title: Chromatin accessibility assay of Fetal Intestine_Small Tissue; DS16822

description:
sample_term_id: UBERON_0002108
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Chromatin accessibility determination via DNase-seq
Library name: DS16822
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.5418
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.5417
****************
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: GSM665835_UW.Fetal_Intestine_Small.ChromatinAccessibility.H-23663.DS16822.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS16822.hg19.level.1.release.3
ANALYSIS TITLE: Mapping of Fetal Intestine Small Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fetal Intestine Small, Donor H-23663, Library DS16822 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.6370
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 3

QUALITY SCORES:
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 39
FINDPEAKS_SCORE: 0.37
FINDPEAKS_PERCENTILE: 49
HOTSPOT_SCORE: 0.3638
HOTSPOT_PERCENTILE: 49
IROC_SCORE: 0.9957
IROC_PERCENTILE: 74
POISSON_SCORE: 0.4147
POISSON_PERCENTILE: 36

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

ANALYSIS FILE NAME: GSM665835_UW.Fetal_Intestine_Small.ChromatinAccessibility.H-23663.DS16822.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS16822.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Intestine Small Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from  Fetal Intestine Small, Donor H-23663, Library DS16822 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.6409
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 3
BROWSER_TRACK_NAME: FIS DNase 63 22
BROWSER_TRACK_DESCRIPTION: UW Fetal Intestine Small DNase Hypersensitivity Donor H-23663 Library DS16822 EA Release 3

QUALITY SCORES:
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 39
FINDPEAKS_SCORE: 0.37
FINDPEAKS_PERCENTILE: 49
HOTSPOT_SCORE: 0.3638
HOTSPOT_PERCENTILE: 49
IROC_SCORE: 0.9957
IROC_PERCENTILE: 74
POISSON_SCORE: 0.4147
POISSON_PERCENTILE: 36

source_name: Fetal Intestine, Small primary tissue, day 105; DS16822

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

value: Primary Tissue

value: day 105


title: Chromatin accessibility assay of Fetal Kidney_Right Tissue; DS16801

status: Public on Feb 02 2011

type: SRA

city: Seattle

first: Northwest

last: REMC

state: WA

country: USA

institute: University of Washington

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: DS16801
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.5390
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.5389
****************
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: GSM665833_UW.Fetal_Kidney_Right.ChromatinAccessibility.H-23640.DS16801.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS16801.hg19.level.1.release.3
ANALYSIS TITLE: Mapping of Fetal Kidney Right Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fetal Kidney Right, Donor H-23640, Library DS16801 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.6398
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 3

QUALITY SCORES:
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 39
FINDPEAKS_SCORE: 0.4637
FINDPEAKS_PERCENTILE: 79
HOTSPOT_SCORE: 0.4546
HOTSPOT_PERCENTILE: 79
IROC_SCORE: 0.9941
IROC_PERCENTILE: 54
POISSON_SCORE: 0.5204
POISSON_PERCENTILE: 82

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

ANALYSIS FILE NAME: GSM665833_UW.Fetal_Kidney_Right.ChromatinAccessibility.H-23640.DS16801.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS16801.hg19.level.2
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-23640, Library DS16801 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.6437
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 3
BROWSER_TRACK_NAME: FKR DNase 40 01
BROWSER_TRACK_DESCRIPTION: UW Fetal Kidney Right DNase Hypersensitivity Donor H-23640 Library DS16801 EA Release 3

QUALITY SCORES:
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 39
FINDPEAKS_SCORE: 0.4637
FINDPEAKS_PERCENTILE: 79
HOTSPOT_SCORE: 0.4546
HOTSPOT_PERCENTILE: 79
IROC_SCORE: 0.9941
IROC_PERCENTILE: 54
POISSON_SCORE: 0.5204
POISSON_PERCENTILE: 82

molecule: genomic DNA

organism: Homo sapiens

source_name: Fetal Kidney, Right primary tissue, day 115; DS16801

extract_protocol: Library construction protocol: Single read - Illumina

tag: sample alias

tag: sample common name

value: Fetal Kidney, Right

tag: molecule

value: genomic DNA

tag: disease

value: UW

value: fetal

value: day 115

value: Male

value: Chromatin Accessibility

value: Qiagen minElut

value: Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)


title: Chromatin accessibility assay of Fetal Lung_Right Tissue; DS16566

description:
sample_term_id: UBERON_0002167
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Chromatin accessibility determination via DNase-seq
Library name: DS16566
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.5374
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.5373
****************
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: GSM665827_UW.Fetal_Lung_Right.ChromatinAccessibility.H-23604.DS16566.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS16566.hg19.level.1.release.3
ANALYSIS TITLE: Mapping of Fetal Lung Right Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fetal Lung Right, Donor H-23604, Library DS16566 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.6381
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 3

QUALITY SCORES:
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 39
FINDPEAKS_SCORE: 0.4574
FINDPEAKS_PERCENTILE: 74
HOTSPOT_SCORE: 0.4497
HOTSPOT_PERCENTILE: 77
IROC_SCORE: 0.9949
IROC_PERCENTILE: 64
POISSON_SCORE: 0.5246
POISSON_PERCENTILE: 85

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

ANALYSIS FILE NAME: GSM665827_UW.Fetal_Lung_Right.ChromatinAccessibility.H-23604.DS16566.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS16566.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Lung Right Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from  Fetal Lung Right, Donor H-23604, Library DS16566 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.6420
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 3
BROWSER_TRACK_NAME: FLR DNase 04 66
BROWSER_TRACK_DESCRIPTION: UW Fetal Lung Right DNase Hypersensitivity Donor H-23604 Library DS16566 EA Release 3

QUALITY SCORES:
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 39
FINDPEAKS_SCORE: 0.4574
FINDPEAKS_PERCENTILE: 74
HOTSPOT_SCORE: 0.4497
HOTSPOT_PERCENTILE: 77
IROC_SCORE: 0.9949
IROC_PERCENTILE: 64
POISSON_SCORE: 0.5246
POISSON_PERCENTILE: 85

source_name: Fetal Lung, Right primary tissue, day 110; DS16566

value: Fetal Lung, Right

value: day 110

value: Female


title: Chromatin accessibility assay of CD8+ Primary cells; DS17203

description:
sample_term_id: CL_0000625
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Chromatin accessibility determination via DNase-seq
Library name: DS17203
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.5353
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.5352
****************
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: GSM665838_UW.CD8_Primary_Cells.ChromatinAccessibility.RO_01679.DS17203.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS17203.hg19.level.1.release.3
ANALYSIS TITLE: Mapping of CD8 Primary Cells Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on CD8 Primary Cells, Donor RO 01679, Library DS17203 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.6404
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 3

QUALITY SCORES:
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 39
FINDPEAKS_SCORE: 0.6535
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.6695
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.9962
IROC_PERCENTILE: 79
POISSON_SCORE: 0.626
POISSON_PERCENTILE: 95

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

ANALYSIS FILE NAME: GSM665838_UW.CD8_Primary_Cells.ChromatinAccessibility.RO_01679.DS17203.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS17203.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of CD8 Primary Cells Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from  CD8 Primary Cells, Donor RO 01679, Library DS17203 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.6443
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 3
BROWSER_TRACK_NAME: CD8 DNase 21 03
BROWSER_TRACK_DESCRIPTION: UW CD8 Primary Cells DNase Hypersensitivity Donor RO 01679 Library DS17203 EA Release 3

QUALITY SCORES:
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 39
FINDPEAKS_SCORE: 0.6535
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.6695
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.9962
IROC_PERCENTILE: 79
POISSON_SCORE: 0.626
POISSON_PERCENTILE: 95

source_name: flow sorted CD8+ Cells,year 21; DS17203

value: CD8 Primary Cells

value: FHCRC HEIMFELD

value: Primary Cell

tag: markers

value: year 21

value: Caucasian


title: Chromatin accessibility assay of Fetal Thymus Tissue; DS16490

description:
sample_term_id: UBERON_0002370
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Chromatin accessibility determination via DNase-seq
Library name: DS16490
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.5362
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.5361
****************
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: GSM665823_UW.Fetal_Thymus.ChromatinAccessibility.H-23589.DS16490.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS16490.hg19.level.1.release.3
ANALYSIS TITLE: Mapping of Fetal Thymus Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fetal Thymus, Donor H-23589, Library DS16490 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.6391
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 3

QUALITY SCORES:
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 39
FINDPEAKS_SCORE: 0.304
FINDPEAKS_PERCENTILE: 26
HOTSPOT_SCORE: 0.301
HOTSPOT_PERCENTILE: 15
IROC_SCORE: 0.9963
IROC_PERCENTILE: 82
POISSON_SCORE: 0.3506
POISSON_PERCENTILE: 8

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

ANALYSIS FILE NAME: GSM665823_UW.Fetal_Thymus.ChromatinAccessibility.H-23589.DS16490.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS16490.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Thymus Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from  Fetal Thymus, Donor H-23589, Library DS16490 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.6430
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 3
BROWSER_TRACK_NAME: FT DNase 89 90
BROWSER_TRACK_DESCRIPTION: UW Fetal Thymus DNase Hypersensitivity Donor H-23589 Library DS16490 EA Release 3

QUALITY SCORES:
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 39
FINDPEAKS_SCORE: 0.304
FINDPEAKS_PERCENTILE: 26
HOTSPOT_SCORE: 0.301
HOTSPOT_PERCENTILE: 15
IROC_SCORE: 0.9963
IROC_PERCENTILE: 82
POISSON_SCORE: 0.3506
POISSON_PERCENTILE: 8

source_name: Fetal Thymus primary tissue, day 147; DS16490

value: Fetal Thymus

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

value: Primary Tissue

value: day 147


title: Chromatin accessibility assay of Fetal Heart Tissue; DS16621

description:
sample_term_id: UBERON_0000948
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Chromatin accessibility determination via DNase-seq
Library name: DS16621
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.5287
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.5286
****************
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: GSM665831_UW.Fetal_Heart.ChromatinAccessibility.H-23617.DS16621.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS16621.hg19.level.1.release.3
ANALYSIS TITLE: Mapping of Fetal Heart Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fetal Heart, Donor H-23617, Library DS16621 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.6372
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 3

QUALITY SCORES:
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 39
FINDPEAKS_SCORE: 0.5235
FINDPEAKS_PERCENTILE: 90
HOTSPOT_SCORE: 0.5164
HOTSPOT_PERCENTILE: 90
IROC_SCORE: 0.9959
IROC_PERCENTILE: 77
POISSON_SCORE: 0.5904
POISSON_PERCENTILE: 90

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

ANALYSIS FILE NAME: GSM665831_UW.Fetal_Heart.ChromatinAccessibility.H-23617.DS16621.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS16621.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Heart Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from  Fetal Heart, Donor H-23617, Library DS16621 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.6411
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 3
BROWSER_TRACK_NAME: FH DNase 17 21
BROWSER_TRACK_DESCRIPTION: UW Fetal Heart DNase Hypersensitivity Donor H-23617 Library DS16621 EA Release 3

QUALITY SCORES:
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 39
FINDPEAKS_SCORE: 0.5235
FINDPEAKS_PERCENTILE: 90
HOTSPOT_SCORE: 0.5164
HOTSPOT_PERCENTILE: 90
IROC_SCORE: 0.9959
IROC_PERCENTILE: 77
POISSON_SCORE: 0.5904
POISSON_PERCENTILE: 90

source_name: Fetal Heart primary tissue, day 110; DS16621

value: Fetal Heart

value: genomic DNA

value: UW

value: fetal


title: [E-TABM-828] SA1_breast_ab4457_hsaMCF7_treat 2

status: Public on Feb 05 2011

city: Hinxton

first: ArrayExpress

last: EBI

state: Cambridgeshire

address: Wellcome Trust Genome Campus

country: United Kingdom

institute: European Bioinformatics Institute

description: Provider: CRUK-CRI

data_processing:
bioassay_data_transformation | We merged the data from the MAQ aligned replicates, filtering out non-unique reads as well as reads with a MAQ quality score below 10. Positive binding events were discovered using a dynamic programming algorithm (Swembl), which incorporates a scoring function that is increased by alignments of ChIP reads and decreased by alignments of input reads by a general decay function after read observation (S. Wilder et al in preparation).
processed data files:
SA1_treat.gff
Cohesin_treat.gff

source_name: SA1_breast_ab4457_hsaMCF7_treat 2

growth_protocol: growth | MCF7 human breast cancer cells were grown as previously described (Neve et al. 2006). Unless otherwise stated, during all experiments oestrogen was added at a final concentration of 100 nM for 45 minutes (ChIP) or 24 hours (cell cycle analysis). HepG2 cells were grown in DMEM supplemented with 10% FBS.

extract_protocol:
immunoprecipitate | ChIP experiments were performed with well-characterized antibodies against CTCF (Millipore, 07-729), STAG1 (abcam, ab4457), RAD21 (abcam, ab992), ERa (santa cruz, sc-543), CEBPa (santa cruz, sc-9314) and MED12 (abcam, ab70842). ChIP-seq experiments were performed as recently described (Schmidt et al. 2009)
sequencing | The flowcells were prepared and processed according to the manufacturer's protocols, with single-end sequencing for 36 to 45 cycles.

tag: material type

value: cell

tag: cellline

tag: Sex

value: female

tag: organismpart

value: breast

tag: chip antibody

tag: chip antibody catalog

value: abcam, ab4457

tag: compound

value: oestrogen

tag: sirna knockdown

value: not applicable


title: Chromatin accessibility assay of Moblized CD56+ Primary cells; DS16376

description:
sample_term_id: CL_0000623
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Chromatin accessibility determination via DNase-seq
Library name: DS16376
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.5330
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.5329
****************
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: GSM665820_UW.Mobilized_CD56_Primary_Cells.ChromatinAccessibility.RO_01689.DS16376.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS16376.hg19.level.1.release.3
ANALYSIS TITLE: Mapping of Mobilized CD56 Primary Cells Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Mobilized CD56 Primary Cells, Donor RO 01689, Library DS16376 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.6395
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 3

QUALITY SCORES:
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 39
FINDPEAKS_SCORE: 0.2682
FINDPEAKS_PERCENTILE: 13
HOTSPOT_SCORE: 0.266
HOTSPOT_PERCENTILE: 8
IROC_SCORE: 0.9976
IROC_PERCENTILE: 100
POISSON_SCORE: 0.31
POISSON_PERCENTILE: 5

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

ANALYSIS FILE NAME: GSM665820_UW.Mobilized_CD56_Primary_Cells.ChromatinAccessibility.RO_01689.DS16376.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS16376.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Mobilized CD56 Primary Cells Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from  Mobilized CD56 Primary Cells, Donor RO 01689, Library DS16376 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.6434
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 3
BROWSER_TRACK_NAME: MCD56 DNase 89 76
BROWSER_TRACK_DESCRIPTION: UW Mobilized CD56 Primary Cells DNase Hypersensitivity Donor RO 01689 Library DS16376 EA Release 3

QUALITY SCORES:
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 39
FINDPEAKS_SCORE: 0.2682
FINDPEAKS_PERCENTILE: 13
HOTSPOT_SCORE: 0.266
HOTSPOT_PERCENTILE: 8
IROC_SCORE: 0.9976
IROC_PERCENTILE: 100
POISSON_SCORE: 0.31
POISSON_PERCENTILE: 5

source_name: flow sorted CD56+ Primary Cells, Mobilized, year 34; DS16376

value: Mobilized CD56 Primary Cells

value: FHCRC HEIMFELD

value: Primary Cell

value: year 34

value: Female

value: Chromatin Accessibility

value: Qiagen minElut

value: Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)


title: Chromatin accessibility assay of Fetal Kidney_Left Tissue; DS16446

description:
sample_term_id: UBERON_0004538
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Chromatin accessibility determination via DNase-seq
Library name: DS16446
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.5394
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.5393
****************
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: GSM665822_UW.Fetal_Kidney_Left.ChromatinAccessibility.H-23589.DS16446.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS16446.hg19.level.1.release.3
ANALYSIS TITLE: Mapping of Fetal Kidney Left Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fetal Kidney Left, Donor H-23589, Library DS16446 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.6386
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 3

QUALITY SCORES:
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 39
FINDPEAKS_SCORE: 0.2532
FINDPEAKS_PERCENTILE: 10
HOTSPOT_SCORE: 0.2565
HOTSPOT_PERCENTILE: 5
IROC_SCORE: 0.9857
IROC_PERCENTILE: 5
POISSON_SCORE: 0.3514
POISSON_PERCENTILE: 10

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

ANALYSIS FILE NAME: GSM665822_UW.Fetal_Kidney_Left.ChromatinAccessibility.H-23589.DS16446.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS16446.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Kidney Left Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from  Fetal Kidney Left, Donor H-23589, Library DS16446 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.6425
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 3
BROWSER_TRACK_NAME: FKL DNase 89 46
BROWSER_TRACK_DESCRIPTION: UW Fetal Kidney Left DNase Hypersensitivity Donor H-23589 Library DS16446 EA Release 3

QUALITY SCORES:
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 39
FINDPEAKS_SCORE: 0.2532
FINDPEAKS_PERCENTILE: 10
HOTSPOT_SCORE: 0.2565
HOTSPOT_PERCENTILE: 5
IROC_SCORE: 0.9857
IROC_PERCENTILE: 5
POISSON_SCORE: 0.3514
POISSON_PERCENTILE: 10

source_name: Fetal Kidney, Left primary tissue, day 147; DS16446

value: Fetal Kidney, Left

value: genomic DNA

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

value: Primary Tissue

value: day 147


title: Chromatin accessibility assay of Fetal Kidney_Right Tissue; DS16441

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: DS16441
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.5402
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.5401
****************
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: GSM665821_UW.Fetal_Kidney_Right.ChromatinAccessibility.H-23589.DS16441.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS16441.hg19.level.1.release.3
ANALYSIS TITLE: Mapping of Fetal Kidney Right Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fetal Kidney Right, Donor H-23589, Library DS16441 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.6385
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 3

QUALITY SCORES:
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 39
FINDPEAKS_SCORE: 0.3276
FINDPEAKS_PERCENTILE: 33
HOTSPOT_SCORE: 0.317
HOTSPOT_PERCENTILE: 26
IROC_SCORE: 0.9879
IROC_PERCENTILE: 8
POISSON_SCORE: 0.4009
POISSON_PERCENTILE: 31

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

ANALYSIS FILE NAME: GSM665821_UW.Fetal_Kidney_Right.ChromatinAccessibility.H-23589.DS16441.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS16441.hg19.level.2
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-23589, Library DS16441 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.6424
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 3
BROWSER_TRACK_NAME: FKR DNase 89 41
BROWSER_TRACK_DESCRIPTION: UW Fetal Kidney Right DNase Hypersensitivity Donor H-23589 Library DS16441 EA Release 3

QUALITY SCORES:
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 39
FINDPEAKS_SCORE: 0.3276
FINDPEAKS_PERCENTILE: 33
HOTSPOT_SCORE: 0.317
HOTSPOT_PERCENTILE: 26
IROC_SCORE: 0.9879
IROC_PERCENTILE: 8
POISSON_SCORE: 0.4009
POISSON_PERCENTILE: 31

source_name: Fetal Kidney, Right primary tissue, day 147; DS16441

value: Fetal Kidney, Right

value: UW

value: fetal


title: Chromatin accessibility assay of Fetal Brain Tissue; DS16302

description:
sample_term_id: UBERON_0000955
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Chromatin accessibility determination via DNase-seq
Library name: DS16302
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.5300
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.5299
****************
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: GSM665819_UW.Fetal_Brain.ChromatinAccessibility.H-23548.DS16302.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS16302.hg19.level.1.release.3
ANALYSIS TITLE: Mapping of Fetal Brain Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fetal Brain, Donor H-23548, Library DS16302 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.6382
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 3

QUALITY SCORES:
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 39
FINDPEAKS_SCORE: 0.4211
FINDPEAKS_PERCENTILE: 62
HOTSPOT_SCORE: 0.4057
HOTSPOT_PERCENTILE: 62
IROC_SCORE: 0.9952
IROC_PERCENTILE: 69
POISSON_SCORE: 0.4854
POISSON_PERCENTILE: 62

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

ANALYSIS FILE NAME: GSM665819_UW.Fetal_Brain.ChromatinAccessibility.H-23548.DS16302.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS16302.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Brain Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from  Fetal Brain, Donor H-23548, Library DS16302 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.6421
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 3
BROWSER_TRACK_NAME: FB DNase 48 02
BROWSER_TRACK_DESCRIPTION: UW Fetal Brain DNase Hypersensitivity Donor H-23548 Library DS16302 EA Release 3

QUALITY SCORES:
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 39
FINDPEAKS_SCORE: 0.4211
FINDPEAKS_PERCENTILE: 62
HOTSPOT_SCORE: 0.4057
HOTSPOT_PERCENTILE: 62
IROC_SCORE: 0.9952
IROC_PERCENTILE: 69
POISSON_SCORE: 0.4854
POISSON_PERCENTILE: 62

source_name: Fetal Brain primary tissue, day 142; DS16302

value: Fetal Brain

value: day 142


title: [E-TABM-828] Era_breast_sc543_hsaMCF7_vehicle

description: Provider: CRUK-CRI

value: cell

value: female

value: breast

value: Era

value: santa cruz, sc-543

value: vehicle

value: not applicable


title: Chromatin accessibility assay of Fetal Intestine_Large Tissue; DS16164

description:
sample_term_id: UBERON_0000059
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Chromatin accessibility determination via DNase-seq
Library name: DS16164
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.5422
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.5421
****************
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: GSM665818_UW.Fetal_Intestine_Large.ChromatinAccessibility.H-23524.DS16164.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS16164.hg19.level.1.release.3
ANALYSIS TITLE: Mapping of Fetal Intestine Large Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fetal Intestine Large, Donor H-23524, Library DS16164 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.6368
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 3

QUALITY SCORES:
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 39
FINDPEAKS_SCORE: 0.4466
FINDPEAKS_PERCENTILE: 69
HOTSPOT_SCORE: 0.4383
HOTSPOT_PERCENTILE: 72
IROC_SCORE: 0.9973
IROC_PERCENTILE: 95
POISSON_SCORE: 0.4866
POISSON_PERCENTILE: 64

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

ANALYSIS FILE NAME: GSM665818_UW.Fetal_Intestine_Large.ChromatinAccessibility.H-23524.DS16164.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS16164.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Intestine Large Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from  Fetal Intestine Large, Donor H-23524, Library DS16164 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.6407
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 3
BROWSER_TRACK_NAME: FIL DNase 24 64
BROWSER_TRACK_DESCRIPTION: UW Fetal Intestine Large DNase Hypersensitivity Donor H-23524 Library DS16164 EA Release 3

QUALITY SCORES:
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 39
FINDPEAKS_SCORE: 0.4466
FINDPEAKS_PERCENTILE: 69
HOTSPOT_SCORE: 0.4383
HOTSPOT_PERCENTILE: 72
IROC_SCORE: 0.9973
IROC_PERCENTILE: 95
POISSON_SCORE: 0.4866
POISSON_PERCENTILE: 64

source_name: Fetal Intestine, Large primary tissue, day 105; DS16164

value: Fetal Intestine, Large

value: day 105

value: Male

value: Chromatin Accessibility

value: Qiagen minElut

value: Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)


title: Chromatin accessibility assay of Fetal Kidney Tissue; DS16139

description:
sample_term_id: UBERON_0002113
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Chromatin accessibility determination via DNase-seq
Library name: DS16139
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.5304
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.5303
****************
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: GSM665816_UW.Fetal_Kidney.ChromatinAccessibility.H-23524.DS16139.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS16139.hg19.level.1.release.3
ANALYSIS TITLE: Mapping of Fetal Kidney Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fetal Kidney, Donor H-23524, Library DS16139 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.6397
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 3

QUALITY SCORES:
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 39
FINDPEAKS_SCORE: 0.2999
FINDPEAKS_PERCENTILE: 23
HOTSPOT_SCORE: 0.3424
HOTSPOT_PERCENTILE: 36
IROC_SCORE: 0.9701
IROC_PERCENTILE: 3
POISSON_SCORE: 0.3977
POISSON_PERCENTILE: 28

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

ANALYSIS FILE NAME: GSM665816_UW.Fetal_Kidney.ChromatinAccessibility.H-23524.DS16139.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS16139.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Kidney Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from  Fetal Kidney, Donor H-23524, Library DS16139 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.6436
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 3
BROWSER_TRACK_NAME: FK DNase 24 39
BROWSER_TRACK_DESCRIPTION: UW Fetal Kidney DNase Hypersensitivity Donor H-23524 Library DS16139 EA Release 3

QUALITY SCORES:
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 39
FINDPEAKS_SCORE: 0.2999
FINDPEAKS_PERCENTILE: 23
HOTSPOT_SCORE: 0.3424
HOTSPOT_PERCENTILE: 36
IROC_SCORE: 0.9701
IROC_PERCENTILE: 3
POISSON_SCORE: 0.3977
POISSON_PERCENTILE: 28

source_name: Fetal Kidney primary tissue, day 105; DS16139

value: Fetal Kidney

value: genomic DNA

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

value: Primary Tissue

value: UW


title: Chromatin accessibility assay of Fetal Heart Tissue; DS16146

description:
sample_term_id: UBERON_0000948
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Chromatin accessibility determination via DNase-seq
Library name: DS16146
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.5275
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.5274
****************
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: GSM665817_UW.Fetal_Heart.ChromatinAccessibility.H-23524.DS16146.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS16146.hg19.level.1.release.3
ANALYSIS TITLE: Mapping of Fetal Heart Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fetal Heart, Donor H-23524, Library DS16146 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.6400
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 3

QUALITY SCORES:
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 39
FINDPEAKS_SCORE: 0.4475
FINDPEAKS_PERCENTILE: 72
HOTSPOT_SCORE: 0.4354
HOTSPOT_PERCENTILE: 69
IROC_SCORE: 0.9948
IROC_PERCENTILE: 62
POISSON_SCORE: 0.5059
POISSON_PERCENTILE: 74

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

ANALYSIS FILE NAME: GSM665817_UW.Fetal_Heart.ChromatinAccessibility.H-23524.DS16146.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS16146.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Heart Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from  Fetal Heart, Donor H-23524, Library DS16146 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.6439
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 3
BROWSER_TRACK_NAME: FH DNase 24 46
BROWSER_TRACK_DESCRIPTION: UW Fetal Heart DNase Hypersensitivity Donor H-23524 Library DS16146 EA Release 3

QUALITY SCORES:
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 39
FINDPEAKS_SCORE: 0.4475
FINDPEAKS_PERCENTILE: 72
HOTSPOT_SCORE: 0.4354
HOTSPOT_PERCENTILE: 69
IROC_SCORE: 0.9948
IROC_PERCENTILE: 62
POISSON_SCORE: 0.5059
POISSON_PERCENTILE: 74

source_name: Fetal Heart primary tissue, day 105; DS16146

value: Fetal Heart

value: fetal


title: Chromatin accessibility assay of Fetal Intestine_Large Tissue; DS16027

description:
sample_term_id: UBERON_0000059
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Chromatin accessibility determination via DNase-seq
Library name: DS16027
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.5410
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.5409
****************
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: GSM665815_UW.Fetal_Intestine_Large.ChromatinAccessibility.H-23500.DS16027.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS16027.hg19.level.1.release.3
ANALYSIS TITLE: Mapping of Fetal Intestine Large Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fetal Intestine Large, Donor H-23500, Library DS16027 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.6405
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 3

QUALITY SCORES:
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 39
FINDPEAKS_SCORE: 0.2993
FINDPEAKS_PERCENTILE: 21
HOTSPOT_SCORE: 0.3019
HOTSPOT_PERCENTILE: 18
IROC_SCORE: 0.9912
IROC_PERCENTILE: 21
POISSON_SCORE: 0.3732
POISSON_PERCENTILE: 21

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

ANALYSIS FILE NAME: GSM665815_UW.Fetal_Intestine_Large.ChromatinAccessibility.H-23500.DS16027.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS16027.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Intestine Large Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from  Fetal Intestine Large, Donor H-23500, Library DS16027 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.6444
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 3
BROWSER_TRACK_NAME: FIL DNase 00 27
BROWSER_TRACK_DESCRIPTION: UW Fetal Intestine Large DNase Hypersensitivity Donor H-23500 Library DS16027 EA Release 3

QUALITY SCORES:
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 39
FINDPEAKS_SCORE: 0.2993
FINDPEAKS_PERCENTILE: 21
HOTSPOT_SCORE: 0.3019
HOTSPOT_PERCENTILE: 18
IROC_SCORE: 0.9912
IROC_PERCENTILE: 21
POISSON_SCORE: 0.3732
POISSON_PERCENTILE: 21

source_name: Fetal Intestine, Large primary tissue, day 103; DS16027

value: day 103

value: Female


title: Chromatin accessibility assay of Fetal Heart Tissue; DS16018

description:
sample_term_id: UBERON_0000948
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Chromatin accessibility determination via DNase-seq
Library name: DS16018
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.5271
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.5270
****************
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: GSM665814_UW.Fetal_Heart.ChromatinAccessibility.H-23500.DS16018.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS16018.hg19.level.1.release.3
ANALYSIS TITLE: Mapping of Fetal Heart Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fetal Heart, Donor H-23500, Library DS16018 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.6402
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 3

QUALITY SCORES:
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 39
FINDPEAKS_SCORE: 0.5109
FINDPEAKS_PERCENTILE: 87
HOTSPOT_SCORE: 0.514
HOTSPOT_PERCENTILE: 87
IROC_SCORE: 0.9972
IROC_PERCENTILE: 90
POISSON_SCORE: 0.603
POISSON_PERCENTILE: 92

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

ANALYSIS FILE NAME: GSM665814_UW.Fetal_Heart.ChromatinAccessibility.H-23500.DS16018.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS16018.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Heart Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from  Fetal Heart, Donor H-23500, Library DS16018 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.6441
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 3
BROWSER_TRACK_NAME: FH DNase 00 18
BROWSER_TRACK_DESCRIPTION: UW Fetal Heart DNase Hypersensitivity Donor H-23500 Library DS16018 EA Release 3

QUALITY SCORES:
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 39
FINDPEAKS_SCORE: 0.5109
FINDPEAKS_PERCENTILE: 87
HOTSPOT_SCORE: 0.514
HOTSPOT_PERCENTILE: 87
IROC_SCORE: 0.9972
IROC_PERCENTILE: 90
POISSON_SCORE: 0.603
POISSON_PERCENTILE: 92

source_name: Fetal Heart primary tissue, day 103; DS16018


title: Chromatin accessibility assay of CD4+ Primary cells; DS15947

description:
sample_term_id: CL_0000492
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Chromatin accessibility determination via DNase-seq
Library name: DS15947
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.5326
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.5325
****************
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: GSM665812_UW.CD4_Primary_Cells.ChromatinAccessibility.RO_01549.DS15947.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS15947.hg19.level.1.release.3
ANALYSIS TITLE: Mapping of CD4 Primary Cells Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on CD4 Primary Cells, Donor RO 01549, Library DS15947 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.6389
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 3

QUALITY SCORES:
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 39
FINDPEAKS_SCORE: 0.335
FINDPEAKS_PERCENTILE: 38
HOTSPOT_SCORE: 0.356
HOTSPOT_PERCENTILE: 44
IROC_SCORE: 0.9937
IROC_PERCENTILE: 46
POISSON_SCORE: 0.3675
POISSON_PERCENTILE: 15

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

ANALYSIS FILE NAME: GSM665812_UW.CD4_Primary_Cells.ChromatinAccessibility.RO_01549.DS15947.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS15947.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of CD4 Primary Cells Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from  CD4 Primary Cells, Donor RO 01549, Library DS15947 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.6428
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 3
BROWSER_TRACK_NAME: CD4 DNase 70 47
BROWSER_TRACK_DESCRIPTION: UW CD4 Primary Cells DNase Hypersensitivity Donor RO 01549 Library DS15947 EA Release 3

QUALITY SCORES:
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 39
FINDPEAKS_SCORE: 0.335
FINDPEAKS_PERCENTILE: 38
HOTSPOT_SCORE: 0.356
HOTSPOT_PERCENTILE: 44
IROC_SCORE: 0.9937
IROC_PERCENTILE: 46
POISSON_SCORE: 0.3675
POISSON_PERCENTILE: 15

source_name: flow sorted CD4+ Cells,year 33; DS15947

value: CD4 Primary Cells

value: FHCRC HEIMFELD

value: Primary Cell

value: year 33

value: Caucasian


title: Chromatin accessibility assay of Fetal Heart Tissue; DS15839

description:
sample_term_id: UBERON_0000948
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Chromatin accessibility determination via DNase-seq
Library name: DS15839
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.5291
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.5290
****************
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: GSM665811_UW.Fetal_Heart.ChromatinAccessibility.H-23468.DS15839.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS15839.hg19.level.1.release.3
ANALYSIS TITLE: Mapping of Fetal Heart Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fetal Heart, Donor H-23468, Library DS15839 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.6393
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 3

QUALITY SCORES:
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 39
FINDPEAKS_SCORE: 0.3632
FINDPEAKS_PERCENTILE: 44
HOTSPOT_SCORE: 0.3943
HOTSPOT_PERCENTILE: 54
IROC_SCORE: 0.9934
IROC_PERCENTILE: 44
POISSON_SCORE: 0.4961
POISSON_PERCENTILE: 72

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

ANALYSIS FILE NAME: GSM665811_UW.Fetal_Heart.ChromatinAccessibility.H-23468.DS15839.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS15839.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Heart Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from  Fetal Heart, Donor H-23468, Library DS15839 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.6432
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 3
BROWSER_TRACK_NAME: FH DNase 68 39
BROWSER_TRACK_DESCRIPTION: UW Fetal Heart DNase Hypersensitivity Donor H-23468 Library DS15839 EA Release 3

QUALITY SCORES:
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 39
FINDPEAKS_SCORE: 0.3632
FINDPEAKS_PERCENTILE: 44
HOTSPOT_SCORE: 0.3943
HOTSPOT_PERCENTILE: 54
IROC_SCORE: 0.9934
IROC_PERCENTILE: 44
POISSON_SCORE: 0.4961
POISSON_PERCENTILE: 72

source_name: Fetal Heart primary tissue, day 96; DS15839

value: day 96

value: Male

value: Chromatin Accessibility


title: Chromatin accessibility assay of Fetal Kidney_Right Tissue; DS15651

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: DS15651
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.5366
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.5365
****************
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: GSM665810_UW.Fetal_Kidney_Right.ChromatinAccessibility.H-23435.DS15651.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS15651.hg19.level.1.release.3
ANALYSIS TITLE: Mapping of Fetal Kidney Right Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fetal Kidney Right, Donor H-23435, Library DS15651 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.6371
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 3

QUALITY SCORES:
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 39
FINDPEAKS_SCORE: 0.3134
FINDPEAKS_PERCENTILE: 28
HOTSPOT_SCORE: 0.3156
HOTSPOT_PERCENTILE: 23
IROC_SCORE: 0.9885
IROC_PERCENTILE: 10
POISSON_SCORE: 0.4195
POISSON_PERCENTILE: 38

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

ANALYSIS FILE NAME: GSM665810_UW.Fetal_Kidney_Right.ChromatinAccessibility.H-23435.DS15651.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS15651.hg19.level.2
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-23435, Library DS15651 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.6410
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 3
BROWSER_TRACK_NAME: FKR DNase 35 51
BROWSER_TRACK_DESCRIPTION: UW Fetal Kidney Right DNase Hypersensitivity Donor H-23435 Library DS15651 EA Release 3

QUALITY SCORES:
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 39
FINDPEAKS_SCORE: 0.3134
FINDPEAKS_PERCENTILE: 28
HOTSPOT_SCORE: 0.3156
HOTSPOT_PERCENTILE: 23
IROC_SCORE: 0.9885
IROC_PERCENTILE: 10
POISSON_SCORE: 0.4195
POISSON_PERCENTILE: 38

source_name: Fetal Kidney, Right primary tissue, day 117; DS15651

value: Fetal Kidney, Right

value: day 117

value: Qiagen minElut

value: Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)


title: Chromatin accessibility assay of Fetal Heart Tissue; DS15643

description:
sample_term_id: UBERON_0000948
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Chromatin accessibility determination via DNase-seq
Library name: DS15643
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.5267
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.5266
****************
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: Fetal Heart primary tissue, day 117; DS15643

value: genomic DNA

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

value: Primary Tissue

value: UW


title: Chromatin accessibility assay of Fetal Intestine_Large Tissue; DS16563

description:
sample_term_id: UBERON_0000059
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Chromatin accessibility determination via DNase-seq
Library name: DS16563
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.5427
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.5426
****************
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: GSM665826_UW.Fetal_Intestine_Large.ChromatinAccessibility.H-23604.DS16563.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS16563.hg19.level.1.release.3
ANALYSIS TITLE: Mapping of Fetal Intestine Large Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fetal Intestine Large, Donor H-23604, Library DS16563 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.6380
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 3

QUALITY SCORES:
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 39
FINDPEAKS_SCORE: 0.3569
FINDPEAKS_PERCENTILE: 41
HOTSPOT_SCORE: 0.3485
HOTSPOT_PERCENTILE: 38
IROC_SCORE: 0.995
IROC_PERCENTILE: 67
POISSON_SCORE: 0.4078
POISSON_PERCENTILE: 33

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

ANALYSIS FILE NAME: GSM665826_UW.Fetal_Intestine_Large.ChromatinAccessibility.H-23604.DS16563.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS16563.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Intestine Large Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from  Fetal Intestine Large, Donor H-23604, Library DS16563 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.6419
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 3
BROWSER_TRACK_NAME: FIL DNase 04 63
BROWSER_TRACK_DESCRIPTION: UW Fetal Intestine Large DNase Hypersensitivity Donor H-23604 Library DS16563 EA Release 3

QUALITY SCORES:
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 39
FINDPEAKS_SCORE: 0.3569
FINDPEAKS_PERCENTILE: 41
HOTSPOT_SCORE: 0.3485
HOTSPOT_PERCENTILE: 38
IROC_SCORE: 0.995
IROC_PERCENTILE: 67
POISSON_SCORE: 0.4078
POISSON_PERCENTILE: 33

source_name: Fetal Intestine, Large primary tissue, day 110; DS16563

value: Fetal Intestine, Large

value: fetal

value: day 110

value: Female


title: Chromatin accessibility assay of Fetal Lung Tissue; DS15573

description:
sample_term_id: UBERON_0002048
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Chromatin accessibility determination via DNase-seq
Library name: DS15573
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.5312
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.5311
****************
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: GSM665806_UW.Fetal_Lung.ChromatinAccessibility.H-23419.DS15573.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS15573.hg19.level.1.release.3
ANALYSIS TITLE: Mapping of Fetal Lung Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fetal Lung, Donor H-23419, Library DS15573 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.6374
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 3

QUALITY SCORES:
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 39
FINDPEAKS_SCORE: 0.3656
FINDPEAKS_PERCENTILE: 46
HOTSPOT_SCORE: 0.3539
HOTSPOT_PERCENTILE: 41
IROC_SCORE: 0.9925
IROC_PERCENTILE: 28
POISSON_SCORE: 0.4314
POISSON_PERCENTILE: 44

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

ANALYSIS FILE NAME: GSM665806_UW.Fetal_Lung.ChromatinAccessibility.H-23419.DS15573.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS15573.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Lung Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from  Fetal Lung, Donor H-23419, Library DS15573 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.6413
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 3
BROWSER_TRACK_NAME: FL DNase 19 73
BROWSER_TRACK_DESCRIPTION: UW Fetal Lung DNase Hypersensitivity Donor H-23419 Library DS15573 EA Release 3

QUALITY SCORES:
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 39
FINDPEAKS_SCORE: 0.3656
FINDPEAKS_PERCENTILE: 46
HOTSPOT_SCORE: 0.3539
HOTSPOT_PERCENTILE: 41
IROC_SCORE: 0.9925
IROC_PERCENTILE: 28
POISSON_SCORE: 0.4314
POISSON_PERCENTILE: 44

source_name: Fetal Lung primary tissue, day 82; DS15573

value: Fetal Lung

value: day 82


title: Chromatin accessibility assay of Fetal Lung_Right Tissue; DS15632

description:
sample_term_id: UBERON_0002167
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Chromatin accessibility determination via DNase-seq
Library name: DS15632
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.5406
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.5405
****************
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: GSM665807_UW.Fetal_Lung_Right.ChromatinAccessibility.H-23435.DS15632.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS15632.hg19.level.1.release.3
ANALYSIS TITLE: Mapping of Fetal Lung Right Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fetal Lung Right, Donor H-23435, Library DS15632 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.6403
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 3

QUALITY SCORES:
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 39
FINDPEAKS_SCORE: 0.4306
FINDPEAKS_PERCENTILE: 64
HOTSPOT_SCORE: 0.4206
HOTSPOT_PERCENTILE: 64
IROC_SCORE: 0.9938
IROC_PERCENTILE: 49
POISSON_SCORE: 0.4901
POISSON_PERCENTILE: 67

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

ANALYSIS FILE NAME: GSM665807_UW.Fetal_Lung_Right.ChromatinAccessibility.H-23435.DS15632.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS15632.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Lung Right Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from  Fetal Lung Right, Donor H-23435, Library DS15632 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.6442
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 3
BROWSER_TRACK_NAME: FLR DNase 35 32
BROWSER_TRACK_DESCRIPTION: UW Fetal Lung Right DNase Hypersensitivity Donor H-23435 Library DS15632 EA Release 3

QUALITY SCORES:
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 39
FINDPEAKS_SCORE: 0.4306
FINDPEAKS_PERCENTILE: 64
HOTSPOT_SCORE: 0.4206
HOTSPOT_PERCENTILE: 64
IROC_SCORE: 0.9938
IROC_PERCENTILE: 49
POISSON_SCORE: 0.4901
POISSON_PERCENTILE: 67

source_name: Fetal Lung, Right primary tissue, day 117; DS15632

value: Fetal Lung, Right


title: Chromatin accessibility assay of Fetal Brain Tissue; DS15453

description:
sample_term_id: UBERON_0000955
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Chromatin accessibility determination via DNase-seq
Library name: DS15453
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.5296
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.5295
****************
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: GSM665804_UW.Fetal_Brain.ChromatinAccessibility.H-23399.DS15453.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS15453.hg19.level.1.release.3
ANALYSIS TITLE: Mapping of Fetal Brain Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fetal Brain, Donor H-23399, Library DS15453 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.6376
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 3

QUALITY SCORES:
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 39
FINDPEAKS_SCORE: 0.3342
FINDPEAKS_PERCENTILE: 36
HOTSPOT_SCORE: 0.3261
HOTSPOT_PERCENTILE: 31
IROC_SCORE: 0.9913
IROC_PERCENTILE: 23
POISSON_SCORE: 0.4304
POISSON_PERCENTILE: 41

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

ANALYSIS FILE NAME: GSM665804_UW.Fetal_Brain.ChromatinAccessibility.H-23399.DS15453.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS15453.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Brain Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from  Fetal Brain, Donor H-23399, Library DS15453 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.6415
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 3
BROWSER_TRACK_NAME: FB DNase 99 53
BROWSER_TRACK_DESCRIPTION: UW Fetal Brain DNase Hypersensitivity Donor H-23399 Library DS15453 EA Release 3

QUALITY SCORES:
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 39
FINDPEAKS_SCORE: 0.3342
FINDPEAKS_PERCENTILE: 36
HOTSPOT_SCORE: 0.3261
HOTSPOT_PERCENTILE: 31
IROC_SCORE: 0.9913
IROC_PERCENTILE: 23
POISSON_SCORE: 0.4304
POISSON_PERCENTILE: 41

source_name: Fetal Brain primary tissue, day 112; DS15453

value: Fetal Brain

value: day 112

value: Unknown


title: Chromatin accessibility assay of Fetal Adrenal Tissue; DS15123

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: DS15123
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.5319
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.5318
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

source_name: Fetal Adrenal Gland primary tissue, day 85; DS15123

value: Fetal Adrenal Gland

value: day 85

value: Male

value: Chromatin Accessibility


title: Chromatin accessibility assay of Fetal Lung_Left Tissue; DS15637

description:
sample_term_id: UBERON_0002168
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Chromatin accessibility determination via DNase-seq
Library name: DS15637
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.5398
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.5397
****************
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: GSM665808_UW.Fetal_Lung_Left.ChromatinAccessibility.H-23435.DS15637.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS15637.hg19.level.1.release.3
ANALYSIS TITLE: Mapping of Fetal Lung Left Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fetal Lung Left, Donor H-23435, Library DS15637 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.6406
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 3

QUALITY SCORES:
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 39
FINDPEAKS_SCORE: 0.3959
FINDPEAKS_PERCENTILE: 54
HOTSPOT_SCORE: 0.378
HOTSPOT_PERCENTILE: 51
IROC_SCORE: 0.9932
IROC_PERCENTILE: 36
POISSON_SCORE: 0.4521
POISSON_PERCENTILE: 51

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

ANALYSIS FILE NAME: GSM665808_UW.Fetal_Lung_Left.ChromatinAccessibility.H-23435.DS15637.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS15637.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Lung Left Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from  Fetal Lung Left, Donor H-23435, Library DS15637 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.6445
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 3
BROWSER_TRACK_NAME: FLL DNase 35 37
BROWSER_TRACK_DESCRIPTION: UW Fetal Lung Left DNase Hypersensitivity Donor H-23435 Library DS15637 EA Release 3

QUALITY SCORES:
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 39
FINDPEAKS_SCORE: 0.3959
FINDPEAKS_PERCENTILE: 54
HOTSPOT_SCORE: 0.378
HOTSPOT_PERCENTILE: 51
IROC_SCORE: 0.9932
IROC_PERCENTILE: 36
POISSON_SCORE: 0.4521
POISSON_PERCENTILE: 51

source_name: Fetal Lung, Left primary tissue, day 117; DS15637

value: Fetal Lung, Left

value: genomic DNA

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

value: day 117

value: Qiagen minElut

value: Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)


title: Chromatin accessibility assay of iPS DF 19.11 Cell line; DS15153

description:
sample_term_id: NTR_0001173
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Chromatin accessibility determination via DNase-seq
Library name: DS15153
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.5334
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.5333
****************
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: GSM665801_UW.iPS_DF_19.11.ChromatinAccessibility.DS15153.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS15153.hg19.level.1.release.3
ANALYSIS TITLE: Mapping of iPS DF 19.11 Cell Line Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on the iPS DF 19.11 Cell Line, Library DS15153 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.6392
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 3

QUALITY SCORES:
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 39
FINDPEAKS_SCORE: 0.2874
FINDPEAKS_PERCENTILE: 18
HOTSPOT_SCORE: 0.3406
HOTSPOT_PERCENTILE: 33
IROC_SCORE: 0.9933
IROC_PERCENTILE: 41
POISSON_SCORE: 0.394
POISSON_PERCENTILE: 26

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

ANALYSIS FILE NAME: GSM665801_UW.iPS_DF_19.11.ChromatinAccessibility.DS15153.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS15153.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of iPS DF 19.11 Cell Line Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from  the iPS DF 19.11 Cell Line, Library DS15153 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.6431
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 3
BROWSER_TRACK_NAME: iD19.11 DNase 53 53
BROWSER_TRACK_DESCRIPTION: UW iPS DF 19.11 Cell Line DNase Hypersensitivity Library DS15153 EA Release 3

QUALITY SCORES:
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 39
FINDPEAKS_SCORE: 0.2874
FINDPEAKS_PERCENTILE: 18
HOTSPOT_SCORE: 0.3406
HOTSPOT_PERCENTILE: 33
IROC_SCORE: 0.9933
IROC_PERCENTILE: 41
POISSON_SCORE: 0.394
POISSON_PERCENTILE: 26

source_name: iPS DF 19.11 Cell Line, Induced pluripotent stem cel, derived from fibroblast. the first set of numbers before the period refer to different clones, the number after the period indicates the sub-clone.; DS15153

value: iPS DF 19.11 Cell Line

value: James Thomson, Morgridge Institute for Research, University of Wisconsin-Madison

value: Cell Line

tag: line

tag: lineage

value: Derived from newborn foreskin fibroblast:Cat# CRL-2097TM, ATCC

value: Induced pluripotent stem cell

tag: passage

tag: medium

tag: batch


title: Chromatin accessibility assay of Fetal Lung Tissue; DS15461

description:
sample_term_id: UBERON_0002048
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Chromatin accessibility determination via DNase-seq
Library name: DS15461
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.5308
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.5307
****************
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: GSM665805_UW.Fetal_Lung.ChromatinAccessibility.H-23399.DS15461.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS15461.hg19.level.1.release.3
ANALYSIS TITLE: Mapping of Fetal Lung Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fetal Lung, Donor H-23399, Library DS15461 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.6377
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 3

QUALITY SCORES:
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 39
FINDPEAKS_SCORE: 0.4375
FINDPEAKS_PERCENTILE: 67
HOTSPOT_SCORE: 0.4228
HOTSPOT_PERCENTILE: 67
IROC_SCORE: 0.9931
IROC_PERCENTILE: 33
POISSON_SCORE: 0.4915
POISSON_PERCENTILE: 69

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

ANALYSIS FILE NAME: GSM665805_UW.Fetal_Lung.ChromatinAccessibility.H-23399.DS15461.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS15461.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Lung Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from  Fetal Lung, Donor H-23399, Library DS15461 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.6416
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 3
BROWSER_TRACK_NAME: FL DNase 99 61
BROWSER_TRACK_DESCRIPTION: UW Fetal Lung DNase Hypersensitivity Donor H-23399 Library DS15461 EA Release 3

QUALITY SCORES:
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 39
FINDPEAKS_SCORE: 0.4375
FINDPEAKS_PERCENTILE: 67
HOTSPOT_SCORE: 0.4228
HOTSPOT_PERCENTILE: 67
IROC_SCORE: 0.9931
IROC_PERCENTILE: 33
POISSON_SCORE: 0.4915
POISSON_PERCENTILE: 69

source_name: Fetal Lung primary tissue, day 112; DS15461

tag: sample alias

tag: sample common name

value: Fetal Lung

value: Primary Tissue

value: UW

value: fetal

value: day 112