title: Chromatin accessibility assay of Fetal Intestine, Small; DS18495

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: DS18495
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.10039
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.10038
****************
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: GSM817187_UW.Fetal_Intestine_Small.ChromatinAccessibility.H-24111.DS18495.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS18495.hg19.level.1.release.6
ANALYSIS TITLE: Mapping of Fetal Intestine Small Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fetal Intestine Small, Donor H-24111, Library DS18495 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.12607
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 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 41,285,837
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 63
FINDPEAKS_SCORE: 0.2197
FINDPEAKS_PERCENTILE: 3
HOTSPOT_SCORE: 0.2214
HOTSPOT_PERCENTILE: 3
IROC_SCORE: 0.9937
IROC_PERCENTILE: 59
POISSON_SCORE: 0.289
POISSON_PERCENTILE: 5
MAXIMUM_REPLICATE_CORRELATION: 0.99

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

ANALYSIS FILE NAME: GSM817187_UW.Fetal_Intestine_Small.ChromatinAccessibility.H-24111.DS18495.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS18495.hg19.level.2.release.6
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-24111, Library DS18495 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.12670
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 6
BROWSER_TRACK_NAME: FIS DNase 11 95
BROWSER_TRACK_DESCRIPTION: UW Fetal Intestine Small DNase Hypersensitivity Donor H-24111 Library DS18495 EA Release 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 41,285,837
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 63
FINDPEAKS_SCORE: 0.2197
FINDPEAKS_PERCENTILE: 3
HOTSPOT_SCORE: 0.2214
HOTSPOT_PERCENTILE: 3
IROC_SCORE: 0.9937
IROC_PERCENTILE: 59
POISSON_SCORE: 0.289
POISSON_PERCENTILE: 5
MAXIMUM_REPLICATE_CORRELATION: 0.99

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

source_name: Fetal Intestine, Small primary tissue, day 105; DS18495

value: Fetal Intestine, Small

value: day 105

value: Qiagen minElut

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


title: Chromatin accessibility assay of Fetal Intestine, Large; DS18499

status: Public on Oct 15 2011

type: SRA

city: Seattle

first: Northwest

last: REMC

state: WA

country: USA

institute: University of Washington

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: DS18499
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.10047
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.10046
****************
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: GSM817188_UW.Fetal_Intestine_Large.ChromatinAccessibility.H-24111.DS18499.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS18499.hg19.level.1.release.6
ANALYSIS TITLE: Mapping of Fetal Intestine Large Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fetal Intestine Large, Donor H-24111, Library DS18499 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.12608
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 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 35,862,633
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 63
FINDPEAKS_SCORE: 0.2394
FINDPEAKS_PERCENTILE: 5
HOTSPOT_SCORE: 0.2489
HOTSPOT_PERCENTILE: 5
IROC_SCORE: 0.9926
IROC_PERCENTILE: 41
POISSON_SCORE: 0.3406
POISSON_PERCENTILE: 10
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

ANALYSIS FILE NAME: GSM817188_UW.Fetal_Intestine_Large.ChromatinAccessibility.H-24111.DS18499.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS18499.hg19.level.2.release.6
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-24111, Library DS18499 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.12671
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 6
BROWSER_TRACK_NAME: FIL DNase 11 99
BROWSER_TRACK_DESCRIPTION: UW Fetal Intestine Large DNase Hypersensitivity Donor H-24111 Library DS18499 EA Release 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 35,862,633
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 63
FINDPEAKS_SCORE: 0.2394
FINDPEAKS_PERCENTILE: 5
HOTSPOT_SCORE: 0.2489
HOTSPOT_PERCENTILE: 5
IROC_SCORE: 0.9926
IROC_PERCENTILE: 41
POISSON_SCORE: 0.3406
POISSON_PERCENTILE: 10
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

molecule: genomic DNA

organism: Homo sapiens

source_name: Fetal Intestine, Large primary tissue, day 105; DS18499

extract_protocol: Library construction protocol: Single read - Illumina

tag: sample alias

tag: sample common name

value: Fetal Intestine, Large

tag: molecule

value: genomic DNA

tag: disease

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

value: Primary Tissue

value: UW

value: fetal

value: Male

value: Chromatin Accessibility


title: Chromatin accessibility assay of Fetal Muscle, Back; DS18842

description:
sample_term_id: UBERON_0002324
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Chromatin accessibility determination via DNase-seq
Library name: DS18842
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.9872
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.9871
****************
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: GSM817200_UW.Fetal_Muscle_Back.ChromatinAccessibility.H-24143.DS18842.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS18842.hg19.level.1.release.6
ANALYSIS TITLE: Mapping of Fetal Muscle Back Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fetal Muscle Back, Donor H-24143, Library DS18842 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.12620
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 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 29,277,338
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 63
FINDPEAKS_SCORE: 0.3724
FINDPEAKS_PERCENTILE: 49
HOTSPOT_SCORE: 0.362
HOTSPOT_PERCENTILE: 46
IROC_SCORE: 0.9924
IROC_PERCENTILE: 40
POISSON_SCORE: 0.4422
POISSON_PERCENTILE: 48
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

ANALYSIS FILE NAME: GSM817200_UW.Fetal_Muscle_Back.ChromatinAccessibility.H-24143.DS18842.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS18842.hg19.level.2.release.6
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Muscle Back Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from  Fetal Muscle Back, Donor H-24143, Library DS18842 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.12683
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 6
BROWSER_TRACK_NAME: FMB DNase 43 42
BROWSER_TRACK_DESCRIPTION: UW Fetal Muscle Back DNase Hypersensitivity Donor H-24143 Library DS18842 EA Release 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 29,277,338
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 63
FINDPEAKS_SCORE: 0.3724
FINDPEAKS_PERCENTILE: 49
HOTSPOT_SCORE: 0.362
HOTSPOT_PERCENTILE: 46
IROC_SCORE: 0.9924
IROC_PERCENTILE: 40
POISSON_SCORE: 0.4422
POISSON_PERCENTILE: 48
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

source_name: Fetal Muscle, Back primary tissue, day 115; DS18842

value: Fetal Muscle, Back

value: day 115

value: Female


title: Chromatin accessibility assay of Fetal Muscle, Arm; DS18473

description:
sample_term_id: UBERON_0001499
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Chromatin accessibility determination via DNase-seq
Library name: DS18473
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.9900
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.9899
****************
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: GSM817184_UW.Fetal_Muscle_Arm.ChromatinAccessibility.H-24111.DS18473.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS18473.hg19.level.1.release.6
ANALYSIS TITLE: Mapping of Fetal Muscle Arm Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fetal Muscle Arm, Donor H-24111, Library DS18473 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.12604
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 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 36,006,708
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 63
FINDPEAKS_SCORE: 0.3043
FINDPEAKS_PERCENTILE: 24
HOTSPOT_SCORE: 0.3031
HOTSPOT_PERCENTILE: 22
IROC_SCORE: 0.991
IROC_PERCENTILE: 25
POISSON_SCORE: 0.4143
POISSON_PERCENTILE: 35
MAXIMUM_REPLICATE_CORRELATION: 0.99

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

ANALYSIS FILE NAME: GSM817184_UW.Fetal_Muscle_Arm.ChromatinAccessibility.H-24111.DS18473.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS18473.hg19.level.2.release.6
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Muscle Arm Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from  Fetal Muscle Arm, Donor H-24111, Library DS18473 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.12667
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 6
BROWSER_TRACK_NAME: FMA DNase 11 73
BROWSER_TRACK_DESCRIPTION: UW Fetal Muscle Arm DNase Hypersensitivity Donor H-24111 Library DS18473 EA Release 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 36,006,708
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 63
FINDPEAKS_SCORE: 0.3043
FINDPEAKS_PERCENTILE: 24
HOTSPOT_SCORE: 0.3031
HOTSPOT_PERCENTILE: 22
IROC_SCORE: 0.991
IROC_PERCENTILE: 25
POISSON_SCORE: 0.4143
POISSON_PERCENTILE: 35
MAXIMUM_REPLICATE_CORRELATION: 0.99

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

source_name: Fetal Muscle, Arm primary tissue, day 105; DS18473

value: Fetal Muscle, Arm


title: Chromatin accessibility assay of Penis Foreskin Fibroblast Primary Cells; DS18252

description:
sample_term_id: CL_1001608
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Chromatin accessibility determination via DNase-seq
Library name: DS18252
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.10119
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSF-UBC%2FSAMPLE%2FEDACC.9574
****************
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: GSM817169_UW.Penis_Foreskin_Fibroblast_Primary_Cells.ChromatinAccessibility.skin02.DS18252.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS18252.hg19.level.1.release.6
ANALYSIS TITLE: Mapping of Penis Foreskin Fibroblast Primary Cells Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Penis Foreskin Fibroblast Primary Cells, Donor skin02, Library DS18252 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.12589
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 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 32,169,657
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 63
FINDPEAKS_SCORE: 0.6688
FINDPEAKS_PERCENTILE: 98
HOTSPOT_SCORE: 0.7011
HOTSPOT_PERCENTILE: 98
IROC_SCORE: 0.999
IROC_PERCENTILE: 98
POISSON_SCORE: 0.6977
POISSON_PERCENTILE: 98
MAXIMUM_REPLICATE_CORRELATION: 1.0

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

ANALYSIS FILE NAME: GSM817169_UW.Penis_Foreskin_Fibroblast_Primary_Cells.ChromatinAccessibility.skin02.DS18252.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS18252.hg19.level.2.release.6
ANALYSIS TITLE: Raw Signal Density Graphs of Penis Foreskin Fibroblast Primary Cells Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from  Penis Foreskin Fibroblast Primary Cells, Donor skin02, Library DS18252 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.12652
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 6
BROWSER_TRACK_NAME: PFF DNase 02 52
BROWSER_TRACK_DESCRIPTION: UW Penis Foreskin Fibroblast Primary Cells DNase Hypersensitivity Donor skin02 Library DS18252 EA Release 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 32,169,657
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 63
FINDPEAKS_SCORE: 0.6688
FINDPEAKS_PERCENTILE: 98
HOTSPOT_SCORE: 0.7011
HOTSPOT_PERCENTILE: 98
IROC_SCORE: 0.999
IROC_PERCENTILE: 98
POISSON_SCORE: 0.6977
POISSON_PERCENTILE: 98
MAXIMUM_REPLICATE_CORRELATION: 1.0

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

source_name: Penis, Foreskin, Fibroblast Primary Cells skin02; DS18252

value: Penis, Foreskin, Fibroblast skin02

value: SFVAMC Dermatology

value: Primary Cell Culture

value: Fibroblast

tag: markers

value: Invitrogen 106 + LSGS

value: Neonate

value: Disease Free

tag: karyotype

tag: parity


title: Chromatin accessibility assay of Penis Foreskin Fibroblast Primary Cells; DS18256

description:
Design description: Chromatin accessibility determination via DNase-seq
Library name: DS18256
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.10116
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSF-UBC%2FSAMPLE%2FEDACC.9574
****************
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: GSM817170_UW.Penis_Foreskin_Fibroblast_Primary_Cells.ChromatinAccessibility.skin02.DS18256.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS18256.hg19.level.1.release.6
ANALYSIS TITLE: Mapping of Penis Foreskin Fibroblast Primary Cells Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Penis Foreskin Fibroblast Primary Cells, Donor skin02, Library DS18256 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.12590
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 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 39,717,304
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 63
FINDPEAKS_SCORE: 0.7582
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.7811
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.9991
IROC_PERCENTILE: 100
POISSON_SCORE: 0.7699
POISSON_PERCENTILE: 100
MAXIMUM_REPLICATE_CORRELATION: 1.0

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

ANALYSIS FILE NAME: GSM817170_UW.Penis_Foreskin_Fibroblast_Primary_Cells.ChromatinAccessibility.skin02.DS18256.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS18256.hg19.level.2.release.6
ANALYSIS TITLE: Raw Signal Density Graphs of Penis Foreskin Fibroblast Primary Cells Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from  Penis Foreskin Fibroblast Primary Cells, Donor skin02, Library DS18256 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.12653
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 6
BROWSER_TRACK_NAME: PFF DNase 02 56
BROWSER_TRACK_DESCRIPTION: UW Penis Foreskin Fibroblast Primary Cells DNase Hypersensitivity Donor skin02 Library DS18256 EA Release 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 39,717,304
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 63
FINDPEAKS_SCORE: 0.7582
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.7811
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.9991
IROC_PERCENTILE: 100
POISSON_SCORE: 0.7699
POISSON_PERCENTILE: 100
MAXIMUM_REPLICATE_CORRELATION: 1.0

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

source_name: Penis, Foreskin, Fibroblast Primary Cells skin02; DS18256

value: genomic DNA

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, Left; DS17959

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: DS17959
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.9935
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.9934
****************
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: GSM817168_UW.Fetal_Lung_Left.ChromatinAccessibility.H-24005.DS17959.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS17959.hg19.level.1.release.6
ANALYSIS TITLE: Mapping of Fetal Lung Left Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fetal Lung Left, Donor H-24005, Library DS17959 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.12588
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 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 34,799,769
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 63
FINDPEAKS_SCORE: 0.4634
FINDPEAKS_PERCENTILE: 75
HOTSPOT_SCORE: 0.455
HOTSPOT_PERCENTILE: 78
IROC_SCORE: 0.9938
IROC_PERCENTILE: 60
POISSON_SCORE: 0.5127
POISSON_PERCENTILE: 68
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

ANALYSIS FILE NAME: GSM817168_UW.Fetal_Lung_Left.ChromatinAccessibility.H-24005.DS17959.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS17959.hg19.level.2.release.6
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-24005, Library DS17959 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.12651
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 6
BROWSER_TRACK_NAME: FLL DNase 05 59
BROWSER_TRACK_DESCRIPTION: UW Fetal Lung Left DNase Hypersensitivity Donor H-24005 Library DS17959 EA Release 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 34,799,769
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 63
FINDPEAKS_SCORE: 0.4634
FINDPEAKS_PERCENTILE: 75
HOTSPOT_SCORE: 0.455
HOTSPOT_PERCENTILE: 78
IROC_SCORE: 0.9938
IROC_PERCENTILE: 60
POISSON_SCORE: 0.5127
POISSON_PERCENTILE: 68
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

source_name: Fetal Lung, Left primary tissue, day 105; DS17959

value: Fetal Lung, Left

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

value: Primary Tissue

value: UW

value: fetal

value: day 105


title: Chromatin accessibility assay of Fetal Lung, Left; DS18487

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: DS18487
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.9926
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.9925
****************
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: GSM817185_UW.Fetal_Lung_Left.ChromatinAccessibility.H-24111.DS18487.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS18487.hg19.level.1.release.6
ANALYSIS TITLE: Mapping of Fetal Lung Left Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fetal Lung Left, Donor H-24111, Library DS18487 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.12605
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 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 47,426,205
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 63
FINDPEAKS_SCORE: 0.4665
FINDPEAKS_PERCENTILE: 78
HOTSPOT_SCORE: 0.4477
HOTSPOT_PERCENTILE: 71
IROC_SCORE: 0.994
IROC_PERCENTILE: 65
POISSON_SCORE: 0.5409
POISSON_PERCENTILE: 87
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

ANALYSIS FILE NAME: GSM817185_UW.Fetal_Lung_Left.ChromatinAccessibility.H-24111.DS18487.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS18487.hg19.level.2.release.6
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-24111, Library DS18487 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.12668
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 6
BROWSER_TRACK_NAME: FLL DNase 11 87
BROWSER_TRACK_DESCRIPTION: UW Fetal Lung Left DNase Hypersensitivity Donor H-24111 Library DS18487 EA Release 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 47,426,205
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 63
FINDPEAKS_SCORE: 0.4665
FINDPEAKS_PERCENTILE: 78
HOTSPOT_SCORE: 0.4477
HOTSPOT_PERCENTILE: 71
IROC_SCORE: 0.994
IROC_PERCENTILE: 65
POISSON_SCORE: 0.5409
POISSON_PERCENTILE: 87
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

source_name: Fetal Lung, Left primary tissue, day 105; DS18487

value: Male

value: Chromatin Accessibility


title: Chromatin accessibility assay of Penis Foreskin Keratinocytes Primary Cells; DS18714

description:
sample_term_id: CL_1001606
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Chromatin accessibility determination via DNase-seq
Library name: DS18714
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.10105
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSF-UBC%2FSAMPLE%2FEDACC.9573
****************
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: GSM817196_UW.Penis_Foreskin_Keratinocyte_Primary_Cells.ChromatinAccessibility.skin02.DS18714.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS18714.hg19.level.1.release.6
ANALYSIS TITLE: Mapping of Penis Foreskin Keratinocyte Primary Cells Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Penis Foreskin Keratinocyte Primary Cells, Donor skin02, Library DS18714 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.12616
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 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 29,643,959
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 63
FINDPEAKS_SCORE: 0.4668
FINDPEAKS_PERCENTILE: 79
HOTSPOT_SCORE: 0.5003
HOTSPOT_PERCENTILE: 89
IROC_SCORE: 0.9972
IROC_PERCENTILE: 94
POISSON_SCORE: 0.5409
POISSON_PERCENTILE: 87
MAXIMUM_REPLICATE_CORRELATION: 0.0

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

ANALYSIS FILE NAME: GSM817196_UW.Penis_Foreskin_Keratinocyte_Primary_Cells.ChromatinAccessibility.skin02.DS18714.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS18714.hg19.level.2.release.6
ANALYSIS TITLE: Raw Signal Density Graphs of Penis Foreskin Keratinocyte Primary Cells Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from  Penis Foreskin Keratinocyte Primary Cells, Donor skin02, Library DS18714 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.12679
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 6
BROWSER_TRACK_NAME: PFK DNase 02 14
BROWSER_TRACK_DESCRIPTION: UW Penis Foreskin Keratinocyte Primary Cells DNase Hypersensitivity Donor skin02 Library DS18714 EA Release 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 29,643,959
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 63
FINDPEAKS_SCORE: 0.4668
FINDPEAKS_PERCENTILE: 79
HOTSPOT_SCORE: 0.5003
HOTSPOT_PERCENTILE: 89
IROC_SCORE: 0.9972
IROC_PERCENTILE: 94
POISSON_SCORE: 0.5409
POISSON_PERCENTILE: 87
MAXIMUM_REPLICATE_CORRELATION: 0.0

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

source_name: Penis, Foreskin, Keratinocyte Primary Cells skin02; DS18714

value: Penis, Foreskin, Keratinocyte skin02

value: SFVAMC Dermatology

value: Keratinocyte

value: Invitrogen 154CF + HKGS + .07mM Ca


title: Chromatin accessibility assay of Fetal Muscle, Leg; DS18471

description:
sample_term_id: UBERON_0001383
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Chromatin accessibility determination via DNase-seq
Library name: DS18471
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.9843
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.9842
****************
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: GSM817183_UW.Fetal_Muscle_Leg.ChromatinAccessibility.H-24111.DS18471.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS18471.hg19.level.1.release.6
ANALYSIS TITLE: Mapping of Fetal Muscle Leg Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fetal Muscle Leg, Donor H-24111, Library DS18471 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.12603
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 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 34,401,261
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 63
FINDPEAKS_SCORE: 0.4509
FINDPEAKS_PERCENTILE: 70
HOTSPOT_SCORE: 0.4384
HOTSPOT_PERCENTILE: 67
IROC_SCORE: 0.9937
IROC_PERCENTILE: 59
POISSON_SCORE: 0.5373
POISSON_PERCENTILE: 79
MAXIMUM_REPLICATE_CORRELATION: 0.97

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

ANALYSIS FILE NAME: GSM817183_UW.Fetal_Muscle_Leg.ChromatinAccessibility.H-24111.DS18471.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS18471.hg19.level.2.release.6
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Muscle Leg Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from  Fetal Muscle Leg, Donor H-24111, Library DS18471 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.12666
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 6
BROWSER_TRACK_NAME: FML DNase 11 71
BROWSER_TRACK_DESCRIPTION: UW Fetal Muscle Leg DNase Hypersensitivity Donor H-24111 Library DS18471 EA Release 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 34,401,261
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 63
FINDPEAKS_SCORE: 0.4509
FINDPEAKS_PERCENTILE: 70
HOTSPOT_SCORE: 0.4384
HOTSPOT_PERCENTILE: 67
IROC_SCORE: 0.9937
IROC_PERCENTILE: 59
POISSON_SCORE: 0.5373
POISSON_PERCENTILE: 79
MAXIMUM_REPLICATE_CORRELATION: 0.97

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

source_name: Fetal Muscle, Leg primary tissue, day 105; DS18471

value: Fetal Muscle, Leg


title: Chromatin accessibility assay of Fetal Muscle, Back; DS18468

description:
sample_term_id: UBERON_0002324
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Chromatin accessibility determination via DNase-seq
Library name: DS18468
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.9876
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.9875
****************
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: GSM817182_UW.Fetal_Muscle_Back.ChromatinAccessibility.H-24111.DS18468.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS18468.hg19.level.1.release.6
ANALYSIS TITLE: Mapping of Fetal Muscle Back Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fetal Muscle Back, Donor H-24111, Library DS18468 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.12602
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 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 32,484,515
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 63
FINDPEAKS_SCORE: 0.4416
FINDPEAKS_PERCENTILE: 67
HOTSPOT_SCORE: 0.429
HOTSPOT_PERCENTILE: 62
IROC_SCORE: 0.9937
IROC_PERCENTILE: 59
POISSON_SCORE: 0.5198
POISSON_PERCENTILE: 75
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

ANALYSIS FILE NAME: GSM817182_UW.Fetal_Muscle_Back.ChromatinAccessibility.H-24111.DS18468.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS18468.hg19.level.2.release.6
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Muscle Back Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from  Fetal Muscle Back, Donor H-24111, Library DS18468 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.12665
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 6
BROWSER_TRACK_NAME: FMB DNase 11 68
BROWSER_TRACK_DESCRIPTION: UW Fetal Muscle Back DNase Hypersensitivity Donor H-24111 Library DS18468 EA Release 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 32,484,515
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 63
FINDPEAKS_SCORE: 0.4416
FINDPEAKS_PERCENTILE: 67
HOTSPOT_SCORE: 0.429
HOTSPOT_PERCENTILE: 62
IROC_SCORE: 0.9937
IROC_PERCENTILE: 59
POISSON_SCORE: 0.5198
POISSON_PERCENTILE: 75
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

source_name: Fetal Muscle, Back primary tissue, day 105; DS18468

value: Fetal Muscle, Back


title: LtaP_WT_smallRNA

city: SEATTLE

first: Gowthaman

last: Ramasamy

state: WASHINGTON

address: 307 WESTLAKE AVE N

department: GHBC

institute: SEATTLE BIOMEDICAL RESEARCH INSTITUTE

library_source: transcriptomic

data_processing: Small RNA reads were trimmed to remove any Illumina adapter sequence present in the tail of the reads. All read data were aligned using the Burrow Wheeler Aligner (BWA) using the default parameters. ChIP-seq data were filtered to remove all reads with a mapping quality equal or less than 21. The small RNA data were filtered to remove the reads with a mapping quality value less than 37 or reads that aligned with mismatches. For all datasets, multimappers were discarded. SL RNA-seq reads were trimmed to remove the first three 5’ bases specific to the SL sequencing primer and subsequently mapped to their respective reference genomes using the BOWTIE (v0.12.1) short read aligner.  Mapping was set to M = -1 which assigns a multi-mapping read randomly to one of the sites within the genome. Samtools (v 0.1.8) was used to convert SAM output into BAM files. bamTobed command from BEDtools(v2.13.3) were used to create bed files from BAM files.

molecule: total RNA

organism: Leishmania tarentolae

source_name: mixed

growth_protocol: Leishmania were grown in SDM-79 medium until the culture reached a density of 108 cells/ml.

extract_protocol: Total RNA from was isolated from the stationary phase wild type L. tarentolae, L. tarentolae JBP2-/- (KO) and KO grown in BrdU (KO+BrdU) using TRIzol reagent (Invitrogen). 2 μg of total RNA was treated with RNase A or RNase T1 or both in a 25-μl reaction at 25oC. The RNA was purified with phenol-chloroform, ethanol precipitated and dissolved in 10 μl RNase-free water.The RNA from each sample was size separated in TBE gel and the 18-35 bp slices were cut and pulverized. The RNA was eluted, precipitated and ligated to the 5’ small RNA adapter 5’ GUUCAGAGUUCUACAGUCCGACGAUC  using T4 RNA ligase and a second size selection was performed to isolate the 40-65 bp fragments. The 3’ adapter 5’-P-UCGUAUGCCGUCUUCUGCUUGUidT was ligated using T4 RNA ligase followed by the third urea TBE gel to collect the 70-120 bp sized molecules that were reverse transcribed with SSII (Invitrogen) and the SRA RT primer 5’ CAAGCAGAAGACGGCATACGA followed by PCR amplification with Phusion polymerase enzyme (Finnzymes Oy) using Illumina primers (GX1: 5’ CAAGCAGAAGACGGCATACGA and GX2: 5’ AATGATACGGCGACCACCGACAGGTTCAGAGTTCTACAGTCCGA).

treatment_protocol: L. tarentolae JBP2 KO in 0.6 μM BrdU containing medium were grown for 5 days before harvesting.

tag: strain

value: Parrot

tag: developmental stage

value: mixed

tag: rna subtype

value: small RNA

tag: genotype/variation

value: WT


title: Chromatin accessibility assay of Fetal Lung, Right; DS18492

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: DS18492
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.9908
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.9907
****************
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: GSM817186_UW.Fetal_Lung_Right.ChromatinAccessibility.H-24111.DS18492.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS18492.hg19.level.1.release.6
ANALYSIS TITLE: Mapping of Fetal Lung Right Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fetal Lung Right, Donor H-24111, Library DS18492 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.12606
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 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 39,509,151
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 63
FINDPEAKS_SCORE: 0.4719
FINDPEAKS_PERCENTILE: 83
HOTSPOT_SCORE: 0.4544
HOTSPOT_PERCENTILE: 76
IROC_SCORE: 0.9942
IROC_PERCENTILE: 68
POISSON_SCORE: 0.5452
POISSON_PERCENTILE: 89
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

ANALYSIS FILE NAME: GSM817186_UW.Fetal_Lung_Right.ChromatinAccessibility.H-24111.DS18492.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS18492.hg19.level.2.release.6
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-24111, Library DS18492 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.12669
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 6
BROWSER_TRACK_NAME: FLR DNase 11 92
BROWSER_TRACK_DESCRIPTION: UW Fetal Lung Right DNase Hypersensitivity Donor H-24111 Library DS18492 EA Release 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 39,509,151
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 63
FINDPEAKS_SCORE: 0.4719
FINDPEAKS_PERCENTILE: 83
HOTSPOT_SCORE: 0.4544
HOTSPOT_PERCENTILE: 76
IROC_SCORE: 0.9942
IROC_PERCENTILE: 68
POISSON_SCORE: 0.5452
POISSON_PERCENTILE: 89
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

source_name: Fetal Lung, Right primary tissue, day 105; DS18492

value: Fetal Lung, Right

value: genomic DNA

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

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; DS17162

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: DS17162
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.9917
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.9916
****************
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: GSM817164_UW.Fetal_Lung_Right.ChromatinAccessibility.H-23758.DS17162.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS17162.hg19.level.1.release.6
ANALYSIS TITLE: Mapping of Fetal Lung Right Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fetal Lung Right, Donor H-23758, Library DS17162 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.12584
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 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 31,602,771
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 63
FINDPEAKS_SCORE: 0.5496
FINDPEAKS_PERCENTILE: 95
HOTSPOT_SCORE: 0.5383
HOTSPOT_PERCENTILE: 94
IROC_SCORE: 0.9949
IROC_PERCENTILE: 78
POISSON_SCORE: 0.6002
POISSON_PERCENTILE: 95
MAXIMUM_REPLICATE_CORRELATION: 0.99

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

ANALYSIS FILE NAME: GSM817164_UW.Fetal_Lung_Right.ChromatinAccessibility.H-23758.DS17162.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS17162.hg19.level.2.release.6
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-23758, Library DS17162 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.12647
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 6
BROWSER_TRACK_NAME: FLR DNase 58 62
BROWSER_TRACK_DESCRIPTION: UW Fetal Lung Right DNase Hypersensitivity Donor H-23758 Library DS17162 EA Release 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 31,602,771
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 63
FINDPEAKS_SCORE: 0.5496
FINDPEAKS_PERCENTILE: 95
HOTSPOT_SCORE: 0.5383
HOTSPOT_PERCENTILE: 94
IROC_SCORE: 0.9949
IROC_PERCENTILE: 78
POISSON_SCORE: 0.6002
POISSON_PERCENTILE: 95
MAXIMUM_REPLICATE_CORRELATION: 0.99

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

source_name: Fetal Lung, Right primary tissue, day 107; DS17162

value: Primary Tissue

value: UW

value: fetal

value: day 107

value: Female


title: Chromatin accessibility assay of Fetal Adrenal Gland; DS17319

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: DS17319
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.10074
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.10073
****************
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: GSM817165_UW.Fetal_Adrenal_Gland.ChromatinAccessibility.H-23769.DS17319.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS17319.hg19.level.1.release.6
ANALYSIS TITLE: Mapping of Fetal Adrenal Gland Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fetal Adrenal Gland, Donor H-23769, Library DS17319 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.12585
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 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 29,587,833
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 63
FINDPEAKS_SCORE: 0.2862
FINDPEAKS_PERCENTILE: 21
HOTSPOT_SCORE: 0.2905
HOTSPOT_PERCENTILE: 16
IROC_SCORE: 0.9955
IROC_PERCENTILE: 83
POISSON_SCORE: 0.3387
POISSON_PERCENTILE: 6
MAXIMUM_REPLICATE_CORRELATION: 0.9

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

ANALYSIS FILE NAME: GSM817165_UW.Fetal_Adrenal_Gland.ChromatinAccessibility.H-23769.DS17319.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS17319.hg19.level.2.release.6
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Adrenal Gland Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from  Fetal Adrenal Gland, Donor H-23769, Library DS17319 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.12648
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 6
BROWSER_TRACK_NAME: FAG DNase 69 19
BROWSER_TRACK_DESCRIPTION: UW Fetal Adrenal Gland DNase Hypersensitivity Donor H-23769 Library DS17319 EA Release 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 29,587,833
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 63
FINDPEAKS_SCORE: 0.2862
FINDPEAKS_PERCENTILE: 21
HOTSPOT_SCORE: 0.2905
HOTSPOT_PERCENTILE: 16
IROC_SCORE: 0.9955
IROC_PERCENTILE: 83
POISSON_SCORE: 0.3387
POISSON_PERCENTILE: 6
MAXIMUM_REPLICATE_CORRELATION: 0.9

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

source_name: Fetal Adrenal Gland primary tissue, day 108; DS17319

value: Fetal Adrenal Gland

value: day 108

value: Male

value: Chromatin Accessibility


title: Chromatin accessibility assay of Fetal Kidney, Left; DS18466

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: DS18466
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.10030
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.10029
****************
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: GSM817181_UW.Fetal_Kidney_Left.ChromatinAccessibility.H-24089.DS18466.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS18466.hg19.level.1.release.6
ANALYSIS TITLE: Mapping of Fetal Kidney Left Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fetal Kidney Left, Donor H-24089, Library DS18466 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.12601
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 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 35,582,244
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 63
FINDPEAKS_SCORE: 0.3079
FINDPEAKS_PERCENTILE: 25
HOTSPOT_SCORE: 0.3121
HOTSPOT_PERCENTILE: 29
IROC_SCORE: 0.9899
IROC_PERCENTILE: 21
POISSON_SCORE: 0.4154
POISSON_PERCENTILE: 37
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

ANALYSIS FILE NAME: GSM817181_UW.Fetal_Kidney_Left.ChromatinAccessibility.H-24089.DS18466.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS18466.hg19.level.2.release.6
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-24089, Library DS18466 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.12664
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 6
BROWSER_TRACK_NAME: FKL DNase 89 66
BROWSER_TRACK_DESCRIPTION: UW Fetal Kidney Left DNase Hypersensitivity Donor H-24089 Library DS18466 EA Release 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 35,582,244
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 63
FINDPEAKS_SCORE: 0.3079
FINDPEAKS_PERCENTILE: 25
HOTSPOT_SCORE: 0.3121
HOTSPOT_PERCENTILE: 29
IROC_SCORE: 0.9899
IROC_PERCENTILE: 21
POISSON_SCORE: 0.4154
POISSON_PERCENTILE: 37
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

source_name: Fetal Kidney, Left primary tissue, day 96; DS18466

value: Fetal Kidney, Left

value: day 96


title: Chromatin accessibility assay of Fetal Adrenal Gland; DS17677

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: DS17677
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.10068
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.10067
****************
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: GSM817167_UW.Fetal_Adrenal_Gland.ChromatinAccessibility.H-23887.DS17677.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS17677.hg19.level.1.release.6
ANALYSIS TITLE: Mapping of Fetal Adrenal Gland Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fetal Adrenal Gland, Donor H-23887, Library DS17677 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.12587
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 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 19,166,947
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 63
FINDPEAKS_SCORE: 0.2842
FINDPEAKS_PERCENTILE: 16
HOTSPOT_SCORE: 0.2842
HOTSPOT_PERCENTILE: 14
IROC_SCORE: 0.994
IROC_PERCENTILE: 65
POISSON_SCORE: 0.2862
POISSON_PERCENTILE: 3
MAXIMUM_REPLICATE_CORRELATION: 0.94

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

ANALYSIS FILE NAME: GSM817167_UW.Fetal_Adrenal_Gland.ChromatinAccessibility.H-23887.DS17677.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS17677.hg19.level.2.release.6
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Adrenal Gland Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from  Fetal Adrenal Gland, Donor H-23887, Library DS17677 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.12650
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 6
BROWSER_TRACK_NAME: FAG DNase 87 77
BROWSER_TRACK_DESCRIPTION: UW Fetal Adrenal Gland DNase Hypersensitivity Donor H-23887 Library DS17677 EA Release 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 19,166,947
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 63
FINDPEAKS_SCORE: 0.2842
FINDPEAKS_PERCENTILE: 16
HOTSPOT_SCORE: 0.2842
HOTSPOT_PERCENTILE: 14
IROC_SCORE: 0.994
IROC_PERCENTILE: 65
POISSON_SCORE: 0.2862
POISSON_PERCENTILE: 3
MAXIMUM_REPLICATE_CORRELATION: 0.94

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

source_name: Fetal Adrenal Gland primary tissue, day 108; DS17677


title: Chromatin accessibility assay of Fetal Muscle, Arm; DS18452

description:
sample_term_id: UBERON_0001499
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Chromatin accessibility determination via DNase-seq
Library name: DS18452
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.9904
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.9903
****************
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: GSM817178_UW.Fetal_Muscle_Arm.ChromatinAccessibility.H-24089.DS18452.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS18452.hg19.level.1.release.6
ANALYSIS TITLE: Mapping of Fetal Muscle Arm Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fetal Muscle Arm, Donor H-24089, Library DS18452 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.12598
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 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 38,955,084
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 63
FINDPEAKS_SCORE: 0.2993
FINDPEAKS_PERCENTILE: 22
HOTSPOT_SCORE: 0.2945
HOTSPOT_PERCENTILE: 21
IROC_SCORE: 0.9916
IROC_PERCENTILE: 30
POISSON_SCORE: 0.3965
POISSON_PERCENTILE: 25
MAXIMUM_REPLICATE_CORRELATION: 0.99

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

ANALYSIS FILE NAME: GSM817178_UW.Fetal_Muscle_Arm.ChromatinAccessibility.H-24089.DS18452.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS18452.hg19.level.2.release.6
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Muscle Arm Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from  Fetal Muscle Arm, Donor H-24089, Library DS18452 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.12661
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 6
BROWSER_TRACK_NAME: FMA DNase 89 52
BROWSER_TRACK_DESCRIPTION: UW Fetal Muscle Arm DNase Hypersensitivity Donor H-24089 Library DS18452 EA Release 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 38,955,084
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 63
FINDPEAKS_SCORE: 0.2993
FINDPEAKS_PERCENTILE: 22
HOTSPOT_SCORE: 0.2945
HOTSPOT_PERCENTILE: 21
IROC_SCORE: 0.9916
IROC_PERCENTILE: 30
POISSON_SCORE: 0.3965
POISSON_PERCENTILE: 25
MAXIMUM_REPLICATE_CORRELATION: 0.99

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

source_name: Fetal Muscle, Arm primary tissue, day 96; DS18452

value: Fetal Muscle, Arm


title: Chromatin accessibility assay of Fetal Kidney, Right; DS17144

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: DS17144
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.10126
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.10125
****************
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: GSM817163_UW.Fetal_Kidney_Right.ChromatinAccessibility.H-23758.DS17144.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS17144.hg19.level.1.release.6
ANALYSIS TITLE: Mapping of Fetal Kidney Right Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fetal Kidney Right, Donor H-23758, Library DS17144 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.12583
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 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 24,933,096
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 63
FINDPEAKS_SCORE: 0.4364
FINDPEAKS_PERCENTILE: 63
HOTSPOT_SCORE: 0.4323
HOTSPOT_PERCENTILE: 63
IROC_SCORE: 0.9944
IROC_PERCENTILE: 70
POISSON_SCORE: 0.4964
POISSON_PERCENTILE: 65
MAXIMUM_REPLICATE_CORRELATION: 0.89

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

ANALYSIS FILE NAME: GSM817163_UW.Fetal_Kidney_Right.ChromatinAccessibility.H-23758.DS17144.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS17144.hg19.level.2.release.6
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-23758, Library DS17144 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.12646
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 6
BROWSER_TRACK_NAME: FKR DNase 58 44
BROWSER_TRACK_DESCRIPTION: UW Fetal Kidney Right DNase Hypersensitivity Donor H-23758 Library DS17144 EA Release 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 24,933,096
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 63
FINDPEAKS_SCORE: 0.4364
FINDPEAKS_PERCENTILE: 63
HOTSPOT_SCORE: 0.4323
HOTSPOT_PERCENTILE: 63
IROC_SCORE: 0.9944
IROC_PERCENTILE: 70
POISSON_SCORE: 0.4964
POISSON_PERCENTILE: 65
MAXIMUM_REPLICATE_CORRELATION: 0.89

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

source_name: Fetal Kidney, Right primary tissue, day 107; DS17144

value: Fetal Kidney, Right


title: Chromatin accessibility assay of CD4 Primary Cells; DS17329

description:
sample_term_id: CL_0000837
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Chromatin accessibility determination via DNase-seq
Library name: DS17329
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.10083
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.10082
****************
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: GSM817166_UW.CD4_Primary_Cells.ChromatinAccessibility.RO_01689.DS17329.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS17329.hg19.level.1.release.6
ANALYSIS TITLE: Mapping of CD4 Primary Cells Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on CD4 Primary Cells, Donor RO 01689, Library DS17329 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.12586
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 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 31,254,527
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 63
FINDPEAKS_SCORE: 0.3096
FINDPEAKS_PERCENTILE: 27
HOTSPOT_SCORE: 0.3171
HOTSPOT_PERCENTILE: 30
IROC_SCORE: 0.9802
IROC_PERCENTILE: 3
POISSON_SCORE: 0.3748
POISSON_PERCENTILE: 19
MAXIMUM_REPLICATE_CORRELATION: 0.93

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

ANALYSIS FILE NAME: GSM817166_UW.CD4_Primary_Cells.ChromatinAccessibility.RO_01689.DS17329.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS17329.hg19.level.2.release.6
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 01689, Library DS17329 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.12649
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 6
BROWSER_TRACK_NAME: CD4 DNase 89 29
BROWSER_TRACK_DESCRIPTION: UW CD4 Primary Cells DNase Hypersensitivity Donor RO 01689 Library DS17329 EA Release 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 31,254,527
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 63
FINDPEAKS_SCORE: 0.3096
FINDPEAKS_PERCENTILE: 27
HOTSPOT_SCORE: 0.3171
HOTSPOT_PERCENTILE: 30
IROC_SCORE: 0.9802
IROC_PERCENTILE: 3
POISSON_SCORE: 0.3748
POISSON_PERCENTILE: 19
MAXIMUM_REPLICATE_CORRELATION: 0.93

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

source_name: flow sorted CD4+ Cells, year 34; DS17329

value: Mobilized CD4 Primary Cells

value: genomic DNA

value: FHCRC HEIMFELD

value: Primary Cell

value: CD4 Primary Cells

value: year 34

value: Caucasian


title: Chromatin accessibility assay of Fetal Muscle, Leg; DS18456

description:
sample_term_id: UBERON_0001383
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Chromatin accessibility determination via DNase-seq
Library name: DS18456
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.9847
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.9846
****************
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: GSM817179_UW.Fetal_Muscle_Leg.ChromatinAccessibility.H-24089.DS18456.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS18456.hg19.level.1.release.6
ANALYSIS TITLE: Mapping of Fetal Muscle Leg Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fetal Muscle Leg, Donor H-24089, Library DS18456 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.12599
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 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 37,943,763
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 63
FINDPEAKS_SCORE: 0.3114
FINDPEAKS_PERCENTILE: 29
HOTSPOT_SCORE: 0.3095
HOTSPOT_PERCENTILE: 27
IROC_SCORE: 0.9911
IROC_PERCENTILE: 27
POISSON_SCORE: 0.4101
POISSON_PERCENTILE: 33
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

ANALYSIS FILE NAME: GSM817179_UW.Fetal_Muscle_Leg.ChromatinAccessibility.H-24089.DS18456.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS18456.hg19.level.2.release.6
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Muscle Leg Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from  Fetal Muscle Leg, Donor H-24089, Library DS18456 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.12662
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 6
BROWSER_TRACK_NAME: FML DNase 89 56
BROWSER_TRACK_DESCRIPTION: UW Fetal Muscle Leg DNase Hypersensitivity Donor H-24089 Library DS18456 EA Release 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 37,943,763
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 63
FINDPEAKS_SCORE: 0.3114
FINDPEAKS_PERCENTILE: 29
HOTSPOT_SCORE: 0.3095
HOTSPOT_PERCENTILE: 27
IROC_SCORE: 0.9911
IROC_PERCENTILE: 27
POISSON_SCORE: 0.4101
POISSON_PERCENTILE: 33
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

source_name: Fetal Muscle, Leg primary tissue, day 96; DS18456

value: Fetal Muscle, Leg

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

value: Primary Tissue

value: UW

value: fetal

value: Qiagen minElut

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


title: Chromatin accessibility assay of Fetal Intestine, Large; DS17094

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: DS17094
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.10051
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.10050
****************
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: GSM817162_UW.Fetal_Intestine_Large.ChromatinAccessibility.H-23744.DS17094.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS17094.hg19.level.1.release.6
ANALYSIS TITLE: Mapping of Fetal Intestine Large Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fetal Intestine Large, Donor H-23744, Library DS17094 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.12582
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 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 35,367,475
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 63
FINDPEAKS_SCORE: 0.3307
FINDPEAKS_PERCENTILE: 33
HOTSPOT_SCORE: 0.3256
HOTSPOT_PERCENTILE: 35
IROC_SCORE: 0.9954
IROC_PERCENTILE: 81
POISSON_SCORE: 0.3898
POISSON_PERCENTILE: 21
MAXIMUM_REPLICATE_CORRELATION: 1.0

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

ANALYSIS FILE NAME: GSM817162_UW.Fetal_Intestine_Large.ChromatinAccessibility.H-23744.DS17094.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS17094.hg19.level.2.release.6
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-23744, Library DS17094 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.12645
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 6
BROWSER_TRACK_NAME: FIL DNase 44 94
BROWSER_TRACK_DESCRIPTION: UW Fetal Intestine Large DNase Hypersensitivity Donor H-23744 Library DS17094 EA Release 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 35,367,475
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 63
FINDPEAKS_SCORE: 0.3307
FINDPEAKS_PERCENTILE: 33
HOTSPOT_SCORE: 0.3256
HOTSPOT_PERCENTILE: 35
IROC_SCORE: 0.9954
IROC_PERCENTILE: 81
POISSON_SCORE: 0.3898
POISSON_PERCENTILE: 21
MAXIMUM_REPLICATE_CORRELATION: 1.0

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

source_name: Fetal Intestine, Large primary tissue, day 91; DS17094

value: Fetal Intestine, Large

value: day 91

value: Female

value: Chromatin Accessibility


title: Chromatin accessibility assay of Fetal Lung, Right; DS18418

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: DS18418
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.9912
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.9911
****************
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: GSM817174_UW.Fetal_Lung_Right.ChromatinAccessibility.H-24089.DS18418.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS18418.hg19.level.1.release.6
ANALYSIS TITLE: Mapping of Fetal Lung Right Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fetal Lung Right, Donor H-24089, Library DS18418 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.12594
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 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 42,846,401
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 63
FINDPEAKS_SCORE: 0.3646
FINDPEAKS_PERCENTILE: 46
HOTSPOT_SCORE: 0.3447
HOTSPOT_PERCENTILE: 43
IROC_SCORE: 0.9912
IROC_PERCENTILE: 29
POISSON_SCORE: 0.4423
POISSON_PERCENTILE: 49
MAXIMUM_REPLICATE_CORRELATION: 0.95

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

ANALYSIS FILE NAME: GSM817174_UW.Fetal_Lung_Right.ChromatinAccessibility.H-24089.DS18418.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS18418.hg19.level.2.release.6
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-24089, Library DS18418 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.12657
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 6
BROWSER_TRACK_NAME: FLR DNase 89 18
BROWSER_TRACK_DESCRIPTION: UW Fetal Lung Right DNase Hypersensitivity Donor H-24089 Library DS18418 EA Release 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 42,846,401
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 63
FINDPEAKS_SCORE: 0.3646
FINDPEAKS_PERCENTILE: 46
HOTSPOT_SCORE: 0.3447
HOTSPOT_PERCENTILE: 43
IROC_SCORE: 0.9912
IROC_PERCENTILE: 29
POISSON_SCORE: 0.4423
POISSON_PERCENTILE: 49
MAXIMUM_REPLICATE_CORRELATION: 0.95

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

source_name: Fetal Lung, Right primary tissue, day 96; DS18418

value: Fetal Lung, Right

value: genomic DNA

value: day 96

value: Male


title: Chromatin accessibility assay of Fetal Intestine, Small; DS16975

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: DS16975
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.10043
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.10042
****************
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: GSM817161_UW.Fetal_Intestine_Small.ChromatinAccessibility.H-23724.DS16975.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS16975.hg19.level.1.release.6
ANALYSIS TITLE: Mapping of Fetal Intestine Small Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fetal Intestine Small, Donor H-23724, Library DS16975 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.12581
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 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 29,393,256
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 63
FINDPEAKS_SCORE: 0.443
FINDPEAKS_PERCENTILE: 68
HOTSPOT_SCORE: 0.4412
HOTSPOT_PERCENTILE: 68
IROC_SCORE: 0.9959
IROC_PERCENTILE: 87
POISSON_SCORE: 0.4821
POISSON_PERCENTILE: 62
MAXIMUM_REPLICATE_CORRELATION: 0.99

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

ANALYSIS FILE NAME: GSM817161_UW.Fetal_Intestine_Small.ChromatinAccessibility.H-23724.DS16975.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS16975.hg19.level.2.release.6
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-23724, Library DS16975 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.12644
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 6
BROWSER_TRACK_NAME: FIS DNase 24 75
BROWSER_TRACK_DESCRIPTION: UW Fetal Intestine Small DNase Hypersensitivity Donor H-23724 Library DS16975 EA Release 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 29,393,256
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 63
FINDPEAKS_SCORE: 0.443
FINDPEAKS_PERCENTILE: 68
HOTSPOT_SCORE: 0.4412
HOTSPOT_PERCENTILE: 68
IROC_SCORE: 0.9959
IROC_PERCENTILE: 87
POISSON_SCORE: 0.4821
POISSON_PERCENTILE: 62
MAXIMUM_REPLICATE_CORRELATION: 0.99

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

source_name: Fetal Intestine, Small primary tissue, day 87; DS16975

value: Fetal Intestine, Small

value: day 87


title: Chromatin accessibility assay of Moblized CD8 Primary Cells; DS16962

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: DS16962
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.9862
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.9861
****************
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: GSM817160_UW.Mobilized_CD8_Primary_Cells.ChromatinAccessibility.RO_01679.DS16962.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS16962.hg19.level.1.release.6
ANALYSIS TITLE: Mapping of Mobilized CD8 Primary Cells Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Mobilized CD8 Primary Cells, Donor RO 01679, Library DS16962 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.12580
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 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 24,581,088
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 63
FINDPEAKS_SCORE: 0.3507
FINDPEAKS_PERCENTILE: 41
HOTSPOT_SCORE: 0.3773
HOTSPOT_PERCENTILE: 54
IROC_SCORE: 0.9957
IROC_PERCENTILE: 84
POISSON_SCORE: 0.4183
POISSON_PERCENTILE: 38
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM817160_UW.Mobilized_CD8_Primary_Cells.ChromatinAccessibility.RO_01679.DS16962.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS16962.hg19.level.2.release.6
ANALYSIS TITLE: Raw Signal Density Graphs of Mobilized CD8 Primary Cells Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from  Mobilized CD8 Primary Cells, Donor RO 01679, Library DS16962 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.12643
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 6
BROWSER_TRACK_NAME: MCD8 DNase 79 62
BROWSER_TRACK_DESCRIPTION: UW Mobilized CD8 Primary Cells DNase Hypersensitivity Donor RO 01679 Library DS16962 EA Release 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 24,581,088
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 63
FINDPEAKS_SCORE: 0.3507
FINDPEAKS_PERCENTILE: 41
HOTSPOT_SCORE: 0.3773
HOTSPOT_PERCENTILE: 54
IROC_SCORE: 0.9957
IROC_PERCENTILE: 84
POISSON_SCORE: 0.4183
POISSON_PERCENTILE: 38
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: flow sorted CD8+ Primary Cells, Mobilized, year 21; DS16962

value: Mobilized CD8 Primary Cells

value: FHCRC HEIMFELD

value: Primary Cell

value: year 21

value: Caucasian