCS H3K27me3 02 13
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Placenta Chorion Smooth Histone H3K27me3 Donor CTL02 Library A21713 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 27,053,313
FINDPEAKS_SCORE: 0.0057
FINDPEAKS_PERCENTILE: 2
HOTSPOT_SCORE: 0.0525
HOTSPOT_PERCENTILE: 4
IROC_SCORE: 0.4094
IROC_PERCENTILE: 2
POISSON_SCORE: 0.2242
POISSON_PERCENTILE: 18
MAXIMUM_REPLICATE_CORRELATION: NA

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

value: Placenta

value: Chorion smooth tissue

value: primary tissue


description:
design description: H3K27ac ChIP-Seq analysis of placenta (smooth chorionic membrane) tissue from CTL02 (A21715) using Illumina HiSeq 2000
library name: A21715
EXPERIMENT_TYPE: Histone H3K27ac
EXTRACTION_PROTOCOL: Refer to document 'Chromatin Immunoprecipitation (ChIP)' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
EXTRACTION_PROTOCOL_TYPE_OF_SONICATOR: Fisher 550 Sonic Dismembrator
EXTRACTION_PROTOCOL_SONICATION_CYCLES: 10 min
CHIP_PROTOCOL: Refer to document 'Chromatin Immunoprecipitation (ChIP)' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
CHIP_PROTOCOL_CHROMATIN_AMOUNT: 4.5 ug
SIZE_FRACTION: 159-482 bp
CHIP_PROTOCOL_BEAD_TYPE: Sepharose A/G Bead Mix
CHIP_PROTOCOL_BEAD_AMOUNT: 20 ul
CHIP_PROTOCOL_ANTIBODY_AMOUNT: 2.5 ug
CHIP_ANTIBODY: H3K27ac
CHIP_ANTIBODY_PROVIDER: Abcam
CHIP_ANTIBODY_CATALOG: ab4729
CHIP_ANTIBODY_LOT: GR55451-1
****************
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: GSM1127147_UCSF-UBC.Placenta_Chorion_Smooth.H3K27ac.CTL02.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A21715-1.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Placenta Chorion Smooth H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K27ac ChIP-Seq on Placenta Chorion Smooth, Donor CTL02 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.17037
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 23,618,884
FINDPEAKS_SCORE: 0.1475
FINDPEAKS_PERCENTILE: 12
HOTSPOT_SCORE: 0.2122
HOTSPOT_PERCENTILE: 15
IROC_SCORE: 0.9541
IROC_PERCENTILE: 7
POISSON_SCORE: 0.3428
POISSON_PERCENTILE: 20
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM1127147_UCSF-UBC.Placenta_Chorion_Smooth.H3K27ac.CTL02.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A21715-1.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Placenta Chorion Smooth H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K27ac ChIP-Seq read mappings from Placenta Chorion Smooth, Donor CTL02 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.17096
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: PCS H3K27ac 02 15
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Placenta Chorion Smooth Histone H3K27ac Donor CTL02 Library A21715 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 23,618,884
FINDPEAKS_SCORE: 0.1475
FINDPEAKS_PERCENTILE: 12
HOTSPOT_SCORE: 0.2122
HOTSPOT_PERCENTILE: 15
IROC_SCORE: 0.9541
IROC_PERCENTILE: 7
POISSON_SCORE: 0.3428
POISSON_PERCENTILE: 20
MAXIMUM_REPLICATE_CORRELATION: NA

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


description:
design description: H3K36me3 ChIP-Seq analysis of placenta (amniotic membrane) tissue from CTL02 (A21721) using Illumina HiSeq 2000
library name: A21721
EXPERIMENT_TYPE: Histone H3K36me3
EXTRACTION_PROTOCOL: Refer to document 'Chromatin Immunoprecipitation (ChIP)' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
EXTRACTION_PROTOCOL_TYPE_OF_SONICATOR: Fisher 550 Sonic Dismembrator
EXTRACTION_PROTOCOL_SONICATION_CYCLES: 15 min
CHIP_PROTOCOL: Refer to document 'Chromatin Immunoprecipitation (ChIP)' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
CHIP_PROTOCOL_CHROMATIN_AMOUNT: 4.5 ug
SIZE_FRACTION: 161-492 bp
CHIP_PROTOCOL_BEAD_TYPE: Sepharose A/G Bead Mix
CHIP_PROTOCOL_BEAD_AMOUNT: 20 ul
CHIP_PROTOCOL_ANTIBODY_AMOUNT: 2.5 ug
CHIP_ANTIBODY: H3K36me3
CHIP_ANTIBODY_PROVIDER: Abcam
CHIP_ANTIBODY_CATALOG: ab9050
CHIP_ANTIBODY_LOT: 947467
****************
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: GSM1127144_UCSF-UBC.Placenta_Amnion.H3K36me3.CTL02.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A21721-1.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Placenta Amnion H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K36me3 ChIP-Seq on Placenta Amnion, Donor CTL02 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.17035
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 22,898,925
FINDPEAKS_SCORE: 0.0838
FINDPEAKS_PERCENTILE: 14
HOTSPOT_SCORE: 0.154
HOTSPOT_PERCENTILE: 5
IROC_SCORE: 0.9056
IROC_PERCENTILE: 16
POISSON_SCORE: 0.3336
POISSON_PERCENTILE: 12
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM1127144_UCSF-UBC.Placenta_Amnion.H3K36me3.CTL02.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A21721-1.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Placenta Amnion H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K36me3 ChIP-Seq read mappings from Placenta Amnion, Donor CTL02 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.17094
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: PA H3K36me3 02 21
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Placenta Amnion Histone H3K36me3 Donor CTL02 Library A21721 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 22,898,925
FINDPEAKS_SCORE: 0.0838
FINDPEAKS_PERCENTILE: 14
HOTSPOT_SCORE: 0.154
HOTSPOT_PERCENTILE: 5
IROC_SCORE: 0.9056
IROC_PERCENTILE: 16
POISSON_SCORE: 0.3336
POISSON_PERCENTILE: 12
MAXIMUM_REPLICATE_CORRELATION: NA

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


description:
design description: H3K4me1 ChIP-Seq analysis of peripheral mononuclear cell from TC015 (A21626) using Illumina HiSeq 2000
library name: A21626
EXPERIMENT_TYPE: Histone H3K4me1
EXTRACTION_PROTOCOL: Refer to document 'Chromatin Immunoprecipitation (ChIP)' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
EXTRACTION_PROTOCOL_TYPE_OF_SONICATOR: Fisher 550 Sonic Dismembrator
EXTRACTION_PROTOCOL_SONICATION_CYCLES: 10 min
CHIP_PROTOCOL: Refer to document 'Chromatin Immunoprecipitation (ChIP)' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
CHIP_PROTOCOL_CHROMATIN_AMOUNT: 5 ug
SIZE_FRACTION: 94-294 bp
CHIP_PROTOCOL_BEAD_TYPE: Sepharose A/G Bead Mix
CHIP_PROTOCOL_BEAD_AMOUNT: 20 ul
CHIP_PROTOCOL_ANTIBODY_AMOUNT: 5 ug
CHIP_ANTIBODY: H3K4me1
CHIP_ANTIBODY_PROVIDER: Diagenode
CHIP_ANTIBODY_CATALOG: pAb-037-050
CHIP_ANTIBODY_LOT: A399-002341P
****************
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: GSM1127143_UCSF-UBC.Peripheral_Blood_Mononuclear_Primary_Cells.H3K4me1.TC015.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A21626-1.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Peripheral Blood Mononuclear Primary Cells H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K4me1 ChIP-Seq on Peripheral Blood Mononuclear Primary Cells, Donor TC015, Library A21626 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.17048
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 20,998,561
FINDPEAKS_SCORE: 0.0934
FINDPEAKS_PERCENTILE: 18
HOTSPOT_SCORE: 0.1953
HOTSPOT_PERCENTILE: 14
IROC_SCORE: 0.9215
IROC_PERCENTILE: 27
POISSON_SCORE: 0.3382
POISSON_PERCENTILE: 14
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

ANALYSIS FILE NAME: GSM1127143_UCSF-UBC.Peripheral_Blood_Mononuclear_Primary_Cells.H3K4me1.TC015.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A21626-1.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Peripheral Blood Mononuclear Primary Cells H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K4me1 ChIP-Seq read mappings from Peripheral Blood Mononuclear Primary Cells, Donor TC015, Library A21626 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.17107
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: PBM H3K4me1 15 26
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Peripheral Blood Mononuclear Primary Cells Histone H3K4me1 Donor TC015 Library A21626 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 20,998,561
FINDPEAKS_SCORE: 0.0934
FINDPEAKS_PERCENTILE: 18
HOTSPOT_SCORE: 0.1953
HOTSPOT_PERCENTILE: 14
IROC_SCORE: 0.9215
IROC_PERCENTILE: 27
POISSON_SCORE: 0.3382
POISSON_PERCENTILE: 14
MAXIMUM_REPLICATE_CORRELATION: 0.98

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


title: Histone H3K36me3 ChIP-Seq of Fetal Adrenal Gland; Histone.DS23068

description:
sample_term_id: UBERON_0002369
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Histone H3K36me3 ChIP-Seq
Library name: Histone.DS23068
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.16274
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.15682
****************
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: GSM1160196_UW.Fetal_Adrenal_Gland.H3K36me3.H-24800.Histone.DS23068.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Histone.DS23068-Histone.DS23068.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Fetal Adrenal Gland H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K36me3 ChIP-Seq on Fetal Adrenal Gland, Donor H-24800, 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.16853
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: 24,484,028
FINDPEAKS_SCORE: 0.5028
FINDPEAKS_PERCENTILE: 95
HOTSPOT_SCORE: 0.4591
HOTSPOT_PERCENTILE: 95
IROC_SCORE: 0.9973
IROC_PERCENTILE: 93
POISSON_SCORE: 0.6477
POISSON_PERCENTILE: 95
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM1160196_UW.Fetal_Adrenal_Gland.H3K36me3.H-24800.Histone.DS23068.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Histone.DS23068-Histone.DS23068.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Adrenal Gland H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K36me3 ChIP-Seq read mappings from Fetal Adrenal Gland, Donor H-24800, 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.16949
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: FAG H3K36me3 00 68
BROWSER_TRACK_DESCRIPTION: UW Fetal Adrenal Gland Histone H3K36me3 Donor H-24800 Library Histone.DS23068 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 24,484,028
FINDPEAKS_SCORE: 0.5028
FINDPEAKS_PERCENTILE: 95
HOTSPOT_SCORE: 0.4591
HOTSPOT_PERCENTILE: 95
IROC_SCORE: 0.9973
IROC_PERCENTILE: 93
POISSON_SCORE: 0.6477
POISSON_PERCENTILE: 95
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: Fetal Adrenal Gland primary tissue, day 97; Histone.DS23068

value: University of Washington, Congenital Defects Lab. Ian Glass

value: Primary Tissue

value: Fetal Adrenal Gland

value: UW

value: fetal

value: day 97

value: Male

value: Histone H3K36me3

value: Millipore A/G agarose beads

value: 30ul A/G bead slurry

value: Active Motif


description:
design description: H3K27me3 ChIP-Seq analysis of peripheral mononuclear cell from TC016 (A21636) using Illumina HiSeq 2000
library name: A21636
EXPERIMENT_TYPE: Histone H3K27me3
EXTRACTION_PROTOCOL: Refer to document 'Chromatin Immunoprecipitation (ChIP)' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
EXTRACTION_PROTOCOL_TYPE_OF_SONICATOR: Fisher 550 Sonic Dismembrator
EXTRACTION_PROTOCOL_SONICATION_CYCLES: 10 min
CHIP_PROTOCOL: Refer to document 'Chromatin Immunoprecipitation (ChIP)' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
CHIP_PROTOCOL_CHROMATIN_AMOUNT: 5 ug
SIZE_FRACTION: 94-294 bp
CHIP_PROTOCOL_BEAD_TYPE: Sepharose A/G Bead Mix
CHIP_PROTOCOL_BEAD_AMOUNT: 20 ul
CHIP_PROTOCOL_ANTIBODY_AMOUNT: 5 ug
CHIP_ANTIBODY: H3K27me3
CHIP_ANTIBODY_PROVIDER: Diagenode
CHIP_ANTIBODY_CATALOG: pAb-069-050
CHIP_ANTIBODY_LOT: A299-00242
****************
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: GSM1127142_UCSF-UBC.Peripheral_Blood_Mononuclear_Primary_Cells.H3K27me3.TC016.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A21636-1.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Peripheral Blood Mononuclear Primary Cells H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K27me3 ChIP-Seq on Peripheral Blood Mononuclear Primary Cells, Donor TC016, Library A21636 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.17049
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: 21,436,989
FINDPEAKS_SCORE: 0.0121
FINDPEAKS_PERCENTILE: 13
HOTSPOT_SCORE: 0.0901
HOTSPOT_PERCENTILE: 13
IROC_SCORE: 0.6847
IROC_PERCENTILE: 11
POISSON_SCORE: 0.1891
POISSON_PERCENTILE: 7
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

ANALYSIS FILE NAME: GSM1127142_UCSF-UBC.Peripheral_Blood_Mononuclear_Primary_Cells.H3K27me3.TC016.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A21636-1.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Peripheral Blood Mononuclear Primary Cells H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K27me3 ChIP-Seq read mappings from Peripheral Blood Mononuclear Primary Cells, Donor TC016, Library A21636 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.17108
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: PBM H3K27me3 16 36
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Peripheral Blood Mononuclear Primary Cells Histone H3K27me3 Donor TC016 Library A21636 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 21,436,989
FINDPEAKS_SCORE: 0.0121
FINDPEAKS_PERCENTILE: 13
HOTSPOT_SCORE: 0.0901
HOTSPOT_PERCENTILE: 13
IROC_SCORE: 0.6847
IROC_PERCENTILE: 11
POISSON_SCORE: 0.1891
POISSON_PERCENTILE: 7
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

value: female

value: Blood

value: Peripheral blood mononuclear cell


title: Histone H3K4me1 ChIP-Seq of Fetal Muscle, Trunk; Histone.DS23308

description:
sample_term_id: UBERON_0001774
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Histone H3K4me1 ChIP-Seq
Library name: Histone.DS23308
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.16268
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.16267
****************
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: GSM1160197_UW.Fetal_Muscle_Trunk.H3K4me1.H-24851.Histone.DS23308.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Histone.DS23308-Histone.DS23308.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Fetal Muscle Trunk H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K4me1 ChIP-Seq on Fetal Muscle Trunk, Donor H-24851, 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.16820
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: 17,690,919
FINDPEAKS_SCORE: 0.5922
FINDPEAKS_PERCENTILE: 95
HOTSPOT_SCORE: 0.604
HOTSPOT_PERCENTILE: 96
IROC_SCORE: 0.9984
IROC_PERCENTILE: 93
POISSON_SCORE: 0.6692
POISSON_PERCENTILE: 96
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM1160197_UW.Fetal_Muscle_Trunk.H3K4me1.H-24851.Histone.DS23308.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Histone.DS23308-Histone.DS23308.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Muscle Trunk H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K4me1 ChIP-Seq read mappings from Fetal Muscle Trunk, Donor H-24851, 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.16916
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: FMT H3K4me1 51 08
BROWSER_TRACK_DESCRIPTION: UW Fetal Muscle Trunk Histone H3K4me1 Donor H-24851 Library Histone.DS23308 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 17,690,919
FINDPEAKS_SCORE: 0.5922
FINDPEAKS_PERCENTILE: 95
HOTSPOT_SCORE: 0.604
HOTSPOT_PERCENTILE: 96
IROC_SCORE: 0.9984
IROC_PERCENTILE: 93
POISSON_SCORE: 0.6692
POISSON_PERCENTILE: 96
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: Fetal Muscle, Trunk primary tissue, day 115; Histone.DS23308

value: Fetal Muscle, Trunk

value: day 115

value: Female

value: Histone H3K4me1

value: Diagenode Bioruptor

value: 20-40 cycles of 0.5 minute on and 0.5 minute off


title: Histone H3K27ac ChIP-Seq of Fetal Muscle, Trunk; Histone.DS23303

description:
sample_term_id: UBERON_0001774
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Histone H3K27ac ChIP-Seq
Library name: Histone.DS23303
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.16286
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.16267
****************
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: GSM1160189_UW.Fetal_Muscle_Trunk.H3K27ac.H-24851.Histone.DS23303.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Histone.DS23303-Histone.DS23303.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Fetal Muscle Trunk H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K27ac ChIP-Seq on Fetal Muscle Trunk, Donor H-24851, 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.16806
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: 17,494,942
FINDPEAKS_SCORE: 0.3078
FINDPEAKS_PERCENTILE: 40
HOTSPOT_SCORE: 0.3516
HOTSPOT_PERCENTILE: 39
IROC_SCORE: 0.9952
IROC_PERCENTILE: 53
POISSON_SCORE: 0.3899
POISSON_PERCENTILE: 27
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM1160189_UW.Fetal_Muscle_Trunk.H3K27ac.H-24851.Histone.DS23303.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Histone.DS23303-Histone.DS23303.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Muscle Trunk H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K27ac ChIP-Seq read mappings from Fetal Muscle Trunk, Donor H-24851, 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.16902
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: FMT H3K27ac 51 03
BROWSER_TRACK_DESCRIPTION: UW Fetal Muscle Trunk Histone H3K27ac Donor H-24851 Library Histone.DS23303 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 17,494,942
FINDPEAKS_SCORE: 0.3078
FINDPEAKS_PERCENTILE: 40
HOTSPOT_SCORE: 0.3516
HOTSPOT_PERCENTILE: 39
IROC_SCORE: 0.9952
IROC_PERCENTILE: 53
POISSON_SCORE: 0.3899
POISSON_PERCENTILE: 27
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: Fetal Muscle, Trunk primary tissue, day 115; Histone.DS23303

value: University of Washington, Congenital Defects Lab. Ian Glass

value: Primary Tissue

value: UW

value: Histone H3K27ac

value: Invitrogen Dynabeads


description:
design description: H3K9me3 ChIP-Seq analysis of placenta (amniotic membrane) tissue from CTL02 (A21719) using Illumina HiSeq 2000
library name: A21719
EXPERIMENT_TYPE: Histone H3K9me3
EXTRACTION_PROTOCOL: Refer to document 'Chromatin Immunoprecipitation (ChIP)' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
EXTRACTION_PROTOCOL_TYPE_OF_SONICATOR: Fisher 550 Sonic Dismembrator
EXTRACTION_PROTOCOL_SONICATION_CYCLES: 15 min
CHIP_PROTOCOL: Refer to document 'Chromatin Immunoprecipitation (ChIP)' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
CHIP_PROTOCOL_CHROMATIN_AMOUNT: 4.5 ug
SIZE_FRACTION: 162-449 bp
CHIP_PROTOCOL_BEAD_TYPE: Sepharose A/G Bead Mix
CHIP_PROTOCOL_BEAD_AMOUNT: 20 ul
CHIP_PROTOCOL_ANTIBODY_AMOUNT: 5 ug
CHIP_ANTIBODY: H3K9me3
CHIP_ANTIBODY_PROVIDER: Diagenode
CHIP_ANTIBODY_CATALOG: pAb-056-050
CHIP_ANTIBODY_LOT: A93-0042
****************
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: GSM1127140_UCSF-UBC.Placenta_Amnion.H3K9me3.CTL02.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A21719-1.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Placenta Amnion H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K9me3 ChIP-Seq on Placenta Amnion, Donor CTL02 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.17069
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 22,804,384
FINDPEAKS_SCORE: 0.0226
FINDPEAKS_PERCENTILE: 26
HOTSPOT_SCORE: 0.0322
HOTSPOT_PERCENTILE: 4
IROC_SCORE: 0.9282
IROC_PERCENTILE: 88
POISSON_SCORE: 0.1195
POISSON_PERCENTILE: 2
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM1127140_UCSF-UBC.Placenta_Amnion.H3K9me3.CTL02.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A21719-1.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Placenta Amnion H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K9me3 ChIP-Seq read mappings from Placenta Amnion, Donor CTL02 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.17128
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: PA H3K9me3 02 19
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Placenta Amnion Histone H3K9me3 Donor CTL02 Library A21719 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 22,804,384
FINDPEAKS_SCORE: 0.0226
FINDPEAKS_PERCENTILE: 26
HOTSPOT_SCORE: 0.0322
HOTSPOT_PERCENTILE: 4
IROC_SCORE: 0.9282
IROC_PERCENTILE: 88
POISSON_SCORE: 0.1195
POISSON_PERCENTILE: 2
MAXIMUM_REPLICATE_CORRELATION: NA

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

value: male

value: Placenta

value: Amnion tissue

value: No

value: primary tissue

value: placenta (amniotic membrane) tissue


title: Reference Epigenome: ChIP-Seq Analysis of H3K36me3 in Human Gastric Tissue; renlab.H3K36me3.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 H3K36me3 in Human Gastric Tissue. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: CY80
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.16011
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: GSM1127180_UCSD.Gastric.H3K36me3.STL001.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K36me3.STL001GA.01.01.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Gastric H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K36me3 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.16406
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: 21,189,882
FINDPEAKS_SCORE: 0.25
FINDPEAKS_PERCENTILE: 45
HOTSPOT_SCORE: 0.33
HOTSPOT_PERCENTILE: 61
IROC_SCORE: 0.98
IROC_PERCENTILE: 55
POISSON_SCORE: 0.48
POISSON_PERCENTILE: 53
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

ANALYSIS FILE NAME: GSM1127180_UCSD.Gastric.H3K36me3.STL001.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K36me3.STL001GA.01.01.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Gastric H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K36me3 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.16560
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 H3K36me3 01 80
BROWSER_TRACK_DESCRIPTION: UCSD Gastric Histone H3K36me3 Donor STL001 Library CY80 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 21,189,882
FINDPEAKS_SCORE: 0.25
FINDPEAKS_PERCENTILE: 45
HOTSPOT_SCORE: 0.33
HOTSPOT_PERCENTILE: 61
IROC_SCORE: 0.98
IROC_PERCENTILE: 55
POISSON_SCORE: 0.48
POISSON_PERCENTILE: 53
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

value: Gastric

value: Shin Lin, Stanford University

value: Autopsy

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

value: Male

value: Caucasian and African American

value: Histone H3K36me3

value: Biorupter

value: 500 micrograms

value: magnetic anti-rabbit

value: 5 micrograms

value: Abcam