title: Chromatin accessibility assay of Fetal Kidney, Right; DNase.DS20951

description:
sample_term_id: UBERON_0004539
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Chromatin accessibility determination via DNase-seq
Library name: DNase.DS20951
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.14341
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.14340
****************
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: GSM1027337_UW.Fetal_Kidney_Right.ChromatinAccessibility.H-24582.DNase.DS20951.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNase.DS20951.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Fetal Kidney Right Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fetal Kidney Right, Donor H-24582, Library DNase.DS20951 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.17606
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: Chromatin Accessibility
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 30,555,411
FINDPEAKS_SCORE: 0.4869
FINDPEAKS_PERCENTILE: 80
HOTSPOT_SCORE: 0.4777
HOTSPOT_PERCENTILE: 80
IROC_SCORE: 0.9945
IROC_PERCENTILE: 76
POISSON_SCORE: 0.5358
POISSON_PERCENTILE: 83
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

ANALYSIS FILE NAME: GSM1027337_UW.Fetal_Kidney_Right.ChromatinAccessibility.H-24582.DNase.DS20951.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNase.DS20951.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Kidney Right Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from  Fetal Kidney Right, Donor H-24582, Library DNase.DS20951 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.17560
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Chromatin Accessibility
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 150bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: FKR DNase 82 51
BROWSER_TRACK_DESCRIPTION: UW Fetal Kidney Right DNase Hypersensitivity Donor H-24582 Library DNase.DS20951 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 30,555,411
FINDPEAKS_SCORE: 0.4869
FINDPEAKS_PERCENTILE: 80
HOTSPOT_SCORE: 0.4777
HOTSPOT_PERCENTILE: 80
IROC_SCORE: 0.9945
IROC_PERCENTILE: 76
POISSON_SCORE: 0.5358
POISSON_PERCENTILE: 83
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

source_name: Fetal Kidney, Right primary tissue, day 87; DNase.DS20951

value: Fetal Kidney, Right

value: day 87


title: ChIP-Seq Input of CD56 Primary Cells; Histone.DS21629

status: Public on Nov 01 2012

type: SRA

city: Seattle

first: Northwest

last: REMC

state: WA

country: USA

institute: University of Washington

description:
sample_term_id: CL_0000623
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Input
Library name: Histone.DS21629
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.14543
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.7027
****************
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: GSM1027305_UW.CD56_Primary_Cells.Input.RO_01701.Histone.DS21629.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Histone.DS21629-Histone.DS21629.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of CD56 Primary Cells Input ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Input ChIP-Seq on CD56 Primary Cells, Donor RO 01701, 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.16847
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: 25,261,311
FINDPEAKS_SCORE: 0.0077
FINDPEAKS_PERCENTILE: 83
HOTSPOT_SCORE: 0.0305
HOTSPOT_PERCENTILE: 62
IROC_SCORE: 0.9761
IROC_PERCENTILE: 70
POISSON_SCORE: 0.0915
POISSON_PERCENTILE: 65
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM1027305_UW.CD56_Primary_Cells.Input.RO_01701.Histone.DS21629.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Histone.DS21629-Histone.DS21629.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of CD56 Primary Cells Input ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Input ChIP-Seq read mappings from CD56 Primary Cells, Donor RO 01701, 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.16943
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: CD56 Input 01 29
BROWSER_TRACK_DESCRIPTION: UW CD56 Primary Cells ChIP-Seq Input Donor RO 01701 Library Histone.DS21629 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 25,261,311
FINDPEAKS_SCORE: 0.0077
FINDPEAKS_PERCENTILE: 83
HOTSPOT_SCORE: 0.0305
HOTSPOT_PERCENTILE: 62
IROC_SCORE: 0.9761
IROC_PERCENTILE: 70
POISSON_SCORE: 0.0915
POISSON_PERCENTILE: 65
MAXIMUM_REPLICATE_CORRELATION: NA

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

molecule: genomic DNA

organism: Homo sapiens

source_name: flow sorted CD56+ Cells, year 37; Histone.DS21629

extract_protocol: Library construction protocol: Single read - Illumina

tag: sample alias

tag: sample common name

value: CD56 Primary Cells

tag: molecule

value: genomic DNA

tag: disease

value: FHCRC HEIMFELD

value: Primary Cell

tag: markers

value: year 37

value: Male

value: Hispanic

value: ChIP-Seq Input

value: Diagenode Bioruptor

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

value: Input


title: Chromatin accessibility assay of Penis Foreskin Melanocytes Primary Cells; DNase.DS18668

description:
Design description: Chromatin accessibility determination via DNase-seq
Library name: DNase.DS18668
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.14280
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSF-UBC%2FSAMPLE%2FEDACC.9575
****************
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: GSM1027307_UW.Penis_Foreskin_Melanocyte_Primary_Cells.ChromatinAccessibility.skin02.DNase.DS18668.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNase.DS18668.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Penis Foreskin Melanocyte Primary Cells Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Penis Foreskin Melanocyte Primary Cells, Donor skin02, Library DNase.DS18668 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.17597
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: Chromatin Accessibility
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 41,085,977
FINDPEAKS_SCORE: 0.292
FINDPEAKS_PERCENTILE: 17
HOTSPOT_SCORE: 0.3407
HOTSPOT_PERCENTILE: 43
IROC_SCORE: 0.9978
IROC_PERCENTILE: 98
POISSON_SCORE: 0.3641
POISSON_PERCENTILE: 24
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

ANALYSIS FILE NAME: GSM1027307_UW.Penis_Foreskin_Melanocyte_Primary_Cells.ChromatinAccessibility.skin02.DNase.DS18668.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNase.DS18668.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Penis Foreskin Melanocyte Primary Cells Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from  Penis Foreskin Melanocyte Primary Cells, Donor skin02, Library DNase.DS18668 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.17551
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Chromatin Accessibility
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 150bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: PFM DNase 02 68
BROWSER_TRACK_DESCRIPTION: UW Penis Foreskin Melanocyte Primary Cells DNase Hypersensitivity Donor skin02 Library DNase.DS18668 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 41,085,977
FINDPEAKS_SCORE: 0.292
FINDPEAKS_PERCENTILE: 17
HOTSPOT_SCORE: 0.3407
HOTSPOT_PERCENTILE: 43
IROC_SCORE: 0.9978
IROC_PERCENTILE: 98
POISSON_SCORE: 0.3641
POISSON_PERCENTILE: 24
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

source_name: Penis, Foreskin, Melanocyte Primary Cells skin02; DNase.DS18668

value: Penis, Foreskin, Melanocyte skin02

value: SFVAMC Dermatology

value: Primary Cell Culture

value: Melanocyte

value: Invitrogen 254 + HMGS

value: Neonate

value: Disease Free

tag: karyotype

tag: parity

value: Chromatin Accessibility

value: Qiagen minElut


title: ChIP-Seq Input of CD19 Primary Cells; Histone.DS21628

description:
sample_term_id: CL_0000236
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Input
Library name: Histone.DS21628
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.14540
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.6973
****************
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: GSM1027304_UW.CD19_Primary_Cells.Input.RO_01701.Histone.DS21628.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Histone.DS21628-Histone.DS21628.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of CD19 Primary Cells Input ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Input ChIP-Seq on CD19 Primary Cells, Donor RO 01701, 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.16800
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 29,816,951
FINDPEAKS_SCORE: 0.0054
FINDPEAKS_PERCENTILE: 37
HOTSPOT_SCORE: 0.0054
HOTSPOT_PERCENTILE: 32
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.0408
POISSON_PERCENTILE: 37
MAXIMUM_REPLICATE_CORRELATION: 0.97

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

ANALYSIS FILE NAME: GSM1027304_UW.CD19_Primary_Cells.Input.RO_01701.Histone.DS21628.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Histone.DS21628-Histone.DS21628.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of CD19 Primary Cells Input ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Input ChIP-Seq read mappings from CD19 Primary Cells, Donor RO 01701, 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.16896
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: CD19 Input 01 28
BROWSER_TRACK_DESCRIPTION: UW CD19 Primary Cells ChIP-Seq Input Donor RO 01701 Library Histone.DS21628 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 29,816,951
FINDPEAKS_SCORE: 0.0054
FINDPEAKS_PERCENTILE: 37
HOTSPOT_SCORE: 0.0054
HOTSPOT_PERCENTILE: 32
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.0408
POISSON_PERCENTILE: 37
MAXIMUM_REPLICATE_CORRELATION: 0.97

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

source_name: flow sorted CD19+ Cells, year 37; Histone.DS21628

value: CD19 Primary Cells

value: genomic DNA

value: FHCRC HEIMFELD

value: Primary Cell


title: Histone H3K9me3 ChIP-Seq of Fetal Thymus; Histone.DS22904

description:
sample_term_id: UBERON_0002370
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Histone H3K9me3 ChIP-Seq
Library name: Histone.DS22904
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.14483
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.14482
****************
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: GSM1027303_UW.Fetal_Thymus.H3K9me3.H-24644.Histone.DS22904.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Histone.DS22904.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Fetal Thymus H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K9me3 ChIP-Seq on Fetal Thymus, 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.16808
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: 14,850,964
FINDPEAKS_SCORE: 0.1249
FINDPEAKS_PERCENTILE: 76
HOTSPOT_SCORE: 0.2483
HOTSPOT_PERCENTILE: 86
IROC_SCORE: 0.8514
IROC_PERCENTILE: 64
POISSON_SCORE: 0.3481
POISSON_PERCENTILE: 70
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM1027303_UW.Fetal_Thymus.H3K9me3.H-24644.Histone.DS22904.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Histone.DS22904.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Thymus H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K9me3 ChIP-Seq read mappings from Fetal Thymus, 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.16904
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: FT H3K9me3 44 04
BROWSER_TRACK_DESCRIPTION: UW Fetal Thymus Histone H3K9me3 Donor H-24644 Library Histone.DS22904 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 14,850,964
FINDPEAKS_SCORE: 0.1249
FINDPEAKS_PERCENTILE: 76
HOTSPOT_SCORE: 0.2483
HOTSPOT_PERCENTILE: 86
IROC_SCORE: 0.8514
IROC_PERCENTILE: 64
POISSON_SCORE: 0.3481
POISSON_PERCENTILE: 70
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: Fetal Thymus primary tissue, day 110; Histone.DS22904

value: Fetal Thymus

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

value: Primary Tissue

value: UW

value: fetal

value: day 110

value: Female

value: Histone H3K9me3

value: Millipore A/G agarose beads

value: 30ul A/G bead slurry

value: Active Motif


title: Histone H3K4me3 ChIP-Seq of CD56 Primary Cells; Histone.DS21715

description:
sample_term_id: CL_0000623
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Histone H3K4me3 ChIP-Seq
Library name: Histone.DS21715
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.14506
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.7027
****************
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: GSM1027301_UW.CD56_Primary_Cells.H3K4me3.RO_01701.Histone.DS21715.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Histone.DS21715-Histone.DS21715.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of CD56 Primary Cells H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K4me3 ChIP-Seq on CD56 Primary Cells, Donor RO 01701, 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.16834
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: 21,978,805
FINDPEAKS_SCORE: 0.3704
FINDPEAKS_PERCENTILE: 43
HOTSPOT_SCORE: 0.3747
HOTSPOT_PERCENTILE: 36
IROC_SCORE: 0.9999
IROC_PERCENTILE: 47
POISSON_SCORE: 0.3729
POISSON_PERCENTILE: 36
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM1027301_UW.CD56_Primary_Cells.H3K4me3.RO_01701.Histone.DS21715.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Histone.DS21715-Histone.DS21715.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of CD56 Primary Cells H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K4me3 ChIP-Seq read mappings from CD56 Primary Cells, Donor RO 01701, 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.16930
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: CD56 H3K4me3 01 15
BROWSER_TRACK_DESCRIPTION: UW CD56 Primary Cells Histone H3K4me3 Donor RO 01701 Library Histone.DS21715 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 21,978,805
FINDPEAKS_SCORE: 0.3704
FINDPEAKS_PERCENTILE: 43
HOTSPOT_SCORE: 0.3747
HOTSPOT_PERCENTILE: 36
IROC_SCORE: 0.9999
IROC_PERCENTILE: 47
POISSON_SCORE: 0.3729
POISSON_PERCENTILE: 36
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: flow sorted CD56+ Cells, year 37; Histone.DS21715

value: CD56 Primary Cells

value: year 37

value: Male

value: Hispanic

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


title: Histone H3K4me1 ChIP-Seq of Fetal Thymus; Histone.DS22601

description:
sample_term_id: UBERON_0002370
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Histone H3K4me1 ChIP-Seq
Library name: Histone.DS22601
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.14488
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.14482
****************
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: GSM1027298_UW.Fetal_Thymus.H3K4me1.H-24644.Histone.DS22601.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Histone.DS22601-Histone.DS22601.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Fetal Thymus H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K4me1 ChIP-Seq on Fetal Thymus, 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.16826
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: 21,330,132
FINDPEAKS_SCORE: 0.5053
FINDPEAKS_PERCENTILE: 91
HOTSPOT_SCORE: 0.5298
HOTSPOT_PERCENTILE: 91
IROC_SCORE: 0.9975
IROC_PERCENTILE: 91
POISSON_SCORE: 0.6066
POISSON_PERCENTILE: 89
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM1027298_UW.Fetal_Thymus.H3K4me1.H-24644.Histone.DS22601.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Histone.DS22601-Histone.DS22601.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Thymus H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K4me1 ChIP-Seq read mappings from Fetal Thymus, 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.16922
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: FT H3K4me1 44 01
BROWSER_TRACK_DESCRIPTION: UW Fetal Thymus Histone H3K4me1 Donor H-24644 Library Histone.DS22601 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 21,330,132
FINDPEAKS_SCORE: 0.5053
FINDPEAKS_PERCENTILE: 91
HOTSPOT_SCORE: 0.5298
HOTSPOT_PERCENTILE: 91
IROC_SCORE: 0.9975
IROC_PERCENTILE: 91
POISSON_SCORE: 0.6066
POISSON_PERCENTILE: 89
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: Fetal Thymus primary tissue, day 110; Histone.DS22601

value: Fetal Thymus

value: genomic DNA

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

value: Primary Tissue

value: UW

value: fetal

value: Histone H3K4me1


title: Chromatin accessibility assay of Fetal Renal Cortex; DNase.DS20024

description:
sample_term_id: UBERON_0001225
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Chromatin accessibility determination via DNase-seq
Library name: DNase.DS20024
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.14360
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.14359
****************
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: GSM1027316_UW.Fetal_Renal_Cortex.ChromatinAccessibility.H-24365.DNase.DS20024.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNase.DS20024.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Fetal Renal Cortex Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fetal Renal Cortex, Donor H-24365, Library DNase.DS20024 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.17627
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: Chromatin Accessibility
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 35,507,688
FINDPEAKS_SCORE: 0.5111
FINDPEAKS_PERCENTILE: 89
HOTSPOT_SCORE: 0.5089
HOTSPOT_PERCENTILE: 89
IROC_SCORE: 0.9943
IROC_PERCENTILE: 70
POISSON_SCORE: 0.5597
POISSON_PERCENTILE: 89
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

ANALYSIS FILE NAME: GSM1027316_UW.Fetal_Renal_Cortex.ChromatinAccessibility.H-24365.DNase.DS20024.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNase.DS20024.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Renal Cortex Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from  Fetal Renal Cortex, Donor H-24365, Library DNase.DS20024 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.17581
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Chromatin Accessibility
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 150bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: FRC DNase 65 24
BROWSER_TRACK_DESCRIPTION: UW Fetal Renal Cortex DNase Hypersensitivity Donor H-24365 Library DNase.DS20024 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 35,507,688
FINDPEAKS_SCORE: 0.5111
FINDPEAKS_PERCENTILE: 89
HOTSPOT_SCORE: 0.5089
HOTSPOT_PERCENTILE: 89
IROC_SCORE: 0.9943
IROC_PERCENTILE: 70
POISSON_SCORE: 0.5597
POISSON_PERCENTILE: 89
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

source_name: Fetal Kidney, renal, cortex primary tissue, day 96; DNase.DS20024

value: Fetal Renal Cortex

value: day 96

value: Female

value: Chromatin Accessibility

value: Qiagen minElut


title: Histone H3K4me3 ChIP-Seq of Fetal Thymus; Histone.DS21539

description:
sample_term_id: UBERON_0002370
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Histone H3K4me3 ChIP-Seq
Library name: Histone.DS21539
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.14524
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.14482
****************
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: GSM1027299_UW.Fetal_Thymus.H3K4me3.H-24644.Histone.DS21539.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Histone.DS21539-Histone.DS21539.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Fetal Thymus H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K4me3 ChIP-Seq on Fetal Thymus, 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.16873
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: 25,565,772
FINDPEAKS_SCORE: 0.3697
FINDPEAKS_PERCENTILE: 39
HOTSPOT_SCORE: 0.3733
HOTSPOT_PERCENTILE: 34
IROC_SCORE: 0.9999
IROC_PERCENTILE: 47
POISSON_SCORE: 0.3727
POISSON_PERCENTILE: 34
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM1027299_UW.Fetal_Thymus.H3K4me3.H-24644.Histone.DS21539.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Histone.DS21539-Histone.DS21539.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Thymus H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K4me3 ChIP-Seq read mappings from Fetal Thymus, 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.16969
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: FT H3K4me3 44 39
BROWSER_TRACK_DESCRIPTION: UW Fetal Thymus Histone H3K4me3 Donor H-24644 Library Histone.DS21539 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 25,565,772
FINDPEAKS_SCORE: 0.3697
FINDPEAKS_PERCENTILE: 39
HOTSPOT_SCORE: 0.3733
HOTSPOT_PERCENTILE: 34
IROC_SCORE: 0.9999
IROC_PERCENTILE: 47
POISSON_SCORE: 0.3727
POISSON_PERCENTILE: 34
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: Fetal Thymus primary tissue, day 110; Histone.DS21539

value: day 110

value: Histone H3K4me3

value: Diagenode Bioruptor


title: Histone H3K4me1 ChIP-Seq of CD19 Primary Cells; Histone.DS22584

description:
sample_term_id: CL_0000236
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Histone H3K4me1 ChIP-Seq
Library name: Histone.DS22584
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.14515
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.6965
****************
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: GSM1027296_UW.CD19_Primary_Cells.H3K4me1.RO_01679.Histone.DS22584.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Histone.DS22584-Histone.DS22584.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of CD19 Primary Cells H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K4me1 ChIP-Seq on CD19 Primary Cells, Donor RO 01679, 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.16795
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 29,452,256
FINDPEAKS_SCORE: 0.5902
FINDPEAKS_PERCENTILE: 93
HOTSPOT_SCORE: 0.567
HOTSPOT_PERCENTILE: 93
IROC_SCORE: 0.9998
IROC_PERCENTILE: 98
POISSON_SCORE: 0.6428
POISSON_PERCENTILE: 93
MAXIMUM_REPLICATE_CORRELATION: 0.75

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

ANALYSIS FILE NAME: GSM1027296_UW.CD19_Primary_Cells.H3K4me1.RO_01679.Histone.DS22584.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Histone.DS22584-Histone.DS22584.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of CD19 Primary Cells H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K4me1 ChIP-Seq read mappings from CD19 Primary Cells, Donor RO 01679, 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.16891
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: CD19 H3K4me1 79 84
BROWSER_TRACK_DESCRIPTION: UW CD19 Primary Cells Histone H3K4me1 Donor RO 01679 Library Histone.DS22584 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 29,452,256
FINDPEAKS_SCORE: 0.5902
FINDPEAKS_PERCENTILE: 93
HOTSPOT_SCORE: 0.567
HOTSPOT_PERCENTILE: 93
IROC_SCORE: 0.9998
IROC_PERCENTILE: 98
POISSON_SCORE: 0.6428
POISSON_PERCENTILE: 93
MAXIMUM_REPLICATE_CORRELATION: 0.75

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

source_name: flow sorted CD19+ Cells, year 21; Histone.DS22584

value: CD19 Primary Cells

value: FHCRC HEIMFELD

value: Primary Cell

value: year 21

value: Male

value: Caucasian

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

value: Active Motif


title: Histone H3K4me1 ChIP-Seq of CD56 Primary Cells; Histone.DS22593

description:
sample_term_id: CL_0000623
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Histone H3K4me1 ChIP-Seq
Library name: Histone.DS22593
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.14500
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.5358
****************
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: GSM1027297_UW.CD56_Primary_Cells.H3K4me1.RO_01679.Histone.DS22593.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Histone.DS22593-Histone.DS22593.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of CD56 Primary Cells H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K4me1 ChIP-Seq on CD56 Primary Cells, Donor RO 01679, 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.16793
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: 22,489,892
FINDPEAKS_SCORE: 0.6751
FINDPEAKS_PERCENTILE: 98
HOTSPOT_SCORE: 0.6558
HOTSPOT_PERCENTILE: 98
IROC_SCORE: 0.9995
IROC_PERCENTILE: 96
POISSON_SCORE: 0.7208
POISSON_PERCENTILE: 98
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM1027297_UW.CD56_Primary_Cells.H3K4me1.RO_01679.Histone.DS22593.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Histone.DS22593-Histone.DS22593.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of CD56 Primary Cells H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K4me1 ChIP-Seq read mappings from CD56 Primary Cells, Donor RO 01679, 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.16889
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: CD56 H3K4me1 79 93
BROWSER_TRACK_DESCRIPTION: UW CD56 Primary Cells Histone H3K4me1 Donor RO 01679 Library Histone.DS22593 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 22,489,892
FINDPEAKS_SCORE: 0.6751
FINDPEAKS_PERCENTILE: 98
HOTSPOT_SCORE: 0.6558
HOTSPOT_PERCENTILE: 98
IROC_SCORE: 0.9995
IROC_PERCENTILE: 96
POISSON_SCORE: 0.7208
POISSON_PERCENTILE: 98
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: flow sorted CD56+ Cells,year 21; Histone.DS22593

value: CD56 Primary Cells

value: genomic DNA

value: Histone H3K4me1


title: Histone H3K4me3 ChIP-Seq of CD19 Primary Cells; Histone.DS21711

description:
sample_term_id: CL_0000236
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Histone H3K4me3 ChIP-Seq
Library name: Histone.DS21711
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.14521
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.6973
****************
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: GSM1027300_UW.CD19_Primary_Cells.H3K4me3.RO_01701.Histone.DS21711.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Histone.DS21711-Histone.DS21711.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of CD19 Primary Cells H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K4me3 ChIP-Seq on CD19 Primary Cells, Donor RO 01701, 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.16851
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: 25,229,334
FINDPEAKS_SCORE: 0.3314
FINDPEAKS_PERCENTILE: 32
HOTSPOT_SCORE: 0.3364
HOTSPOT_PERCENTILE: 29
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.336
POISSON_PERCENTILE: 25
MAXIMUM_REPLICATE_CORRELATION: 0.97

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

ANALYSIS FILE NAME: GSM1027300_UW.CD19_Primary_Cells.H3K4me3.RO_01701.Histone.DS21711.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Histone.DS21711-Histone.DS21711.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of CD19 Primary Cells H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K4me3 ChIP-Seq read mappings from CD19 Primary Cells, Donor RO 01701, 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.16947
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: CD19 H3K4me3 01 11
BROWSER_TRACK_DESCRIPTION: UW CD19 Primary Cells Histone H3K4me3 Donor RO 01701 Library Histone.DS21711 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 25,229,334
FINDPEAKS_SCORE: 0.3314
FINDPEAKS_PERCENTILE: 32
HOTSPOT_SCORE: 0.3364
HOTSPOT_PERCENTILE: 29
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.336
POISSON_PERCENTILE: 25
MAXIMUM_REPLICATE_CORRELATION: 0.97

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

source_name: flow sorted CD19+ Cells, year 37; Histone.DS21711

value: year 37

value: Hispanic

value: Invitrogen Dynabeads

value: Cell Signaling

value: lot 2


title: Histone H3K36me3 ChIP-Seq of Fetal Thymus; Histone.DS22603

description:
sample_term_id: UBERON_0002370
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Histone H3K36me3 ChIP-Seq
Library name: Histone.DS22603
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.14485
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.14482
****************
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: GSM1027295_UW.Fetal_Thymus.H3K36me3.H-24644.Histone.DS22603.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Histone.DS22603-Histone.DS22603.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Fetal Thymus H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K36me3 ChIP-Seq on Fetal Thymus, 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.16796
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: 27,748,390
FINDPEAKS_SCORE: 0.363
FINDPEAKS_PERCENTILE: 72
HOTSPOT_SCORE: 0.3099
HOTSPOT_PERCENTILE: 55
IROC_SCORE: 0.9897
IROC_PERCENTILE: 72
POISSON_SCORE: 0.5456
POISSON_PERCENTILE: 67
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM1027295_UW.Fetal_Thymus.H3K36me3.H-24644.Histone.DS22603.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Histone.DS22603-Histone.DS22603.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Thymus H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K36me3 ChIP-Seq read mappings from Fetal Thymus, 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.16892
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: FT H3K36me3 44 03
BROWSER_TRACK_DESCRIPTION: UW Fetal Thymus Histone H3K36me3 Donor H-24644 Library Histone.DS22603 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 27,748,390
FINDPEAKS_SCORE: 0.363
FINDPEAKS_PERCENTILE: 72
HOTSPOT_SCORE: 0.3099
HOTSPOT_PERCENTILE: 55
IROC_SCORE: 0.9897
IROC_PERCENTILE: 72
POISSON_SCORE: 0.5456
POISSON_PERCENTILE: 67
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: Fetal Thymus primary tissue, day 110; Histone.DS22603

value: Fetal Thymus

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

value: Primary Tissue

value: UW

value: fetal

value: day 110

value: Female

value: Histone H3K36me3

value: Diagenode Bioruptor


title: Chromatin accessibility assay of Fetal Muscle, Leg; DNase.DS19382

description:
sample_term_id: UBERON_0001383
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Chromatin accessibility determination via DNase-seq
Library name: DNase.DS19382
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.14312
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.14311
****************
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: GSM1027309_UW.Fetal_Muscle_Leg.ChromatinAccessibility.H-24272.DNase.DS19382.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNase.DS19382.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Fetal Muscle Leg Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fetal Muscle Leg, Donor H-24272, Library DNase.DS19382 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.17613
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: Chromatin Accessibility
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 36,516,379
FINDPEAKS_SCORE: 0.328
FINDPEAKS_PERCENTILE: 37
HOTSPOT_SCORE: 0.3141
HOTSPOT_PERCENTILE: 35
IROC_SCORE: 0.9921
IROC_PERCENTILE: 39
POISSON_SCORE: 0.3944
POISSON_PERCENTILE: 39
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

ANALYSIS FILE NAME: GSM1027309_UW.Fetal_Muscle_Leg.ChromatinAccessibility.H-24272.DNase.DS19382.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNase.DS19382.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Muscle Leg Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from  Fetal Muscle Leg, Donor H-24272, Library DNase.DS19382 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.17567
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Chromatin Accessibility
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 150bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: FML DNase 72 82
BROWSER_TRACK_DESCRIPTION: UW Fetal Muscle Leg DNase Hypersensitivity Donor H-24272 Library DNase.DS19382 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 36,516,379
FINDPEAKS_SCORE: 0.328
FINDPEAKS_PERCENTILE: 37
HOTSPOT_SCORE: 0.3141
HOTSPOT_PERCENTILE: 35
IROC_SCORE: 0.9921
IROC_PERCENTILE: 39
POISSON_SCORE: 0.3944
POISSON_PERCENTILE: 39
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

source_name: Fetal Muscle, Leg primary tissue, day 85; DNase.DS19382

value: Fetal Muscle, Leg

value: day 85

value: Chromatin Accessibility

value: Qiagen minElut


title: Histone H3K36me3 ChIP-Seq of CD56 Primary Cells; Histone.DS22595

description:
sample_term_id: CL_0000623
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Histone H3K36me3 ChIP-Seq
Library name: Histone.DS22595
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.14493
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.5358
****************
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: GSM1027294_UW.CD56_Primary_Cells.H3K36me3.RO_01679.Histone.DS22595.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Histone.DS22595-Histone.DS22595-Histone.DS22595.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of CD56 Primary Cells H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K36me3 ChIP-Seq on CD56 Primary Cells, Donor RO 01679, 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.16887
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 33,957,611
FINDPEAKS_SCORE: 0.4073
FINDPEAKS_PERCENTILE: 81
HOTSPOT_SCORE: 0.3243
HOTSPOT_PERCENTILE: 60
IROC_SCORE: 0.9937
IROC_PERCENTILE: 81
POISSON_SCORE: 0.5867
POISSON_PERCENTILE: 79
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM1027294_UW.CD56_Primary_Cells.H3K36me3.RO_01679.Histone.DS22595.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Histone.DS22595-Histone.DS22595-Histone.DS22595.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of CD56 Primary Cells H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K36me3 ChIP-Seq read mappings from CD56 Primary Cells, Donor RO 01679, 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.16983
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: CD56 H3K36me3 79 95
BROWSER_TRACK_DESCRIPTION: UW CD56 Primary Cells Histone H3K36me3 Donor RO 01679 Library Histone.DS22595 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 33,957,611
FINDPEAKS_SCORE: 0.4073
FINDPEAKS_PERCENTILE: 81
HOTSPOT_SCORE: 0.3243
HOTSPOT_PERCENTILE: 60
IROC_SCORE: 0.9937
IROC_PERCENTILE: 81
POISSON_SCORE: 0.5867
POISSON_PERCENTILE: 79
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: flow sorted CD56+ Cells,year 21; Histone.DS22595

value: CD56 Primary Cells

value: genomic DNA

value: FHCRC HEIMFELD

value: Primary Cell

value: year 21

value: Male

value: Caucasian

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

value: Active Motif


title: Chromatin accessibility assay of Penis Foreskin Melanocytes Primary Cells; DNase.DS19662

description:
sample_term_id: CL_2000045
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Chromatin accessibility determination via DNase-seq
Library name: DNase.DS19662
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.14283
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSF-UBC%2FSAMPLE%2FEDACC.9575
****************
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: GSM1027312_UW.Penis_Foreskin_Melanocyte_Primary_Cells.ChromatinAccessibility.skin02.DNase.DS19662.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNase.DS19662.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Penis Foreskin Melanocyte Primary Cells Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Penis Foreskin Melanocyte Primary Cells, Donor skin02, Library DNase.DS19662 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.17622
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: Chromatin Accessibility
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 45,958,227
FINDPEAKS_SCORE: 0.2486
FINDPEAKS_PERCENTILE: 4
HOTSPOT_SCORE: 0.2686
HOTSPOT_PERCENTILE: 9
IROC_SCORE: 0.9972
IROC_PERCENTILE: 93
POISSON_SCORE: 0.3075
POISSON_PERCENTILE: 4
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

ANALYSIS FILE NAME: GSM1027312_UW.Penis_Foreskin_Melanocyte_Primary_Cells.ChromatinAccessibility.skin02.DNase.DS19662.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNase.DS19662.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Penis Foreskin Melanocyte Primary Cells Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from  Penis Foreskin Melanocyte Primary Cells, Donor skin02, Library DNase.DS19662 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.17576
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Chromatin Accessibility
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 150bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: PFM DNase 02 62
BROWSER_TRACK_DESCRIPTION: UW Penis Foreskin Melanocyte Primary Cells DNase Hypersensitivity Donor skin02 Library DNase.DS19662 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 45,958,227
FINDPEAKS_SCORE: 0.2486
FINDPEAKS_PERCENTILE: 4
HOTSPOT_SCORE: 0.2686
HOTSPOT_PERCENTILE: 9
IROC_SCORE: 0.9972
IROC_PERCENTILE: 93
POISSON_SCORE: 0.3075
POISSON_PERCENTILE: 4
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

source_name: Penis, Foreskin, Melanocyte Primary Cells skin02; DNase.DS19662

value: Penis, Foreskin, Melanocyte skin02

value: SFVAMC Dermatology

value: Primary Cell Culture

value: Melanocyte

value: Invitrogen 254 + HMGS

value: Neonate

value: Disease Free


title: Chromatin accessibility assay of Fetal Adrenal Gland; DNase.DS19395

description:
sample_term_id: UBERON_0002369
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Chromatin accessibility determination via DNase-seq
Library name: DNase.DS19395
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.14475
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.14474
****************
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: GSM1027310_UW.Fetal_Adrenal_Gland.ChromatinAccessibility.H-24272.DNase.DS19395.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNase.DS19395.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Fetal Adrenal Gland Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fetal Adrenal Gland, Donor H-24272, Library DNase.DS19395 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.17592
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: Chromatin Accessibility
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 30,129,755
FINDPEAKS_SCORE: 0.3025
FINDPEAKS_PERCENTILE: 26
HOTSPOT_SCORE: 0.3016
HOTSPOT_PERCENTILE: 30
IROC_SCORE: 0.99
IROC_PERCENTILE: 26
POISSON_SCORE: 0.3735
POISSON_PERCENTILE: 28
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

ANALYSIS FILE NAME: GSM1027310_UW.Fetal_Adrenal_Gland.ChromatinAccessibility.H-24272.DNase.DS19395.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNase.DS19395.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Adrenal Gland Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from  Fetal Adrenal Gland, Donor H-24272, Library DNase.DS19395 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.17546
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Chromatin Accessibility
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 150bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: FAG DNase 72 95
BROWSER_TRACK_DESCRIPTION: UW Fetal Adrenal Gland DNase Hypersensitivity Donor H-24272 Library DNase.DS19395 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 30,129,755
FINDPEAKS_SCORE: 0.3025
FINDPEAKS_PERCENTILE: 26
HOTSPOT_SCORE: 0.3016
HOTSPOT_PERCENTILE: 30
IROC_SCORE: 0.99
IROC_PERCENTILE: 26
POISSON_SCORE: 0.3735
POISSON_PERCENTILE: 28
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

source_name: Fetal Adrenal Gland primary tissue, day 85; DNase.DS19395

value: Fetal Adrenal Gland

value: genomic DNA

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

value: Primary Tissue

value: UW

value: fetal

value: day 85

value: Female

value: Chromatin Accessibility

value: Qiagen minElut


title: Histone H3K27ac ChIP-Seq of Fetal Thymus; Histone.DS21783

description:
sample_term_id: UBERON_0002370
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Histone H3K27ac ChIP-Seq
Library name: Histone.DS21783
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.14530
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.14482
****************
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: GSM1027289_UW.Fetal_Thymus.H3K27ac.H-24644.Histone.DS21783.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Histone.DS21783-Histone.DS21783.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Fetal Thymus H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K27ac ChIP-Seq on Fetal Thymus, 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.16841
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: 41,152,869
FINDPEAKS_SCORE: 0.2988
FINDPEAKS_PERCENTILE: 38
HOTSPOT_SCORE: 0.3192
HOTSPOT_PERCENTILE: 32
IROC_SCORE: 0.9966
IROC_PERCENTILE: 64
POISSON_SCORE: 0.3707
POISSON_PERCENTILE: 21
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM1027289_UW.Fetal_Thymus.H3K27ac.H-24644.Histone.DS21783.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Histone.DS21783-Histone.DS21783.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Thymus H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K27ac ChIP-Seq read mappings from Fetal Thymus, 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.16937
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: FT H3K27ac 44 83
BROWSER_TRACK_DESCRIPTION: UW Fetal Thymus Histone H3K27ac Donor H-24644 Library Histone.DS21783 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 41,152,869
FINDPEAKS_SCORE: 0.2988
FINDPEAKS_PERCENTILE: 38
HOTSPOT_SCORE: 0.3192
HOTSPOT_PERCENTILE: 32
IROC_SCORE: 0.9966
IROC_PERCENTILE: 64
POISSON_SCORE: 0.3707
POISSON_PERCENTILE: 21
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: Fetal Thymus primary tissue, day 110; Histone.DS21783

value: Fetal Thymus

value: day 110

value: Histone H3K27ac

value: Diagenode Bioruptor

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

value: Invitrogen Dynabeads

value: Active Motif


title: Histone H3K27me3 ChIP-Seq of CD19 Primary Cells; Histone.DS22585

description:
sample_term_id: CL_0000236
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Histone H3K27me3 ChIP-Seq
Library name: Histone.DS22585
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.14512
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.6965
****************
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: GSM1027290_UW.CD19_Primary_Cells.H3K27me3.RO_01679.Histone.DS22585.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Histone.DS22585-Histone.DS22585.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of CD19 Primary Cells H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K27me3 ChIP-Seq on CD19 Primary Cells, Donor RO 01679, 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.16844
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: 22,827,570
FINDPEAKS_SCORE: 0.0349
FINDPEAKS_PERCENTILE: 27
HOTSPOT_SCORE: 0.1319
HOTSPOT_PERCENTILE: 34
IROC_SCORE: 0.772
IROC_PERCENTILE: 24
POISSON_SCORE: 0.3045
POISSON_PERCENTILE: 43
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

ANALYSIS FILE NAME: GSM1027290_UW.CD19_Primary_Cells.H3K27me3.RO_01679.Histone.DS22585.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Histone.DS22585-Histone.DS22585.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of CD19 Primary Cells H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K27me3 ChIP-Seq read mappings from CD19 Primary Cells, Donor RO 01679, 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.16940
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: CD19 H3K27me3 79 85
BROWSER_TRACK_DESCRIPTION: UW CD19 Primary Cells Histone H3K27me3 Donor RO 01679 Library Histone.DS22585 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 22,827,570
FINDPEAKS_SCORE: 0.0349
FINDPEAKS_PERCENTILE: 27
HOTSPOT_SCORE: 0.1319
HOTSPOT_PERCENTILE: 34
IROC_SCORE: 0.772
IROC_PERCENTILE: 24
POISSON_SCORE: 0.3045
POISSON_PERCENTILE: 43
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

source_name: flow sorted CD19+ Cells, year 21; Histone.DS22585

value: CD19 Primary Cells

value: FHCRC HEIMFELD

value: Primary Cell

value: year 21

value: Male

value: Caucasian

value: Histone H3K27me3

value: Millipore A/G agarose beads

value: 30ul A/G bead slurry

value: Millipore


title: Histone H3K27me3 ChIP-Seq of CD56 Primary Cells; Histone.DS22594

description:
sample_term_id: CL_0000623
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Histone H3K27me3 ChIP-Seq
Library name: Histone.DS22594
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.14497
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.5358
****************
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: GSM1027291_UW.CD56_Primary_Cells.H3K27me3.RO_01679.Histone.DS22594.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Histone.DS22594-Histone.DS22594.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of CD56 Primary Cells H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K27me3 ChIP-Seq on CD56 Primary Cells, Donor RO 01679, 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.16827
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 28,153,557
FINDPEAKS_SCORE: 0.0355
FINDPEAKS_PERCENTILE: 29
HOTSPOT_SCORE: 0.1174
HOTSPOT_PERCENTILE: 29
IROC_SCORE: 0.801
IROC_PERCENTILE: 30
POISSON_SCORE: 0.6428
POISSON_PERCENTILE: 100
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM1027291_UW.CD56_Primary_Cells.H3K27me3.RO_01679.Histone.DS22594.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Histone.DS22594-Histone.DS22594.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of CD56 Primary Cells H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K27me3 ChIP-Seq read mappings from CD56 Primary Cells, Donor RO 01679, 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.16923
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: CD56 H3K27me3 79 94
BROWSER_TRACK_DESCRIPTION: UW CD56 Primary Cells Histone H3K27me3 Donor RO 01679 Library Histone.DS22594 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 28,153,557
FINDPEAKS_SCORE: 0.0355
FINDPEAKS_PERCENTILE: 29
HOTSPOT_SCORE: 0.1174
HOTSPOT_PERCENTILE: 29
IROC_SCORE: 0.801
IROC_PERCENTILE: 30
POISSON_SCORE: 0.6428
POISSON_PERCENTILE: 100
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: flow sorted CD56+ Cells,year 21; Histone.DS22594

value: CD56 Primary Cells

value: genomic DNA


title: Histone H3K27me3 ChIP-Seq of Fetal Thymus; Histone.DS22602

description:
sample_term_id: UBERON_0002370
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Histone H3K27me3 ChIP-Seq
Library name: Histone.DS22602
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.14527
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.14482
****************
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: GSM1027292_UW.Fetal_Thymus.H3K27me3.H-24644.Histone.DS22602.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Histone.DS22602-Histone.DS22602.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Fetal Thymus H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K27me3 ChIP-Seq on Fetal Thymus, 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.16872
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 28,380,906
FINDPEAKS_SCORE: 0.1196
FINDPEAKS_PERCENTILE: 71
HOTSPOT_SCORE: 0.1512
HOTSPOT_PERCENTILE: 43
IROC_SCORE: 0.9968
IROC_PERCENTILE: 100
POISSON_SCORE: 0.2208
POISSON_PERCENTILE: 14
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM1027292_UW.Fetal_Thymus.H3K27me3.H-24644.Histone.DS22602.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Histone.DS22602-Histone.DS22602.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Thymus H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K27me3 ChIP-Seq read mappings from Fetal Thymus, 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.16968
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: FT H3K27me3 44 02
BROWSER_TRACK_DESCRIPTION: UW Fetal Thymus Histone H3K27me3 Donor H-24644 Library Histone.DS22602 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 28,380,906
FINDPEAKS_SCORE: 0.1196
FINDPEAKS_PERCENTILE: 71
HOTSPOT_SCORE: 0.1512
HOTSPOT_PERCENTILE: 43
IROC_SCORE: 0.9968
IROC_PERCENTILE: 100
POISSON_SCORE: 0.2208
POISSON_PERCENTILE: 14
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: Fetal Thymus primary tissue, day 110; Histone.DS22602

value: Fetal Thymus

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

value: Primary Tissue

value: UW

value: fetal

value: day 110

value: Female


title: Histone H3K36me3 ChIP-Seq of CD19 Primary Cells; Histone.DS22586

description:
sample_term_id: CL_0000236
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Histone H3K36me3 ChIP-Seq
Library name: Histone.DS22586
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.14509
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.6965
****************
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: GSM1027293_UW.CD19_Primary_Cells.H3K36me3.RO_01679.Histone.DS22586.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Histone.DS22586-Histone.DS22586.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of CD19 Primary Cells H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K36me3 ChIP-Seq on CD19 Primary Cells, Donor RO 01679, 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.16809
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: 23,018,034
FINDPEAKS_SCORE: 0.4365
FINDPEAKS_PERCENTILE: 84
HOTSPOT_SCORE: 0.3533
HOTSPOT_PERCENTILE: 74
IROC_SCORE: 0.994
IROC_PERCENTILE: 83
POISSON_SCORE: 0.6181
POISSON_PERCENTILE: 90
MAXIMUM_REPLICATE_CORRELATION: 0.96

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

ANALYSIS FILE NAME: GSM1027293_UW.CD19_Primary_Cells.H3K36me3.RO_01679.Histone.DS22586.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Histone.DS22586-Histone.DS22586.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of CD19 Primary Cells H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K36me3 ChIP-Seq read mappings from CD19 Primary Cells, Donor RO 01679, 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.16905
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: CD19 H3K36me3 79 86
BROWSER_TRACK_DESCRIPTION: UW CD19 Primary Cells Histone H3K36me3 Donor RO 01679 Library Histone.DS22586 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 23,018,034
FINDPEAKS_SCORE: 0.4365
FINDPEAKS_PERCENTILE: 84
HOTSPOT_SCORE: 0.3533
HOTSPOT_PERCENTILE: 74
IROC_SCORE: 0.994
IROC_PERCENTILE: 83
POISSON_SCORE: 0.6181
POISSON_PERCENTILE: 90
MAXIMUM_REPLICATE_CORRELATION: 0.96

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

source_name: flow sorted CD19+ Cells, year 21; Histone.DS22586

value: CD19 Primary Cells

value: FHCRC HEIMFELD

value: Primary Cell

value: Histone H3K36me3

value: Diagenode Bioruptor

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

value: Active Motif


title: Histone H3K27ac ChIP-Seq of CD19 Primary Cells; Histone.DS21712

description:
sample_term_id: CL_0000236
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Histone H3K27ac ChIP-Seq
Library name: Histone.DS21712
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.14518
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.6973
****************
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: GSM1027287_UW.CD19_Primary_Cells.H3K27ac.RO_01701.Histone.DS21712.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Histone.DS21712-Histone.DS21712.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of CD19 Primary Cells H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K27ac ChIP-Seq on CD19 Primary Cells, Donor RO 01701, 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.16855
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: 21,640,701
FINDPEAKS_SCORE: 0.3484
FINDPEAKS_PERCENTILE: 48
HOTSPOT_SCORE: 0.3555
HOTSPOT_PERCENTILE: 41
IROC_SCORE: 0.9995
IROC_PERCENTILE: 92
POISSON_SCORE: 0.3817
POISSON_PERCENTILE: 26
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM1027287_UW.CD19_Primary_Cells.H3K27ac.RO_01701.Histone.DS21712.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Histone.DS21712-Histone.DS21712.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of CD19 Primary Cells H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K27ac ChIP-Seq read mappings from CD19 Primary Cells, Donor RO 01701, 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.16951
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: CD19 H3K27ac 01 12
BROWSER_TRACK_DESCRIPTION: UW CD19 Primary Cells Histone H3K27ac Donor RO 01701 Library Histone.DS21712 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 21,640,701
FINDPEAKS_SCORE: 0.3484
FINDPEAKS_PERCENTILE: 48
HOTSPOT_SCORE: 0.3555
HOTSPOT_PERCENTILE: 41
IROC_SCORE: 0.9995
IROC_PERCENTILE: 92
POISSON_SCORE: 0.3817
POISSON_PERCENTILE: 26
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: flow sorted CD19+ Cells, year 37; Histone.DS21712

value: year 37

value: Male

value: Hispanic

value: Histone H3K27ac

value: Invitrogen Dynabeads


title: WT-2

city: Castanet Tolosan

first: Erika

last: Sallet

address: 24 Chemin de Borde Rouge, CS 52627

department: Plant Health and the Environment

country: France

institute: INRA/CNRS

description: small RNA fraction

library_source: transcriptomic

data_processing:
Sequenced reads were trimmed for adaptor sequence (TGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC), rRNA sequences was removed using blastn program (maxmismatch number=2), only sequences of length 18-25nt was kept.
Supplementary_files_format_and_content: tab-delimited text files. First column 'SEQUENCE' = nucleotidic sequence, second column 'COUNT'= number of times sequenced

molecule: total RNA

organism: Medicago truncatula

source_name: Root

growth_protocol: roots of 10 day old plants

extract_protocol:
Small RNA enrichement with the MIRVANA kit (Ambion) - small RNA library construction using the TruSeq small RNA sample preparation kit (Illumina)
small RNA fractions were purified from total RNA using the miRVANA kit (Ambion) and small RNA libraries were constructed following the protocol of the TruSeq small RNA sample preparation kit (Illumina)using Primer Index 1 or Primer index 3.

tag: primer index (truseq small rna sample kit)

value: Primer index 3

tag: organ

value: root

tag: developmental stage

value: 10 day old plants

tag: genotype

value: WT-B


title: H3K36me3

city: Oslo

first: Håvard

last: Aanes

state: Oslo

address: Ullevålsveien 72

department: Biochemistry

country: Norway

institute: Norwegian School of Veterinary Science

data_processing:
Data was basecalled with Illumina RTA 1.6 / Bustard 1.6.1 software
Chip-seq reads were aligned to Zv9 using BWA with the following commands: 1) bwa aln -n 2 -t 8 -R 10, 2) bwa samse -n 1
Mapped reads filtered using samtools with the following command: samtools view -S -b -q
Peak calling was performed using CCAT 3.0, with the following settings: fragmentsize = 200, sliding window size = 500, MovingStep = 50, strandsensitive = yes, minCount = 4, minScore = 3
Genome_build: Zv9

organism: Danio rerio

source_name: Whole embryos

growth_protocol: Embryos for ChIP-seq were collected at 5.3 hpf and chromatin prepared as described (Lindeman et al., 2009).

extract_protocol: Immunoprecipitation was performed using H3K36me3 (Diagenode 058-050) and ChiP enriched DNA and input samples prepared for sequencing according to Illumina standard protocol (#11257047 Rev.A).

tag: strain

value: AB

tag: tissue

value: Whole embryos

value: Post-MBT (5.3 hpf)

tag: chip antibody

tag: chip antibody vendor

value: Diagenode

tag: chip antibody cat. #


title: Input


title: RDR6-2

description: small RNA fraction


title: RDR6-1

description: small RNA fraction

value: Primer index 1


title: WT-1

description: small RNA fraction

value: WT-A


title: Histone H3K9me3 ChIP-Seq of CD56 Primary Cells; Histone.DS22900

description:
sample_term_id: CL_0000623
assay_term_id: OBI_0000716
nucleic_acid_term_id:
Design description: Histone H3K9me3 ChIP-Seq
Library name: Histone.DS22900
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.14491
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.5358
****************
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: Various levels of processed data files will be made available as this project proceeds.

source_name: flow sorted CD56+ Cells,year 21; Histone.DS22900

value: CD56 Primary Cells

value: genomic DNA

value: FHCRC HEIMFELD

value: Primary Cell

value: year 21

value: Caucasian

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