title: Chromatin accessibility assay of Fetal Intestine, Small; DS17844

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: DS17844
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.8405
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.8404
****************
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: GSM774229_UW.Fetal_Intestine_Small.ChromatinAccessibility.H-23864.DS17844.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS17844.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of Fetal Intestine Small Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fetal Intestine Small, Donor H-23864, Library DS17844 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.10377
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 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 35,340,931
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 47
FINDPEAKS_SCORE: 0.4016
FINDPEAKS_PERCENTILE: 43
HOTSPOT_SCORE: 0.4043
HOTSPOT_PERCENTILE: 43
IROC_SCORE: 0.9948
IROC_PERCENTILE: 66
POISSON_SCORE: 0.4408
POISSON_PERCENTILE: 38
MAXIMUM_REPLICATE_CORRELATION: 0.99

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

ANALYSIS FILE NAME: GSM774229_UW.Fetal_Intestine_Small.ChromatinAccessibility.H-23864.DS17844.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS17844.hg19.level.2.release.5
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-23864, Library DS17844 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.10330
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 5
BROWSER_TRACK_NAME: FIS DNase 64 44
BROWSER_TRACK_DESCRIPTION: UW Fetal Intestine Small DNase Hypersensitivity Donor H-23864 Library DS17844 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 35,340,931
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 47
FINDPEAKS_SCORE: 0.4016
FINDPEAKS_PERCENTILE: 43
HOTSPOT_SCORE: 0.4043
HOTSPOT_PERCENTILE: 43
IROC_SCORE: 0.9948
IROC_PERCENTILE: 66
POISSON_SCORE: 0.4408
POISSON_PERCENTILE: 38
MAXIMUM_REPLICATE_CORRELATION: 0.99

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

source_name: Fetal Intestine, Small primary tissue, day 98; DS17844

value: Fetal Intestine, Small


title: Chromatin accessibility assay of Fetal Intestine, Large; DS17841

status: Public on Aug 06 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: DS17841
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.8431
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.8430
****************
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: GSM774228_UW.Fetal_Intestine_Large.ChromatinAccessibility.H-23964.DS17841.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS17841.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of Fetal Intestine Large Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fetal Intestine Large, Donor H-23964, Library DS17841 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.10376
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 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 82,113,249
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 47
FINDPEAKS_SCORE: 0.4382
FINDPEAKS_PERCENTILE: 53
HOTSPOT_SCORE: 0.4457
HOTSPOT_PERCENTILE: 55
IROC_SCORE: 0.9908
IROC_PERCENTILE: 23
POISSON_SCORE: 0.49
POISSON_PERCENTILE: 51
MAXIMUM_REPLICATE_CORRELATION: 0.99

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

ANALYSIS FILE NAME: GSM774228_UW.Fetal_Intestine_Large.ChromatinAccessibility.H-23964.DS17841.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS17841.hg19.level.2.release.5
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-23964, Library DS17841 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.10329
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 5
BROWSER_TRACK_NAME: FIL DNase 64 41
BROWSER_TRACK_DESCRIPTION: UW Fetal Intestine Large DNase Hypersensitivity Donor H-23964 Library DS17841 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 82,113,249
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 47
FINDPEAKS_SCORE: 0.4382
FINDPEAKS_PERCENTILE: 53
HOTSPOT_SCORE: 0.4457
HOTSPOT_PERCENTILE: 55
IROC_SCORE: 0.9908
IROC_PERCENTILE: 23
POISSON_SCORE: 0.49
POISSON_PERCENTILE: 51
MAXIMUM_REPLICATE_CORRELATION: 0.99

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

molecule: genomic DNA

organism: Homo sapiens

source_name: Fetal Intestine, Large primary tissue, day 98; DS17841

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: day 98

value: Female

value: Chromatin Accessibility

value: Qiagen minElut

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


title: MOLF backcross animal 4547

city: Rockville

first: Ying

last: Hu

email: yhu@mail.nih.gov, hunterk@mail.nih.gov

state: MD

address: 9609 Medical Center Dr.

department: NCI/CCR

institute: NIH

description: mean insert size : 256.3

library_source: transcriptomic

data_processing: Illumina software pipeline ( Basecalls was done by using Illumina RTA 1.6 for GAIIx run, RTA 1.7 for HiSeq run , Alignment was done by using Illumina CASAVA1.6, CASAVA_v1.7.0 pipelines)

molecule: total RNA

organism: Mus musculus

source_name: PyMT-induced mammary tumor

extract_protocol: Illumina mRNA Library Preparation Protocol  (Total RNA extracted from mammary tissue, Purify mRNA by poly-A selection, Fragment mRNA, Synthesize the First Strand cDNA, Synthesize the Second Strand cDNA, Perform End Repair, Adenylate 3' ends, Ligate the Adapters, Purify the cDNA Templates on a gel to select a size range)

tag: strain background

value: ((MOLF x PyMT) x FVB) backcross animal

tag: tissue

value: MOLF x PyMT backcross mammary tumor


title: MOLF backcross animal 4638

description: mean insert size : 267.1


title: Chromatin accessibility assay of Fetal Intestine, Small; DS17808

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: DS17808
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.8409
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.8408
****************
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: GSM774225_UW.Fetal_Intestine_Small.ChromatinAccessibility.H-23941.DS17808.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS17808.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of Fetal Intestine Small Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fetal Intestine Small, Donor H-23941, Library DS17808 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.10360
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 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 63,889,357
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 47
FINDPEAKS_SCORE: 0.3403
FINDPEAKS_PERCENTILE: 23
HOTSPOT_SCORE: 0.3294
HOTSPOT_PERCENTILE: 23
IROC_SCORE: 0.9951
IROC_PERCENTILE: 68
POISSON_SCORE: 0.3781
POISSON_PERCENTILE: 21
MAXIMUM_REPLICATE_CORRELATION: 0.99

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

ANALYSIS FILE NAME: GSM774225_UW.Fetal_Intestine_Small.ChromatinAccessibility.H-23941.DS17808.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS17808.hg19.level.2.release.5
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-23941, Library DS17808 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.10313
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 5
BROWSER_TRACK_NAME: FIS DNase 41 08
BROWSER_TRACK_DESCRIPTION: UW Fetal Intestine Small DNase Hypersensitivity Donor H-23941 Library DS17808 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 63,889,357
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 47
FINDPEAKS_SCORE: 0.3403
FINDPEAKS_PERCENTILE: 23
HOTSPOT_SCORE: 0.3294
HOTSPOT_PERCENTILE: 23
IROC_SCORE: 0.9951
IROC_PERCENTILE: 68
POISSON_SCORE: 0.3781
POISSON_PERCENTILE: 21
MAXIMUM_REPLICATE_CORRELATION: 0.99

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

source_name: Fetal Intestine, Small primary tissue, day 120; DS17808

value: day 120


title: Chromatin accessibility assay of Fetal Muscle, Back; DS17767

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: DS17767
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.8378
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.8377
****************
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: GSM774224_UW.Fetal_Muscle_Back.ChromatinAccessibility.H-23914.DS17767.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS17767.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of Fetal Muscle Back Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fetal Muscle Back, Donor H-23914, Library DS17767 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.10386
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 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 74,672,932
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 47
FINDPEAKS_SCORE: 0.497
FINDPEAKS_PERCENTILE: 81
HOTSPOT_SCORE: 0.4773
HOTSPOT_PERCENTILE: 68
IROC_SCORE: 0.9933
IROC_PERCENTILE: 45
POISSON_SCORE: 0.5572
POISSON_PERCENTILE: 83
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

ANALYSIS FILE NAME: GSM774224_UW.Fetal_Muscle_Back.ChromatinAccessibility.H-23914.DS17767.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS17767.hg19.level.2.release.5
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-23914, Library DS17767 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.10339
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 5
BROWSER_TRACK_NAME: FMB DNase 14 67
BROWSER_TRACK_DESCRIPTION: UW Fetal Muscle Back DNase Hypersensitivity Donor H-23914 Library DS17767 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 74,672,932
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 47
FINDPEAKS_SCORE: 0.497
FINDPEAKS_PERCENTILE: 81
HOTSPOT_SCORE: 0.4773
HOTSPOT_PERCENTILE: 68
IROC_SCORE: 0.9933
IROC_PERCENTILE: 45
POISSON_SCORE: 0.5572
POISSON_PERCENTILE: 83
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

source_name: Fetal Muscle, Back primary tissue, day 91; DS17767

value: Fetal Muscle, Back

value: day 91

value: Male


title: Chromatin accessibility assay of Fetal Muscle, Arm; DS17765

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: DS17765
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.8513
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.8512
****************
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: GSM774223_UW.Fetal_Muscle_Arm.ChromatinAccessibility.H-23914.DS17765.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS17765.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of Fetal Muscle Arm Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fetal Muscle Arm, Donor H-23914, Library DS17765 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.10385
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 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 91,704,270
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 47
FINDPEAKS_SCORE: 0.4788
FINDPEAKS_PERCENTILE: 64
HOTSPOT_SCORE: 0.5029
HOTSPOT_PERCENTILE: 81
IROC_SCORE: 0.987
IROC_PERCENTILE: 4
POISSON_SCORE: 0.5295
POISSON_PERCENTILE: 64
MAXIMUM_REPLICATE_CORRELATION: 0.99

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

ANALYSIS FILE NAME: GSM774223_UW.Fetal_Muscle_Arm.ChromatinAccessibility.H-23914.DS17765.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS17765.hg19.level.2.release.5
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-23914, Library DS17765 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.10338
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 5
BROWSER_TRACK_NAME: FMA DNase 14 65
BROWSER_TRACK_DESCRIPTION: UW Fetal Muscle Arm DNase Hypersensitivity Donor H-23914 Library DS17765 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 91,704,270
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 47
FINDPEAKS_SCORE: 0.4788
FINDPEAKS_PERCENTILE: 64
HOTSPOT_SCORE: 0.5029
HOTSPOT_PERCENTILE: 81
IROC_SCORE: 0.987
IROC_PERCENTILE: 4
POISSON_SCORE: 0.5295
POISSON_PERCENTILE: 64
MAXIMUM_REPLICATE_CORRELATION: 0.99

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

source_name: Fetal Muscle, Arm primary tissue, day 91; DS17765

value: Fetal Muscle, Arm


title: Chromatin accessibility assay of Fetal Renal Pelvis; DS17760

description:
sample_term_id: UBERON_0001224
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Chromatin accessibility determination via DNase-seq
Library name: DS17760
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.8353
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.8352
****************
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: GSM774222_UW.Fetal_Renal_Pelvis.ChromatinAccessibility.H-23914.DS17760.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS17760.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of Fetal Renal Pelvis Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fetal Renal Pelvis, Donor H-23914, Library DS17760 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.10384
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 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 38,704,326
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 47
FINDPEAKS_SCORE: 0.4329
FINDPEAKS_PERCENTILE: 51
HOTSPOT_SCORE: 0.4305
HOTSPOT_PERCENTILE: 51
IROC_SCORE: 0.9881
IROC_PERCENTILE: 9
POISSON_SCORE: 0.4812
POISSON_PERCENTILE: 49
MAXIMUM_REPLICATE_CORRELATION: 0.92

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

ANALYSIS FILE NAME: GSM774222_UW.Fetal_Renal_Pelvis.ChromatinAccessibility.H-23914.DS17760.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS17760.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Renal Pelvis Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from  Fetal Renal Pelvis, Donor H-23914, Library DS17760 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.10337
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 5
BROWSER_TRACK_NAME: FRP DNase 14 60
BROWSER_TRACK_DESCRIPTION: UW Fetal Renal Pelvis DNase Hypersensitivity Donor H-23914 Library DS17760 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 38,704,326
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 47
FINDPEAKS_SCORE: 0.4329
FINDPEAKS_PERCENTILE: 51
HOTSPOT_SCORE: 0.4305
HOTSPOT_PERCENTILE: 51
IROC_SCORE: 0.9881
IROC_PERCENTILE: 9
POISSON_SCORE: 0.4812
POISSON_PERCENTILE: 49
MAXIMUM_REPLICATE_CORRELATION: 0.92

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

source_name: Fetal Kidney, renal, pelvis primary tissue, day 91; DS17760

value: Fetal Renal Pelvis

value: genomic DNA


title: Chromatin accessibility assay of Fetal Intestine, Large; DS17748

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: DS17748
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.8435
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.8434
****************
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: GSM774220_UW.Fetal_Intestine_Large.ChromatinAccessibility.H-23914.DS17748.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS17748.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of Fetal Intestine Large Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fetal Intestine Large, Donor H-23914, Library DS17748 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.10397
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 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 21,330,603
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 47
FINDPEAKS_SCORE: 0.4594
FINDPEAKS_PERCENTILE: 57
HOTSPOT_SCORE: 0.4634
HOTSPOT_PERCENTILE: 60
IROC_SCORE: 0.9967
IROC_PERCENTILE: 89
POISSON_SCORE: 0.5061
POISSON_PERCENTILE: 55
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

ANALYSIS FILE NAME: GSM774220_UW.Fetal_Intestine_Large.ChromatinAccessibility.H-23914.DS17748.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS17748.hg19.level.2.release.5
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-23914, Library DS17748 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.10350
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 5
BROWSER_TRACK_NAME: FIL DNase 14 48
BROWSER_TRACK_DESCRIPTION: UW Fetal Intestine Large DNase Hypersensitivity Donor H-23914 Library DS17748 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 21,330,603
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 47
FINDPEAKS_SCORE: 0.4594
FINDPEAKS_PERCENTILE: 57
HOTSPOT_SCORE: 0.4634
HOTSPOT_PERCENTILE: 60
IROC_SCORE: 0.9967
IROC_PERCENTILE: 89
POISSON_SCORE: 0.5061
POISSON_PERCENTILE: 55
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

source_name: Fetal Intestine, Large primary tissue, day 91; DS17748

value: Fetal Intestine, Large

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

value: Primary Tissue


title: Chromatin accessibility assay of Fetal Muscle, Arm; DS17825

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: DS17825
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.8509
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.8508
****************
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: GSM774226_UW.Fetal_Muscle_Arm.ChromatinAccessibility.H-23941.DS17825.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS17825.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of Fetal Muscle Arm Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fetal Muscle Arm, Donor H-23941, Library DS17825 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.10392
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 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 39,596,842
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 47
FINDPEAKS_SCORE: 0.4578
FINDPEAKS_PERCENTILE: 55
HOTSPOT_SCORE: 0.4585
HOTSPOT_PERCENTILE: 57
IROC_SCORE: 0.9893
IROC_PERCENTILE: 11
POISSON_SCORE: 0.5133
POISSON_PERCENTILE: 57
MAXIMUM_REPLICATE_CORRELATION: 0.99

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

ANALYSIS FILE NAME: GSM774226_UW.Fetal_Muscle_Arm.ChromatinAccessibility.H-23941.DS17825.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS17825.hg19.level.2.release.5
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-23941, Library DS17825 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.10345
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 5
BROWSER_TRACK_NAME: FMA DNase 41 25
BROWSER_TRACK_DESCRIPTION: UW Fetal Muscle Arm DNase Hypersensitivity Donor H-23941 Library DS17825 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 39,596,842
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 47
FINDPEAKS_SCORE: 0.4578
FINDPEAKS_PERCENTILE: 55
HOTSPOT_SCORE: 0.4585
HOTSPOT_PERCENTILE: 57
IROC_SCORE: 0.9893
IROC_PERCENTILE: 11
POISSON_SCORE: 0.5133
POISSON_PERCENTILE: 57
MAXIMUM_REPLICATE_CORRELATION: 0.99

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

source_name: Fetal Muscle, Arm primary tissue, day 120; DS17825

value: UW

value: fetal


title: Chromatin accessibility assay of Fetal Kidney; DS17753

description:
sample_term_id: UBERON_0002113
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Chromatin accessibility determination via DNase-seq
Library name: DS17753
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.8362
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.15169
****************
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: GSM774221_UW.Fetal_Kidney.ChromatinAccessibility.H-23887.DS17753.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS17753.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of Fetal Kidney Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fetal Kidney, Donor H-23887, Library DS17753 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.10391
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 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 24,709,416
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 47
FINDPEAKS_SCORE: 0.4296
FINDPEAKS_PERCENTILE: 49
HOTSPOT_SCORE: 0.4282
HOTSPOT_PERCENTILE: 47
IROC_SCORE: 0.9929
IROC_PERCENTILE: 40
POISSON_SCORE: 0.5011
POISSON_PERCENTILE: 53
MAXIMUM_REPLICATE_CORRELATION: 0.95

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

ANALYSIS FILE NAME: GSM774221_UW.Fetal_Kidney.ChromatinAccessibility.H-23887.DS17753.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS17753.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Kidney Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from  Fetal Kidney, Donor H-23887, Library DS17753 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.10344
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 5
BROWSER_TRACK_NAME: FK DNase 14 53
BROWSER_TRACK_DESCRIPTION: UW Fetal Kidney DNase Hypersensitivity Donor H-23887 Library DS17753 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 24,709,416
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 47
FINDPEAKS_SCORE: 0.4296
FINDPEAKS_PERCENTILE: 49
HOTSPOT_SCORE: 0.4282
HOTSPOT_PERCENTILE: 47
IROC_SCORE: 0.9929
IROC_PERCENTILE: 40
POISSON_SCORE: 0.5011
POISSON_PERCENTILE: 53
MAXIMUM_REPLICATE_CORRELATION: 0.95

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

source_name: Fetal Kidney primary tissue, day 108; DS17753

value: Fetal Kidney

value: day 108

value: Female

value: Chromatin Accessibility


title: MOLF backcross animal 4438

description: mean insert size : 267.2

value: ((MOLF x PyMT) x FVB) backcross animal

value: MOLF x PyMT backcross mammary tumor


title: Chromatin accessibility assay of Fetal Muscle, Upper Trunk; DS17664

description:
sample_term_id: UBERON_0001774
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Chromatin accessibility determination via DNase-seq
Library name: DS17664
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.9485
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.9484
****************
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: GSM774218_UW.Fetal_Muscle_Upper_Trunk.ChromatinAccessibility.H-23887.DS17664.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS17664.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of Fetal Muscle Upper Trunk Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fetal Muscle Upper Trunk, Donor H-23887, Library DS17664 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.10358
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 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 44,623,752
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 47
FINDPEAKS_SCORE: 0.49
FINDPEAKS_PERCENTILE: 72
HOTSPOT_SCORE: 0.4746
HOTSPOT_PERCENTILE: 66
IROC_SCORE: 0.993
IROC_PERCENTILE: 43
POISSON_SCORE: 0.5312
POISSON_PERCENTILE: 66
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM774218_UW.Fetal_Muscle_Upper_Trunk.ChromatinAccessibility.H-23887.DS17664.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS17664.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Muscle Upper Trunk Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from  Fetal Muscle Upper Trunk, Donor H-23887, Library DS17664 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.10311
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 5
BROWSER_TRACK_NAME: FMUT DNase 87 64
BROWSER_TRACK_DESCRIPTION: UW Fetal Muscle Upper Trunk DNase Hypersensitivity Donor H-23887 Library DS17664 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 44,623,752
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 47
FINDPEAKS_SCORE: 0.49
FINDPEAKS_PERCENTILE: 72
HOTSPOT_SCORE: 0.4746
HOTSPOT_PERCENTILE: 66
IROC_SCORE: 0.993
IROC_PERCENTILE: 43
POISSON_SCORE: 0.5312
POISSON_PERCENTILE: 66
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: Fetal Muscle, Upper, trunk primary tissue, day 108; DS17664

value: Fetal Muscle, Upper Trunk

value: Qiagen minElut

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


title: MOLF backcross animal 4516

description: mean insert size : 272.6


title: MOLF backcross animal 4378

description: mean insert size : 256.9


title: Chromatin accessibility assay of Fetal Intestine, Small; DS17643

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: DS17643
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.8413
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.8412
****************
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: GSM774216_UW.Fetal_Intestine_Small.ChromatinAccessibility.H-23887.DS17643.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS17643.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of Fetal Intestine Small Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fetal Intestine Small, Donor H-23887, Library DS17643 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.10374
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 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 46,159,547
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 47
FINDPEAKS_SCORE: 0.2837
FINDPEAKS_PERCENTILE: 9
HOTSPOT_SCORE: 0.2817
HOTSPOT_PERCENTILE: 9
IROC_SCORE: 0.9944
IROC_PERCENTILE: 53
POISSON_SCORE: 0.346
POISSON_PERCENTILE: 9
MAXIMUM_REPLICATE_CORRELATION: 0.99

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

ANALYSIS FILE NAME: GSM774216_UW.Fetal_Intestine_Small.ChromatinAccessibility.H-23887.DS17643.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS17643.hg19.level.2.release.5
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-23887, Library DS17643 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.10327
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 5
BROWSER_TRACK_NAME: FIS DNase 87 43
BROWSER_TRACK_DESCRIPTION: UW Fetal Intestine Small DNase Hypersensitivity Donor H-23887 Library DS17643 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 46,159,547
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 47
FINDPEAKS_SCORE: 0.2837
FINDPEAKS_PERCENTILE: 9
HOTSPOT_SCORE: 0.2817
HOTSPOT_PERCENTILE: 9
IROC_SCORE: 0.9944
IROC_PERCENTILE: 53
POISSON_SCORE: 0.346
POISSON_PERCENTILE: 9
MAXIMUM_REPLICATE_CORRELATION: 0.99

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

source_name: Fetal Intestine, Small primary tissue, day 108; DS17643

value: Fetal Intestine, Small


title: MOLF backcross animal 4357

description: mean insert size : 269.2


title: Chromatin accessibility assay of Fetal Intestine, Large; DS17647

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: DS17647
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.8439
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.8438
****************
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: GSM774217_UW.Fetal_Intestine_Large.ChromatinAccessibility.H-23887.DS17647.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS17647.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of Fetal Intestine Large Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fetal Intestine Large, Donor H-23887, Library DS17647 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.10375
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 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 68,927,465
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 47
FINDPEAKS_SCORE: 0.2856
FINDPEAKS_PERCENTILE: 11
HOTSPOT_SCORE: 0.2778
HOTSPOT_PERCENTILE: 6
IROC_SCORE: 0.9945
IROC_PERCENTILE: 62
POISSON_SCORE: 0.3429
POISSON_PERCENTILE: 6
MAXIMUM_REPLICATE_CORRELATION: 1.0

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

ANALYSIS FILE NAME: GSM774217_UW.Fetal_Intestine_Large.ChromatinAccessibility.H-23887.DS17647.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS17647.hg19.level.2.release.5
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-23887, Library DS17647 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.10328
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 5
BROWSER_TRACK_NAME: FIL DNase 87 47
BROWSER_TRACK_DESCRIPTION: UW Fetal Intestine Large DNase Hypersensitivity Donor H-23887 Library DS17647 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 68,927,465
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 47
FINDPEAKS_SCORE: 0.2856
FINDPEAKS_PERCENTILE: 11
HOTSPOT_SCORE: 0.2778
HOTSPOT_PERCENTILE: 6
IROC_SCORE: 0.9945
IROC_PERCENTILE: 62
POISSON_SCORE: 0.3429
POISSON_PERCENTILE: 6
MAXIMUM_REPLICATE_CORRELATION: 1.0

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

source_name: Fetal Intestine, Large primary tissue, day 108; DS17647


title: MOLF backcross animal 4315

description: mean insert size : 255


title: Chromatin accessibility assay of Fetal Placenta; DS17639

description:
sample_term_id: UBERON_0001987
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Chromatin accessibility determination via DNase-seq
Library name: DS17639
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.9477
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.9476
****************
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: GSM774215_UW.Fetal_Placenta.ChromatinAccessibility.H-23887.DS17639.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS17639.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of Fetal Placenta Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fetal Placenta, Donor H-23887, Library DS17639 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.10380
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 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 74,855,086
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 47
FINDPEAKS_SCORE: 0.3204
FINDPEAKS_PERCENTILE: 19
HOTSPOT_SCORE: 0.3026
HOTSPOT_PERCENTILE: 13
IROC_SCORE: 0.9934
IROC_PERCENTILE: 47
POISSON_SCORE: 0.378
POISSON_PERCENTILE: 19
MAXIMUM_REPLICATE_CORRELATION:

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

ANALYSIS FILE NAME: GSM774215_UW.Fetal_Placenta.ChromatinAccessibility.H-23887.DS17639.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS17639.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Placenta Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from  Fetal Placenta, Donor H-23887, Library DS17639 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.10333
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 5
BROWSER_TRACK_NAME: FP DNase 87 39
BROWSER_TRACK_DESCRIPTION: UW Fetal Placenta DNase Hypersensitivity Donor H-23887 Library DS17639 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 74,855,086
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 47
FINDPEAKS_SCORE: 0.3204
FINDPEAKS_PERCENTILE: 19
HOTSPOT_SCORE: 0.3026
HOTSPOT_PERCENTILE: 13
IROC_SCORE: 0.9934
IROC_PERCENTILE: 47
POISSON_SCORE: 0.378
POISSON_PERCENTILE: 19
MAXIMUM_REPLICATE_CORRELATION:

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

source_name: Fetal Placenta primary tissue, day 108; DS17639

value: Fetal Placenta


title: MOLF backcross animal 4262

description: mean insert size : 257.6


title: Chromatin accessibility assay of Fetal Intestine, Large; DS17462

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: DS17462
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.8443
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.8442
****************
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: GSM774214_UW.Fetal_Intestine_Large.ChromatinAccessibility.H-23833.DS17462.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS17462.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of Fetal Intestine Large Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fetal Intestine Large, Donor H-23833, Library DS17462 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.10399
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 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 54,297,676
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 47
FINDPEAKS_SCORE: 0.2812
FINDPEAKS_PERCENTILE: 4
HOTSPOT_SCORE: 0.276
HOTSPOT_PERCENTILE: 4
IROC_SCORE: 0.9966
IROC_PERCENTILE: 87
POISSON_SCORE: 0.3376
POISSON_PERCENTILE: 4
MAXIMUM_REPLICATE_CORRELATION: 1.0

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

ANALYSIS FILE NAME: GSM774214_UW.Fetal_Intestine_Large.ChromatinAccessibility.H-23833.DS17462.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS17462.hg19.level.2.release.5
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-23833, Library DS17462 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.10352
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 5
BROWSER_TRACK_NAME: FIL DNase 33 62
BROWSER_TRACK_DESCRIPTION: UW Fetal Intestine Large DNase Hypersensitivity Donor H-23833 Library DS17462 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 54,297,676
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 47
FINDPEAKS_SCORE: 0.2812
FINDPEAKS_PERCENTILE: 4
HOTSPOT_SCORE: 0.276
HOTSPOT_PERCENTILE: 4
IROC_SCORE: 0.9966
IROC_PERCENTILE: 87
POISSON_SCORE: 0.3376
POISSON_PERCENTILE: 4
MAXIMUM_REPLICATE_CORRELATION: 1.0

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

source_name: Fetal Intestine, Large primary tissue, day 113; DS17462

value: genomic DNA

value: day 113

value: Male


title: Chromatin accessibility assay of Fetal Intestine, Large; DS17422

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: DS17422
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.8447
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.8446
****************
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: GSM774213_UW.Fetal_Intestine_Large.ChromatinAccessibility.H-23808.DS17422.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS17422.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of Fetal Intestine Large Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fetal Intestine Large, Donor H-23808, Library DS17422 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.10383
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 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 22,607,272
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 47
FINDPEAKS_SCORE: 0.3854
FINDPEAKS_PERCENTILE: 32
HOTSPOT_SCORE: 0.3954
HOTSPOT_PERCENTILE: 38
IROC_SCORE: 0.9935
IROC_PERCENTILE: 49
POISSON_SCORE: 0.4356
POISSON_PERCENTILE: 34
MAXIMUM_REPLICATE_CORRELATION: 0.99

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

ANALYSIS FILE NAME: GSM774213_UW.Fetal_Intestine_Large.ChromatinAccessibility.H-23808.DS17422.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS17422.hg19.level.2.release.5
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-23808, Library DS17422 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.10336
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 5
BROWSER_TRACK_NAME: FIL DNase 08 22
BROWSER_TRACK_DESCRIPTION: UW Fetal Intestine Large DNase Hypersensitivity Donor H-23808 Library DS17422 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 22,607,272
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 47
FINDPEAKS_SCORE: 0.3854
FINDPEAKS_PERCENTILE: 32
HOTSPOT_SCORE: 0.3954
HOTSPOT_PERCENTILE: 38
IROC_SCORE: 0.9935
IROC_PERCENTILE: 49
POISSON_SCORE: 0.4356
POISSON_PERCENTILE: 34
MAXIMUM_REPLICATE_CORRELATION: 0.99

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

source_name: Fetal Intestine, Large primary tissue, day 115; DS17422

value: Fetal Intestine, Large

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

value: Primary Tissue

value: day 115


title: MOLF backcross animal 4164

description: mean insert size : 262.6


title: MOLF backcross animal 4150

description: mean insert size : 227.1


title: Chromatin accessibility assay of Fetal Stomach; DS17172

description:
sample_term_id: UBERON_0000945
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Chromatin accessibility determination via DNase-seq
Library name: DS17172
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.8488
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.8487
****************
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: GSM774212_UW.Fetal_Stomach.ChromatinAccessibility.H-23758.DS17172.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS17172.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of Fetal Stomach Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fetal Stomach, Donor H-23758, Library DS17172 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.10362
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 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 25,677,532
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 47
FINDPEAKS_SCORE: 0.3575
FINDPEAKS_PERCENTILE: 30
HOTSPOT_SCORE: 0.3673
HOTSPOT_PERCENTILE: 30
IROC_SCORE: 0.9926
IROC_PERCENTILE: 36
POISSON_SCORE: 0.4367
POISSON_PERCENTILE: 36
MAXIMUM_REPLICATE_CORRELATION: 1.0

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

ANALYSIS FILE NAME: GSM774212_UW.Fetal_Stomach.ChromatinAccessibility.H-23758.DS17172.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS17172.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Stomach Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from  Fetal Stomach, Donor H-23758, Library DS17172 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.10315
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 5
BROWSER_TRACK_NAME: FS DNase 58 72
BROWSER_TRACK_DESCRIPTION: UW Fetal Stomach DNase Hypersensitivity Donor H-23758 Library DS17172 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 25,677,532
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 47
FINDPEAKS_SCORE: 0.3575
FINDPEAKS_PERCENTILE: 30
HOTSPOT_SCORE: 0.3673
HOTSPOT_PERCENTILE: 30
IROC_SCORE: 0.9926
IROC_PERCENTILE: 36
POISSON_SCORE: 0.4367
POISSON_PERCENTILE: 36
MAXIMUM_REPLICATE_CORRELATION: 1.0

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

source_name: Fetal Stomach primary tissue, day 107; DS17172

value: Fetal Stomach

value: UW

value: fetal

value: day 107


title: MOLF backcross animal 4144

description: mean insert size : 267.7

value: ((MOLF x PyMT) x FVB) backcross animal

value: MOLF x PyMT backcross mammary tumor


title: MOLF backcross animal 4142

description: mean insert size : 269.8


title: Chromatin accessibility assay of Fetal Lung, Right; DS17831

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: DS17831
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.8382
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.8381
****************
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: GSM774227_UW.Fetal_Lung_Right.ChromatinAccessibility.H-23964.DS17831.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS17831.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of Fetal Lung Right Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fetal Lung Right, Donor H-23964, Library DS17831 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.10387
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 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 72,009,537
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 47
FINDPEAKS_SCORE: 0.4951
FINDPEAKS_PERCENTILE: 79
HOTSPOT_SCORE: 0.4807
HOTSPOT_PERCENTILE: 72
IROC_SCORE: 0.9917
IROC_PERCENTILE: 30
POISSON_SCORE: 0.5321
POISSON_PERCENTILE: 68
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

ANALYSIS FILE NAME: GSM774227_UW.Fetal_Lung_Right.ChromatinAccessibility.H-23964.DS17831.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS17831.hg19.level.2.release.5
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-23964, Library DS17831 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.10340
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 5
BROWSER_TRACK_NAME: FLR DNase 64 31
BROWSER_TRACK_DESCRIPTION: UW Fetal Lung Right DNase Hypersensitivity Donor H-23964 Library DS17831 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 72,009,537
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 47
FINDPEAKS_SCORE: 0.4951
FINDPEAKS_PERCENTILE: 79
HOTSPOT_SCORE: 0.4807
HOTSPOT_PERCENTILE: 72
IROC_SCORE: 0.9917
IROC_PERCENTILE: 30
POISSON_SCORE: 0.5321
POISSON_PERCENTILE: 68
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

source_name: Fetal Lung, Right primary tissue, day 98; DS17831

value: Fetal Lung, Right

value: day 98

value: Female

value: Chromatin Accessibility

value: Qiagen minElut


title: Chromatin accessibility assay of Fetal Intestine, Small; DS17150

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: DS17150
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.8418
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.8417
****************
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: GSM774210_UW.Fetal_Intestine_Small.ChromatinAccessibility.H-23758.DS17150.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS17150.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of Fetal Intestine Small Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fetal Intestine Small, Donor H-23758, Library DS17150 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.10378
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 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 23,669,464
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 47
FINDPEAKS_SCORE: 0.3964
FINDPEAKS_PERCENTILE: 38
HOTSPOT_SCORE: 0.3968
HOTSPOT_PERCENTILE: 40
IROC_SCORE: 0.9961
IROC_PERCENTILE: 79
POISSON_SCORE: 0.4481
POISSON_PERCENTILE: 43
MAXIMUM_REPLICATE_CORRELATION: 0.99

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

ANALYSIS FILE NAME: GSM774210_UW.Fetal_Intestine_Small.ChromatinAccessibility.H-23758.DS17150.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS17150.hg19.level.2.release.5
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-23758, Library DS17150 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.10331
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 5
BROWSER_TRACK_NAME: FIS DNase 58 50
BROWSER_TRACK_DESCRIPTION: UW Fetal Intestine Small DNase Hypersensitivity Donor H-23758 Library DS17150 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 23,669,464
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 47
FINDPEAKS_SCORE: 0.3964
FINDPEAKS_PERCENTILE: 38
HOTSPOT_SCORE: 0.3968
HOTSPOT_PERCENTILE: 40
IROC_SCORE: 0.9961
IROC_PERCENTILE: 79
POISSON_SCORE: 0.4481
POISSON_PERCENTILE: 43
MAXIMUM_REPLICATE_CORRELATION: 0.99

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

source_name: Fetal Intestine, Small primary tissue, day 107; DS17150

value: Fetal Intestine, Small

value: genomic DNA

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


title: Chromatin accessibility assay of Fetal Kidney, Left; DS17140

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: DS17140
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.8357
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.8356
****************
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: GSM774209_UW.Fetal_Kidney_Left.ChromatinAccessibility.H-23758.DS17140.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS17140.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of Fetal Kidney Left Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fetal Kidney Left, Donor H-23758, Library DS17140 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.10388
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 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 30,395,163
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 47
FINDPEAKS_SCORE: 0.3944
FINDPEAKS_PERCENTILE: 36
HOTSPOT_SCORE: 0.3909
HOTSPOT_PERCENTILE: 36
IROC_SCORE: 0.9866
IROC_PERCENTILE: 2
POISSON_SCORE: 0.4417
POISSON_PERCENTILE: 40
MAXIMUM_REPLICATE_CORRELATION: 0.92

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

ANALYSIS FILE NAME: GSM774209_UW.Fetal_Kidney_Left.ChromatinAccessibility.H-23758.DS17140.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS17140.hg19.level.2.release.5
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-23758, Library DS17140 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.10341
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 5
BROWSER_TRACK_NAME: FKL DNase 58 40
BROWSER_TRACK_DESCRIPTION: UW Fetal Kidney Left DNase Hypersensitivity Donor H-23758 Library DS17140 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 30,395,163
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 47
FINDPEAKS_SCORE: 0.3944
FINDPEAKS_PERCENTILE: 36
HOTSPOT_SCORE: 0.3909
HOTSPOT_PERCENTILE: 36
IROC_SCORE: 0.9866
IROC_PERCENTILE: 2
POISSON_SCORE: 0.4417
POISSON_PERCENTILE: 40
MAXIMUM_REPLICATE_CORRELATION: 0.92

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

source_name: Fetal Kidney, Left primary tissue, day 107; DS17140

value: Fetal Kidney, Left

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


title: MOLF backcross animal 3939

description: mean insert size : 248.6

data_processing: Illumina software pipeline ( Basecalls was done by using Illumina RTA 1.6 for GAIIx run, RTA 1.7 for HiSeq run , Alignment was done by using Illumina CASAVA1.6, CASAVA_v1.7.0 pipelines)

source_name: PyMT-induced mammary tumor


title: MOLF backcross animal 3540

description: mean insert size : 275.2


title: MOLF backcross animal 3427

description: mean insert size : 253.5


title: Chromatin accessibility assay of Fetal Placenta; DS17744

description:
sample_term_id: UBERON_0001987
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Chromatin accessibility determination via DNase-seq
Library name: DS17744
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.9481
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.9480
****************
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: GSM774219_UW.Fetal_Placenta.ChromatinAccessibility.H-23914.DS17744.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS17744.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of Fetal Placenta Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fetal Placenta, Donor H-23914, Library DS17744 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.10396
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 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 28,704,485
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 47
FINDPEAKS_SCORE: 0.3988
FINDPEAKS_PERCENTILE: 40
HOTSPOT_SCORE: 0.387
HOTSPOT_PERCENTILE: 34
IROC_SCORE: 0.9963
IROC_PERCENTILE: 81
POISSON_SCORE: 0.4525
POISSON_PERCENTILE: 45
MAXIMUM_REPLICATE_CORRELATION:

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

ANALYSIS FILE NAME: GSM774219_UW.Fetal_Placenta.ChromatinAccessibility.H-23914.DS17744.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS17744.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Placenta Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from  Fetal Placenta, Donor H-23914, Library DS17744 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.10349
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 5
BROWSER_TRACK_NAME: FP DNase 14 44
BROWSER_TRACK_DESCRIPTION: UW Fetal Placenta DNase Hypersensitivity Donor H-23914 Library DS17744 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 28,704,485
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 47
FINDPEAKS_SCORE: 0.3988
FINDPEAKS_PERCENTILE: 40
HOTSPOT_SCORE: 0.387
HOTSPOT_PERCENTILE: 34
IROC_SCORE: 0.9963
IROC_PERCENTILE: 81
POISSON_SCORE: 0.4525
POISSON_PERCENTILE: 45
MAXIMUM_REPLICATE_CORRELATION:

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

source_name: Fetal Placenta primary tissue, day 91; DS17744

value: Fetal Placenta

value: Primary Tissue

value: day 91

value: Male


title: MOLF backcross animal 3273

description: mean insert size : 275.7


title: Chromatin accessibility assay of Fetal Intestine, Small; DS17092

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: DS17092
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.8422
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.8421
****************
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: GSM774205_UW.Fetal_Intestine_Small.ChromatinAccessibility.H-23744.DS17092.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS17092.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of Fetal Intestine Small Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fetal Intestine Small, Donor H-23744, Library DS17092 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.10369
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 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 22,515,407
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 47
FINDPEAKS_SCORE: 0.487
FINDPEAKS_PERCENTILE: 68
HOTSPOT_SCORE: 0.4888
HOTSPOT_PERCENTILE: 77
IROC_SCORE: 0.9974
IROC_PERCENTILE: 94
POISSON_SCORE: 0.5349
POISSON_PERCENTILE: 70
MAXIMUM_REPLICATE_CORRELATION: 0.99

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

ANALYSIS FILE NAME: GSM774205_UW.Fetal_Intestine_Small.ChromatinAccessibility.H-23744.DS17092.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS17092.hg19.level.2.release.5
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-23744, Library DS17092 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.10322
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 5
BROWSER_TRACK_NAME: FIS DNase 44 92
BROWSER_TRACK_DESCRIPTION: UW Fetal Intestine Small DNase Hypersensitivity Donor H-23744 Library DS17092 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 22,515,407
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 47
FINDPEAKS_SCORE: 0.487
FINDPEAKS_PERCENTILE: 68
HOTSPOT_SCORE: 0.4888
HOTSPOT_PERCENTILE: 77
IROC_SCORE: 0.9974
IROC_PERCENTILE: 94
POISSON_SCORE: 0.5349
POISSON_PERCENTILE: 70
MAXIMUM_REPLICATE_CORRELATION: 0.99

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

source_name: Fetal Intestine, Small primary tissue, day 91; DS17092

value: UW

value: fetal


title: Chromatin accessibility assay of Fetal Thymus; DS16841

description:
sample_term_id: UBERON_0002370
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Chromatin accessibility determination via DNase-seq
Library name: DS16841
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.8479
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.8478
****************
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: GSM774204_UW.Fetal_Thymus.ChromatinAccessibility.H-23663.DS16841.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS16841.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of Fetal Thymus Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fetal Thymus, Donor H-23663, Library DS16841 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.10364
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 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 29,128,747
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 47
FINDPEAKS_SCORE: 0.3169
FINDPEAKS_PERCENTILE: 17
HOTSPOT_SCORE: 0.3222
HOTSPOT_PERCENTILE: 21
IROC_SCORE: 0.9916
IROC_PERCENTILE: 28
POISSON_SCORE: 0.3626
POISSON_PERCENTILE: 15
MAXIMUM_REPLICATE_CORRELATION: 0.99

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

ANALYSIS FILE NAME: GSM774204_UW.Fetal_Thymus.ChromatinAccessibility.H-23663.DS16841.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS16841.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Thymus Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from  Fetal Thymus, Donor H-23663, Library DS16841 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.10317
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 5
BROWSER_TRACK_NAME: FT DNase 63 41
BROWSER_TRACK_DESCRIPTION: UW Fetal Thymus DNase Hypersensitivity Donor H-23663 Library DS16841 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 29,128,747
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 47
FINDPEAKS_SCORE: 0.3169
FINDPEAKS_PERCENTILE: 17
HOTSPOT_SCORE: 0.3222
HOTSPOT_PERCENTILE: 21
IROC_SCORE: 0.9916
IROC_PERCENTILE: 28
POISSON_SCORE: 0.3626
POISSON_PERCENTILE: 15
MAXIMUM_REPLICATE_CORRELATION: 0.99

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

source_name: Fetal Thymus primary tissue, day 105; DS16841

value: Fetal Thymus

value: day 105


title: Chromatin accessibility assay of Fetal Heart; DS16819

description:
sample_term_id: UBERON_0000948
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Chromatin accessibility determination via DNase-seq
Library name: DS16819
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.8366
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.8365
****************
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: GSM774203_UW.Fetal_Heart.ChromatinAccessibility.H-23663.DS16819.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS16819.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of Fetal Heart Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fetal Heart, Donor H-23663, Library DS16819 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.10390
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 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 57,721,502
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 47
FINDPEAKS_SCORE: 0.618
FINDPEAKS_PERCENTILE: 94
HOTSPOT_SCORE: 0.6053
HOTSPOT_PERCENTILE: 94
IROC_SCORE: 0.9956
IROC_PERCENTILE: 72
POISSON_SCORE: 0.6462
POISSON_PERCENTILE: 94
MAXIMUM_REPLICATE_CORRELATION: 0.99

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

ANALYSIS FILE NAME: GSM774203_UW.Fetal_Heart.ChromatinAccessibility.H-23663.DS16819.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS16819.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Heart Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from  Fetal Heart, Donor H-23663, Library DS16819 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.10343
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 5
BROWSER_TRACK_NAME: FH DNase 63 19
BROWSER_TRACK_DESCRIPTION: UW Fetal Heart DNase Hypersensitivity Donor H-23663 Library DS16819 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 57,721,502
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 47
FINDPEAKS_SCORE: 0.618
FINDPEAKS_PERCENTILE: 94
HOTSPOT_SCORE: 0.6053
HOTSPOT_PERCENTILE: 94
IROC_SCORE: 0.9956
IROC_PERCENTILE: 72
POISSON_SCORE: 0.6462
POISSON_PERCENTILE: 94
MAXIMUM_REPLICATE_CORRELATION: 0.99

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

source_name: Fetal Heart primary tissue, day 105; DS16819

value: Fetal Heart


title: Chromatin accessibility assay of Fetal Stomach; DS16530

description:
sample_term_id: UBERON_0000945
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Chromatin accessibility determination via DNase-seq
Library name: DS16530
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.8493
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.8492
****************
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: GSM774202_UW.Fetal_Stomach.ChromatinAccessibility.H-23589.DS16530.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS16530.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of Fetal Stomach Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fetal Stomach, Donor H-23589, Library DS16530 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.10400
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 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 29,925,437
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 47
FINDPEAKS_SCORE: 0.3053
FINDPEAKS_PERCENTILE: 13
HOTSPOT_SCORE: 0.3137
HOTSPOT_PERCENTILE: 17
IROC_SCORE: 0.9902
IROC_PERCENTILE: 15
POISSON_SCORE: 0.396
POISSON_PERCENTILE: 26
MAXIMUM_REPLICATE_CORRELATION: 0.99

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

ANALYSIS FILE NAME: GSM774202_UW.Fetal_Stomach.ChromatinAccessibility.H-23589.DS16530.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS16530.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Stomach Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from  Fetal Stomach, Donor H-23589, Library DS16530 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.10353
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 5
BROWSER_TRACK_NAME: FS DNase 89 30
BROWSER_TRACK_DESCRIPTION: UW Fetal Stomach DNase Hypersensitivity Donor H-23589 Library DS16530 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 29,925,437
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 47
FINDPEAKS_SCORE: 0.3053
FINDPEAKS_PERCENTILE: 13
HOTSPOT_SCORE: 0.3137
HOTSPOT_PERCENTILE: 17
IROC_SCORE: 0.9902
IROC_PERCENTILE: 15
POISSON_SCORE: 0.396
POISSON_PERCENTILE: 26
MAXIMUM_REPLICATE_CORRELATION: 0.99

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

source_name: Fetal Stomach primary tissue, day 147; DS16530

value: Fetal Stomach

value: day 147

value: Female


title: H3K4me3_ChIPSeq_Th2

status: Public on Aug 05 2011

city: Chiba

first: Atsushi

last: Onodera

address: Chuo-ku Inohana 1-8-1

department: Immunology

country: Japan

institute: Chiba University

description: Chromatin IP against H3K4me3

data_processing: A total of 170,000â250,000 clusters was generated per tile, and 36 cycles of the sequencing reactions were performed. Short-read sequences were aligned to the mouse genome sequences (mm9 from University of California, Santa Cruz Genome Browser; http://genome.ucsc.edu/) using the Eland program. Sequences allowing no more than two mismatches per sequence were used for the analysis.

growth_protocol: Splenic CD4 T cells were prepared using a magnetic cell sorter (AutoMACS; Miltenyi Biotec) yielding a purity of >98%. Where indicated, cells from C57BL/6 mice were stimulated with immobilized anti-TCR mAb (H57â597; 3 mg/ml) and anti-CD28 mAb under Th1- or Th2-culture conditions for 2 days in vitro.  Th1 conditions; 25 U/ml IL-2, 10 U/ml IL-12, and antiï¾IL-4 mAb.  Th2 conditions; 25 U/ml IL-2, 100 U/ml IL-4. After culturing under Th1- or Th2-culture conditions for 3 more days, the cells were harvested.

extract_protocol: For ChIP-Seq analysis, IP and input samples were prepared using ChIP-Seq Sample Prep kit (Illumina). Adaptor-ligated DNA fragments were size fractionated by 12% acrylamide gel, and the 170- to 250-bp fraction was recovered. DNA thus obtained was amplified by 18 cycles of PCR. One nanogram of DNA was used for the sequencing reaction of the Illumina GAIIx, according to the manufacturerâs instructions.

tag: strain

value: spleen

tag: cell type

value: primary CD4 T cells

tag: culture condition

tag: chip antibody

tag: chip antibody vendor

value: Lake Placid Biologicals

tag: chip antibody cat. & batch number