title: Chromatin accessibility assay of Fetal Renal Cortex; DS17756

description:
sample_term_id: UBERON_0001225
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Chromatin accessibility determination via DNase-seq
Library name: DS17756
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.7081
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.7080
****************
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: GSM701529_UW.Fetal_Renal_Cortex.ChromatinAccessibility.H-23914.DS17756.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS17756.hg19.level.1.release.4
ANALYSIS TITLE: Mapping of Fetal Renal Cortex Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fetal Renal Cortex, Donor H-23914, Library DS17756 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.7696
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 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 21,902,507
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 54
FINDPEAKS_SCORE: 0.3524
FINDPEAKS_PERCENTILE: 33
HOTSPOT_SCORE: 0.3606
HOTSPOT_PERCENTILE: 41
IROC_SCORE: 0.9926
IROC_PERCENTILE: 33
POISSON_SCORE: 0.4075
POISSON_PERCENTILE: 39
MAXIMUM_REPLICATE_CORRELATION: 0.92

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

ANALYSIS FILE NAME: GSM701529_UW.Fetal_Renal_Cortex.ChromatinAccessibility.H-23914.DS17756.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS17756.hg19.level.2.release.4
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Renal Cortex Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from  Fetal Renal Cortex, Donor H-23914, Library DS17756 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.7750
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 4
BROWSER_TRACK_NAME: FRC DNase 14 56
BROWSER_TRACK_DESCRIPTION: UW Fetal Renal Cortex DNase Hypersensitivity Donor H-23914 Library DS17756 EA Release 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 21,902,507
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 52
FINDPEAKS_SCORE: 0.3524
FINDPEAKS_PERCENTILE: 33
HOTSPOT_SCORE: 0.3606
HOTSPOT_PERCENTILE: 41
IROC_SCORE: 0.9926
IROC_PERCENTILE: 33
POISSON_SCORE: 0.4075
POISSON_PERCENTILE: 39
MAXIMUM_REPLICATE_CORRELATION: 0.92

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

source_name: Fetal  primary tissue, day 91; DS17756

value: Fetal Renal Cortex


title: WT-leaf

status: Public on Apr 19 2011

type: SRA

city: New York

first: Huan

last: Wang

state: New York

address: 1230 York Avenue

country: USA

institute: The Rockefeller University

description: smRNA sequencing data of total smRNAs in leaves

library_source: transcriptomic

data_processing: Adapters were removed by Perl script, if a hit with at most 1 mismatch to the first 4-nt of the adapter sequence could be found. After adapter removal, only 19-28 nt reads were aligned to the Arabidopsis thaliana genome (TAIR9) using C program. The small RNAs with perfect genomic matches are used for further analysis.

molecule: total RNA

organism: Arabidopsis thaliana

source_name: total leaf

growth_protocol: Flowers were collected from 6-week-old plants grown on soil in a growth chamber under 12 hr light/12 hr dark at 21°C. Leaves and roots were harvested from 4-week-old plants grown hydroponically under 12 hr light/12 hr dark at 21°C in the MGRL medium. Seedlings were grown on MS plates in a growth chamber under 16 hr light/8 hr dark at 21°C.

extract_protocol: For two-step purification of AGO/smRNA complexes, cleared extracts were fractioned on Superdex 200 10/300 columns (Akta-FPLC, GE) and further immunoprecipitated. After size-fractionation, total RNA or RNA recovered from the purified AGO-smRNA complexes were ligated to 3'² adapter (AppTCGTATGCCGTCTTCTGCTTG-L) and 5'² adapter (rGrUrUrCrArGrArGrUrUrCrUrArCrArGrUrCrCrGrArCrGrArUrC) sequentially. The ligated products were amplified by RT-PCR and used for Illumina's deep sequencing.

tag: tissue

value: leaf

tag: smrna

value: total small RNAs


title: Chromatin accessibility assay of Fetal Stomach; DS17750

status: Public on Apr 14 2011

city: Seattle

first: Northwest

last: REMC

state: WA

institute: University of Washington

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: DS17750
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.7166
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.7165
****************
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: GSM701528_UW.Fetal_Stomach.ChromatinAccessibility.H-23914.DS17750.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS17750.hg19.level.1.release.4
ANALYSIS TITLE: Mapping of Fetal Stomach Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fetal Stomach, Donor H-23914, Library DS17750 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.7694
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 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 22,797,043
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 54
FINDPEAKS_SCORE: 0.2569
FINDPEAKS_PERCENTILE: 6
HOTSPOT_SCORE: 0.268
HOTSPOT_PERCENTILE: 7
IROC_SCORE: 0.9889
IROC_PERCENTILE: 11
POISSON_SCORE: 0.3335
POISSON_PERCENTILE: 11
MAXIMUM_REPLICATE_CORRELATION: 0.99

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

ANALYSIS FILE NAME: GSM701528_UW.Fetal_Stomach.ChromatinAccessibility.H-23914.DS17750.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS17750.hg19.level.2.release.4
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Stomach Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from  Fetal Stomach, Donor H-23914, Library DS17750 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.7748
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 4
BROWSER_TRACK_NAME: FS DNase 14 50
BROWSER_TRACK_DESCRIPTION: UW Fetal Stomach DNase Hypersensitivity Donor H-23914 Library DS17750 EA Release 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 22,797,043
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 52
FINDPEAKS_SCORE: 0.2569
FINDPEAKS_PERCENTILE: 6
HOTSPOT_SCORE: 0.268
HOTSPOT_PERCENTILE: 7
IROC_SCORE: 0.9889
IROC_PERCENTILE: 11
POISSON_SCORE: 0.3335
POISSON_PERCENTILE: 11
MAXIMUM_REPLICATE_CORRELATION: 0.99

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

molecule: genomic DNA

organism: Homo sapiens

source_name: Fetal  primary tissue, day 91; DS17750

extract_protocol: Library construction protocol: Single read - Illumina

tag: sample alias

tag: sample common name

value: Fetal Stomach

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 91

value: Male

value: Chromatin Accessibility

value: Qiagen minElut

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


title: Chromatin accessibility assay of Fetal Lung, Left; DS17739

description:
sample_term_id: UBERON_0002168
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Chromatin accessibility determination via DNase-seq
Library name: DS17739
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.7243
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.7242
****************
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: GSM701527_UW.Fetal_Lung_Left.ChromatinAccessibility.H-23914.DS17739.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS17739.hg19.level.1.release.4
ANALYSIS TITLE: Mapping of Fetal Lung Left Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fetal Lung Left, Donor H-23914, Library DS17739 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.7689
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 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 22,605,963
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 54
FINDPEAKS_SCORE: 0.5091
FINDPEAKS_PERCENTILE: 85
HOTSPOT_SCORE: 0.5168
HOTSPOT_PERCENTILE: 87
IROC_SCORE: 0.9952
IROC_PERCENTILE: 61
POISSON_SCORE: 0.5304
POISSON_PERCENTILE: 81
MAXIMUM_REPLICATE_CORRELATION: 0.96

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

ANALYSIS FILE NAME: GSM701527_UW.Fetal_Lung_Left.ChromatinAccessibility.H-23914.DS17739.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS17739.hg19.level.2.release.4
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Lung Left Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from  Fetal Lung Left, Donor H-23914, Library DS17739 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.7743
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 4
BROWSER_TRACK_NAME: FLL DNase 14 39
BROWSER_TRACK_DESCRIPTION: UW Fetal Lung Left DNase Hypersensitivity Donor H-23914 Library DS17739 EA Release 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 22,605,963
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 52
FINDPEAKS_SCORE: 0.5091
FINDPEAKS_PERCENTILE: 85
HOTSPOT_SCORE: 0.5168
HOTSPOT_PERCENTILE: 87
IROC_SCORE: 0.9952
IROC_PERCENTILE: 61
POISSON_SCORE: 0.5304
POISSON_PERCENTILE: 81
MAXIMUM_REPLICATE_CORRELATION: 0.96

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

source_name: Fetal  primary tissue, day 91; DS17739

value: Fetal Lung, Left


title: Chromatin accessibility assay of CD3 Primary Cells, cord blood; DS17702

description:
sample_term_id: CL_0000084
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Chromatin accessibility determination via DNase-seq
Library name: DS17702
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.7025
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.7024
****************
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: GSM701525_UW.CD3_Primary_Cells.ChromatinAccessibility.CB1_1-3-2011.DS17702.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS17702.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of CD3 Primary Cells Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on CD3 Primary Cells, Donor CB1 1-3-2011, Library DS17702 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.10381
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: 20,929,382
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 47
FINDPEAKS_SCORE: 0.3432
FINDPEAKS_PERCENTILE: 26
HOTSPOT_SCORE: 0.3555
HOTSPOT_PERCENTILE: 28
IROC_SCORE: 0.996
IROC_PERCENTILE: 77
POISSON_SCORE: 0.3655
POISSON_PERCENTILE: 17
MAXIMUM_REPLICATE_CORRELATION: 0.99

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

ANALYSIS FILE NAME: GSM701525_UW.CD3_Primary_Cells.ChromatinAccessibility.CB1_1-3-2011.DS17702.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS17702.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of CD3 Primary Cells Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from  CD3 Primary Cells, Donor CB1 1-3-2011, Library DS17702 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.10334
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: CD3 DNase 11 02
BROWSER_TRACK_DESCRIPTION: UW CD3 Primary Cells DNase Hypersensitivity Donor CB1 1-3-2011 Library DS17702 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 20,929,382
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 47
FINDPEAKS_SCORE: 0.3432
FINDPEAKS_PERCENTILE: 26
HOTSPOT_SCORE: 0.3555
HOTSPOT_PERCENTILE: 28
IROC_SCORE: 0.996
IROC_PERCENTILE: 77
POISSON_SCORE: 0.3655
POISSON_PERCENTILE: 17
MAXIMUM_REPLICATE_CORRELATION: 0.99

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

source_name: flow sorted CD3+ Primary Cells, from cord blood; DS17702

value: CD3 Cord Blood Primary Cells

value: FHCRC HEIMFELD

value: Primary Cell

value: CD3 Primary Cells

tag: markers

value: Unknown


title: Chromatin accessibility assay of CD3 Primary Cells, cord blood; DS17706

description:
sample_term_id: CL_0000084
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Chromatin accessibility determination via DNase-seq
Library name: DS17706
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.7022
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.7021
****************
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: GSM701526_UW.CD3_Primary_Cells.ChromatinAccessibility.CB6_1-4-2011.DS17706.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS17706.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of CD3 Primary Cells Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on CD3 Primary Cells, Donor CB6 1-4-2011, Library DS17706 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.10382
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: 21,594,260
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 47
FINDPEAKS_SCORE: 0.4226
FINDPEAKS_PERCENTILE: 47
HOTSPOT_SCORE: 0.4283
HOTSPOT_PERCENTILE: 49
IROC_SCORE: 0.9954
IROC_PERCENTILE: 70
POISSON_SCORE: 0.4188
POISSON_PERCENTILE: 28
MAXIMUM_REPLICATE_CORRELATION: 0.97

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

ANALYSIS FILE NAME: GSM701526_UW.CD3_Primary_Cells.ChromatinAccessibility.CB6_1-4-2011.DS17706.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS17706.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of CD3 Primary Cells Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from  CD3 Primary Cells, Donor CB6 1-4-2011, Library DS17706 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.10335
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: CD3 DNase 11 06
BROWSER_TRACK_DESCRIPTION: UW CD3 Primary Cells DNase Hypersensitivity Donor CB6 1-4-2011 Library DS17706 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 21,594,260
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 47
FINDPEAKS_SCORE: 0.4226
FINDPEAKS_PERCENTILE: 47
HOTSPOT_SCORE: 0.4283
HOTSPOT_PERCENTILE: 49
IROC_SCORE: 0.9954
IROC_PERCENTILE: 70
POISSON_SCORE: 0.4188
POISSON_PERCENTILE: 28
MAXIMUM_REPLICATE_CORRELATION: 0.97

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

source_name: flow sorted CD3+ Primary Cells, from cord blood; DS17706


title: Chromatin accessibility assay of Fetal Lung, Left; DS17674

description:
sample_term_id: UBERON_0002168
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Chromatin accessibility determination via DNase-seq
Library name: DS17674
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.7237
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.7236
****************
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: GSM701524_UW.Fetal_Lung_Left.ChromatinAccessibility.H-23887.DS17674.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS17674.hg19.level.1.release.4
ANALYSIS TITLE: Mapping of Fetal Lung Left Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fetal Lung Left, Donor H-23887, Library DS17674 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.7707
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 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 24,151,105
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 54
FINDPEAKS_SCORE: 0.5915
FINDPEAKS_PERCENTILE: 94
HOTSPOT_SCORE: 0.5852
HOTSPOT_PERCENTILE: 96
IROC_SCORE: 0.9966
IROC_PERCENTILE: 76
POISSON_SCORE: 0.5926
POISSON_PERCENTILE: 96
MAXIMUM_REPLICATE_CORRELATION: 0.92

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

ANALYSIS FILE NAME: GSM701524_UW.Fetal_Lung_Left.ChromatinAccessibility.H-23887.DS17674.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS17674.hg19.level.2.release.4
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Lung Left Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from  Fetal Lung Left, Donor H-23887, Library DS17674 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.7761
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 4
BROWSER_TRACK_NAME: FLL DNase 87 74
BROWSER_TRACK_DESCRIPTION: UW Fetal Lung Left DNase Hypersensitivity Donor H-23887 Library DS17674 EA Release 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 24,151,105
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 52
FINDPEAKS_SCORE: 0.5915
FINDPEAKS_PERCENTILE: 94
HOTSPOT_SCORE: 0.5852
HOTSPOT_PERCENTILE: 96
IROC_SCORE: 0.9966
IROC_PERCENTILE: 76
POISSON_SCORE: 0.5926
POISSON_PERCENTILE: 96
MAXIMUM_REPLICATE_CORRELATION: 0.92

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

source_name: Fetal  primary tissue, day 108; DS17674

value: day 108

value: Female


title: Chromatin accessibility assay of Fetal Renal Pelvis, Left; DS17553

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: DS17553
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.7262
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.7261
****************
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: GSM701520_UW.Fetal_Renal_Pelvis_Left.ChromatinAccessibility.H-23871.DS17553.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS17553.hg19.level.1.release.4
ANALYSIS TITLE: Mapping of Fetal Renal Pelvis Left Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fetal Renal Pelvis Left, Donor H-23871, Library DS17553 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.7711
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 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 29,053,023
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 54
FINDPEAKS_SCORE: 0.3897
FINDPEAKS_PERCENTILE: 54
HOTSPOT_SCORE: 0.3836
HOTSPOT_PERCENTILE: 50
IROC_SCORE: 0.9906
IROC_PERCENTILE: 19
POISSON_SCORE: 0.4731
POISSON_PERCENTILE: 61
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM701520_UW.Fetal_Renal_Pelvis_Left.ChromatinAccessibility.H-23871.DS17553.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS17553.hg19.level.2.release.4
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Renal Pelvis Left Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from  Fetal Renal Pelvis Left, Donor H-23871, Library DS17553 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.7765
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 4
BROWSER_TRACK_NAME: FRPL DNase 71 53
BROWSER_TRACK_DESCRIPTION: UW Fetal Renal Pelvis Left DNase Hypersensitivity Donor H-23871 Library DS17553 EA Release 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 29,053,023
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 52
FINDPEAKS_SCORE: 0.3897
FINDPEAKS_PERCENTILE: 54
HOTSPOT_SCORE: 0.3836
HOTSPOT_PERCENTILE: 50
IROC_SCORE: 0.9906
IROC_PERCENTILE: 19
POISSON_SCORE: 0.4731
POISSON_PERCENTILE: 61
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: Fetal  primary tissue, day 105; DS17553

value: Fetal Renal Pelvis, Left

value: genomic DNA

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

value: day 105


title: Chromatin accessibility assay of Fetal Renal Cortex, Left; DS17550

description:
sample_term_id: UBERON_0001225
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Chromatin accessibility determination via DNase-seq
Library name: DS17550
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.7228
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.7227
****************
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: GSM701519_UW.Fetal_Renal_Cortex_Left.ChromatinAccessibility.H-23871.DS17550.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS17550.hg19.level.1.release.4
ANALYSIS TITLE: Mapping of Fetal Renal Cortex Left Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fetal Renal Cortex Left, Donor H-23871, Library DS17550 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.7710
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 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 33,274,534
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 54
FINDPEAKS_SCORE: 0.4319
FINDPEAKS_PERCENTILE: 70
HOTSPOT_SCORE: 0.4242
HOTSPOT_PERCENTILE: 63
IROC_SCORE: 0.9928
IROC_PERCENTILE: 35
POISSON_SCORE: 0.5081
POISSON_PERCENTILE: 72
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM701519_UW.Fetal_Renal_Cortex_Left.ChromatinAccessibility.H-23871.DS17550.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS17550.hg19.level.2.release.4
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Renal Cortex Left Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from  Fetal Renal Cortex Left, Donor H-23871, Library DS17550 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.7764
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 4
BROWSER_TRACK_NAME: FRCL DNase 71 50
BROWSER_TRACK_DESCRIPTION: UW Fetal Renal Cortex Left DNase Hypersensitivity Donor H-23871 Library DS17550 EA Release 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 33,274,534
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 52
FINDPEAKS_SCORE: 0.4319
FINDPEAKS_PERCENTILE: 70
HOTSPOT_SCORE: 0.4242
HOTSPOT_PERCENTILE: 63
IROC_SCORE: 0.9928
IROC_PERCENTILE: 35
POISSON_SCORE: 0.5081
POISSON_PERCENTILE: 72
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: Fetal  primary tissue, day 105; DS17550

value: Fetal Renal Cortex, Left

value: Primary Tissue

value: UW

value: fetal


title: Chromatin accessibility assay of Fetal Muscle, Upper Limb Skeletal; DS17661

description:
sample_term_id: UBERON_0003662
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Chromatin accessibility determination via DNase-seq
Library name: DS17661
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.7256
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.7255
****************
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: GSM701522_UW.Fetal_Muscle_Upper_Limb_Skeletal.ChromatinAccessibility.H-23887.DS17661.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS17661.hg19.level.1.release.4
ANALYSIS TITLE: Mapping of Fetal Muscle Upper Limb Skeletal Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fetal Muscle Upper Limb Skeletal, Donor H-23887, Library DS17661 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.7704
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 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 23,065,190
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 54
FINDPEAKS_SCORE: 0.4767
FINDPEAKS_PERCENTILE: 80
HOTSPOT_SCORE: 0.4759
HOTSPOT_PERCENTILE: 76
IROC_SCORE: 0.9945
IROC_PERCENTILE: 54
POISSON_SCORE: 0.5307
POISSON_PERCENTILE: 83
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM701522_UW.Fetal_Muscle_Upper_Limb_Skeletal.ChromatinAccessibility.H-23887.DS17661.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS17661.hg19.level.2.release.4
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Muscle Upper Limb Skeletal Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from  Fetal Muscle Upper Limb Skeletal, Donor H-23887, Library DS17661 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.7758
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 4
BROWSER_TRACK_NAME: FMULS DNase 87 61
BROWSER_TRACK_DESCRIPTION: UW Fetal Muscle Upper Limb Skeletal DNase Hypersensitivity Donor H-23887 Library DS17661 EA Release 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 23,065,190
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 52
FINDPEAKS_SCORE: 0.4767
FINDPEAKS_PERCENTILE: 80
HOTSPOT_SCORE: 0.4759
HOTSPOT_PERCENTILE: 76
IROC_SCORE: 0.9945
IROC_PERCENTILE: 54
POISSON_SCORE: 0.5307
POISSON_PERCENTILE: 83
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: Fetal  primary tissue, day 108; DS17661

value: Fetal Muscle, Upper Limb Skeletal

value: Chromatin Accessibility

value: Qiagen minElut

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


title: Chromatin accessibility assay of Fetal Lung, Right; DS17670

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: DS17670
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.7246
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.7245
****************
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: GSM701523_UW.Fetal_Lung_Right.ChromatinAccessibility.H-23887.DS17670.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS17670.hg19.level.1.release.4
ANALYSIS TITLE: Mapping of Fetal Lung Right Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fetal Lung Right, Donor H-23887, Library DS17670 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.7706
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 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 45,460,415
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 54
FINDPEAKS_SCORE: 0.5062
FINDPEAKS_PERCENTILE: 83
HOTSPOT_SCORE: 0.5026
HOTSPOT_PERCENTILE: 83
IROC_SCORE: 0.9935
IROC_PERCENTILE: 43
POISSON_SCORE: 0.5325
POISSON_PERCENTILE: 85
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

ANALYSIS FILE NAME: GSM701523_UW.Fetal_Lung_Right.ChromatinAccessibility.H-23887.DS17670.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS17670.hg19.level.2.release.4
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-23887, Library DS17670 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.7760
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 4
BROWSER_TRACK_NAME: FLR DNase 87 70
BROWSER_TRACK_DESCRIPTION: UW Fetal Lung Right DNase Hypersensitivity Donor H-23887 Library DS17670 EA Release 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 45,460,415
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 52
FINDPEAKS_SCORE: 0.5062
FINDPEAKS_PERCENTILE: 83
HOTSPOT_SCORE: 0.5026
HOTSPOT_PERCENTILE: 83
IROC_SCORE: 0.9935
IROC_PERCENTILE: 43
POISSON_SCORE: 0.5325
POISSON_PERCENTILE: 85
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

source_name: Fetal  primary tissue, day 108; DS17670

value: Fetal Lung, Right


title: Chromatin accessibility assay of Fetal Stomach; DS17659

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: DS17659
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.7127
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.7126
****************
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: GSM701521_UW.Fetal_Stomach.ChromatinAccessibility.H-23887.DS17659.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS17659.hg19.level.1.release.4
ANALYSIS TITLE: Mapping of Fetal Stomach Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fetal Stomach, Donor H-23887, Library DS17659 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.7703
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 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 22,445,235
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 54
FINDPEAKS_SCORE: 0.3162
FINDPEAKS_PERCENTILE: 20
HOTSPOT_SCORE: 0.3238
HOTSPOT_PERCENTILE: 22
IROC_SCORE: 0.989
IROC_PERCENTILE: 13
POISSON_SCORE: 0.3831
POISSON_PERCENTILE: 24
MAXIMUM_REPLICATE_CORRELATION: 0.99

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

ANALYSIS FILE NAME: GSM701521_UW.Fetal_Stomach.ChromatinAccessibility.H-23887.DS17659.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS17659.hg19.level.2.release.4
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Stomach Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from  Fetal Stomach, Donor H-23887, Library DS17659 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.7757
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 4
BROWSER_TRACK_NAME: FS DNase 87 59
BROWSER_TRACK_DESCRIPTION: UW Fetal Stomach DNase Hypersensitivity Donor H-23887 Library DS17659 EA Release 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 22,445,235
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 52
FINDPEAKS_SCORE: 0.3162
FINDPEAKS_PERCENTILE: 20
HOTSPOT_SCORE: 0.3238
HOTSPOT_PERCENTILE: 22
IROC_SCORE: 0.989
IROC_PERCENTILE: 13
POISSON_SCORE: 0.3831
POISSON_PERCENTILE: 24
MAXIMUM_REPLICATE_CORRELATION: 0.99

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

source_name: Fetal  primary tissue, day 108; DS17659

value: Fetal Stomach


title: Chromatin accessibility assay of CD3 Primary Cells; DS17534

description:
sample_term_id: CL_0000084
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Chromatin accessibility determination via DNase-seq
Library name: DS17534
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.6985
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.6984
****************
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: GSM701516_UW.CD3_Primary_Cells.ChromatinAccessibility.RO_01701.DS17534.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS17534.hg19.level.1.release.4
ANALYSIS TITLE: Mapping of CD3 Primary Cells Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on CD3 Primary Cells, Donor RO 01701, Library DS17534 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.7705
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 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 37,463,214
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 54
FINDPEAKS_SCORE: 0.3801
FINDPEAKS_PERCENTILE: 48
HOTSPOT_SCORE: 0.364
HOTSPOT_PERCENTILE: 43
IROC_SCORE: 0.9876
IROC_PERCENTILE: 9
POISSON_SCORE: 0.4339
POISSON_PERCENTILE: 50
MAXIMUM_REPLICATE_CORRELATION: 0.94

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

ANALYSIS FILE NAME: GSM701516_UW.CD3_Primary_Cells.ChromatinAccessibility.RO_01701.DS17534.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS17534.hg19.level.2.release.4
ANALYSIS TITLE: Raw Signal Density Graphs of CD3 Primary Cells Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from  CD3 Primary Cells, Donor RO 01701, Library DS17534 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.7759
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 4
BROWSER_TRACK_NAME: CD3 DNase 36 34
BROWSER_TRACK_DESCRIPTION: UW CD3 Primary Cells DNase Hypersensitivity Donor RO 01701 Library DS17534 EA Release 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 37,463,214
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 52
FINDPEAKS_SCORE: 0.3801
FINDPEAKS_PERCENTILE: 48
HOTSPOT_SCORE: 0.364
HOTSPOT_PERCENTILE: 43
IROC_SCORE: 0.9876
IROC_PERCENTILE: 9
POISSON_SCORE: 0.4339
POISSON_PERCENTILE: 50
MAXIMUM_REPLICATE_CORRELATION: 0.94

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

source_name: flow sorted CD3+ Cells, year 37; DS17534

value: CD3 Primary Cells

value: FHCRC HEIMFELD

value: Primary Cell

value: year 37

value: Male

value: Hispanic


title: Chromatin accessibility assay of Fetal Kidney; DS17522

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: DS17522
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.7066
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.7065
****************
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: GSM701515_UW.Fetal_Kidney.ChromatinAccessibility.H-23855.DS17522.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS17522.hg19.level.1.release.4
ANALYSIS TITLE: Mapping of Fetal Kidney Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fetal Kidney, Donor H-23855, Library DS17522 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.7702
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 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 37,648,545
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 54
FINDPEAKS_SCORE: 0.269
FINDPEAKS_PERCENTILE: 11
HOTSPOT_SCORE: 0.2777
HOTSPOT_PERCENTILE: 15
IROC_SCORE: 0.9847
IROC_PERCENTILE: 6
POISSON_SCORE: 0.3969
POISSON_PERCENTILE: 33
MAXIMUM_REPLICATE_CORRELATION: 0.91

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

ANALYSIS FILE NAME: GSM701515_UW.Fetal_Kidney.ChromatinAccessibility.H-23855.DS17522.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS17522.hg19.level.2.release.4
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Kidney Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from  Fetal Kidney, Donor H-23855, Library DS17522 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.7756
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 4
BROWSER_TRACK_NAME: FK DNase 55 22
BROWSER_TRACK_DESCRIPTION: UW Fetal Kidney DNase Hypersensitivity Donor H-23855 Library DS17522 EA Release 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 37,648,545
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 52
FINDPEAKS_SCORE: 0.269
FINDPEAKS_PERCENTILE: 11
HOTSPOT_SCORE: 0.2777
HOTSPOT_PERCENTILE: 15
IROC_SCORE: 0.9847
IROC_PERCENTILE: 6
POISSON_SCORE: 0.3969
POISSON_PERCENTILE: 33
MAXIMUM_REPLICATE_CORRELATION: 0.91

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

source_name: Fetal  primary tissue, day 85; DS17522

value: Fetal Kidney

value: genomic DNA

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

value: day 85

value: Female


title: Chromatin accessibility assay of Fetal Renal Cortex, Right; DS17545

description:
sample_term_id: UBERON_0001225
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Chromatin accessibility determination via DNase-seq
Library name: DS17545
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.7232
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.7231
****************
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: GSM701517_UW.Fetal_Renal_Cortex_Right.ChromatinAccessibility.H-23871.DS17545.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS17545.hg19.level.1.release.4
ANALYSIS TITLE: Mapping of Fetal Renal Cortex Right Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fetal Renal Cortex Right, Donor H-23871, Library DS17545 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.7708
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 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 38,809,773
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 54
FINDPEAKS_SCORE: 0.2461
FINDPEAKS_PERCENTILE: 4
HOTSPOT_SCORE: 0.2521
HOTSPOT_PERCENTILE: 6
IROC_SCORE: 0.984
IROC_PERCENTILE: 4
POISSON_SCORE: 0.3564
POISSON_PERCENTILE: 17
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM701517_UW.Fetal_Renal_Cortex_Right.ChromatinAccessibility.H-23871.DS17545.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS17545.hg19.level.2.release.4
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Renal Cortex Right Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from  Fetal Renal Cortex Right, Donor H-23871, Library DS17545 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.7762
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 4
BROWSER_TRACK_NAME: FRCR DNase 71 45
BROWSER_TRACK_DESCRIPTION: UW Fetal Renal Cortex Right DNase Hypersensitivity Donor H-23871 Library DS17545 EA Release 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 38,809,773
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 52
FINDPEAKS_SCORE: 0.2461
FINDPEAKS_PERCENTILE: 4
HOTSPOT_SCORE: 0.2521
HOTSPOT_PERCENTILE: 6
IROC_SCORE: 0.984
IROC_PERCENTILE: 4
POISSON_SCORE: 0.3564
POISSON_PERCENTILE: 17
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: Fetal  primary tissue, day 105; DS17545

value: Fetal Renal Cortex, Right

value: Primary Tissue

value: UW

value: fetal

value: day 105


title: Chromatin accessibility assay of CD56 Primary Cells; DS17443

description:
sample_term_id: CL_0000623
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Chromatin accessibility determination via DNase-seq
Library name: DS17443
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.7028
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.7027
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

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

ANALYSIS FILE NAME: GSM701508_UW.CD56_Primary_Cells.ChromatinAccessibility.RO_01701.DS17443.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS17443.hg19.level.1.release.4
ANALYSIS TITLE: Mapping of CD56 Primary Cells Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on CD56 Primary Cells, Donor RO 01701, Library DS17443 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.7717
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 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 30,212,749
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 54
FINDPEAKS_SCORE: 0.2299
FINDPEAKS_PERCENTILE: 2
HOTSPOT_SCORE: 0.2282
HOTSPOT_PERCENTILE: 2
IROC_SCORE: 0.9969
IROC_PERCENTILE: 85
POISSON_SCORE: 0.2621
POISSON_PERCENTILE: 2
MAXIMUM_REPLICATE_CORRELATION: 0.86

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

ANALYSIS FILE NAME: GSM701508_UW.CD56_Primary_Cells.ChromatinAccessibility.RO_01701.DS17443.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS17443.hg19.level.2.release.4
ANALYSIS TITLE: Raw Signal Density Graphs of CD56 Primary Cells Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from  CD56 Primary Cells, Donor RO 01701, Library DS17443 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.7771
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 4
BROWSER_TRACK_NAME: CD56 DNase 36 43
BROWSER_TRACK_DESCRIPTION: UW CD56 Primary Cells DNase Hypersensitivity Donor RO 01701 Library DS17443 EA Release 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 30,212,749
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 52
FINDPEAKS_SCORE: 0.2299
FINDPEAKS_PERCENTILE: 2
HOTSPOT_SCORE: 0.2282
HOTSPOT_PERCENTILE: 2
IROC_SCORE: 0.9969
IROC_PERCENTILE: 85
POISSON_SCORE: 0.2621
POISSON_PERCENTILE: 2
MAXIMUM_REPLICATE_CORRELATION: 0.86

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

source_name: flow sorted CD56+ Cells, year 37; DS17443

value: CD56 Primary Cells

value: Chromatin Accessibility

value: Qiagen minElut

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


title: Chromatin accessibility assay of Fetal Renal Pelvis, Right; DS17548

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: DS17548
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.7267
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.7266
****************
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: GSM701518_UW.Fetal_Renal_Pelvis_Right.ChromatinAccessibility.H-23871.DS17548.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS17548.hg19.level.1.release.4
ANALYSIS TITLE: Mapping of Fetal Renal Pelvis Right Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fetal Renal Pelvis Right, Donor H-23871, Library DS17548 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.7709
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 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 35,958,758
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 54
FINDPEAKS_SCORE: 0.3689
FINDPEAKS_PERCENTILE: 39
HOTSPOT_SCORE: 0.3599
HOTSPOT_PERCENTILE: 39
IROC_SCORE: 0.9899
IROC_PERCENTILE: 15
POISSON_SCORE: 0.4484
POISSON_PERCENTILE: 56
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM701518_UW.Fetal_Renal_Pelvis_Right.ChromatinAccessibility.H-23871.DS17548.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS17548.hg19.level.2.release.4
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Renal Pelvis Right Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from  Fetal Renal Pelvis Right, Donor H-23871, Library DS17548 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.7763
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 4
BROWSER_TRACK_NAME: FRPR DNase 71 48
BROWSER_TRACK_DESCRIPTION: UW Fetal Renal Pelvis Right DNase Hypersensitivity Donor H-23871 Library DS17548 EA Release 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 35,958,758
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 52
FINDPEAKS_SCORE: 0.3689
FINDPEAKS_PERCENTILE: 39
HOTSPOT_SCORE: 0.3599
HOTSPOT_PERCENTILE: 39
IROC_SCORE: 0.9899
IROC_PERCENTILE: 15
POISSON_SCORE: 0.4484
POISSON_PERCENTILE: 56
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: Fetal  primary tissue, day 105; DS17548

value: Fetal Renal Pelvis, Right


title: Chromatin accessibility assay of Fetal Thymus; DS17474

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: DS17474
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.7176
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.7175
****************
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: GSM701513_UW.Fetal_Thymus.ChromatinAccessibility.H-23833.DS17474.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS17474.hg19.level.1.release.4
ANALYSIS TITLE: Mapping of Fetal Thymus Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fetal Thymus, Donor H-23833, Library DS17474 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.7673
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 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 40,557,402
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 54
FINDPEAKS_SCORE: 0.2615
FINDPEAKS_PERCENTILE: 7
HOTSPOT_SCORE: 0.2517
HOTSPOT_PERCENTILE: 4
IROC_SCORE: 0.9976
IROC_PERCENTILE: 94
POISSON_SCORE: 0.3022
POISSON_PERCENTILE: 4
MAXIMUM_REPLICATE_CORRELATION: 0.92

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

ANALYSIS FILE NAME: GSM701513_UW.Fetal_Thymus.ChromatinAccessibility.H-23833.DS17474.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS17474.hg19.level.2.release.4
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Thymus Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from  Fetal Thymus, Donor H-23833, Library DS17474 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.7727
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 4
BROWSER_TRACK_NAME: FT DNase 33 74
BROWSER_TRACK_DESCRIPTION: UW Fetal Thymus DNase Hypersensitivity Donor H-23833 Library DS17474 EA Release 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 40,557,402
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 52
FINDPEAKS_SCORE: 0.2615
FINDPEAKS_PERCENTILE: 7
HOTSPOT_SCORE: 0.2517
HOTSPOT_PERCENTILE: 4
IROC_SCORE: 0.9976
IROC_PERCENTILE: 94
POISSON_SCORE: 0.3022
POISSON_PERCENTILE: 4
MAXIMUM_REPLICATE_CORRELATION: 0.92

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

source_name: Fetal  primary tissue, day 113; DS17474

value: Fetal Thymus

value: day 113

value: Male


title: Chromatin accessibility assay of Fetal Intestine, Large; DS17502

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: DS17502
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.7046
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.7045
****************
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: GSM701514_UW.Fetal_Intestine_Large.ChromatinAccessibility.H-23855.DS17502.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS17502.hg19.level.1.release.4
ANALYSIS TITLE: Mapping of Fetal Intestine Large Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fetal Intestine Large, Donor H-23855, Library DS17502 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.7700
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 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 31,196,282
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 54
FINDPEAKS_SCORE: 0.3462
FINDPEAKS_PERCENTILE: 30
HOTSPOT_SCORE: 0.3448
HOTSPOT_PERCENTILE: 33
IROC_SCORE: 0.9965
IROC_PERCENTILE: 74
POISSON_SCORE: 0.3361
POISSON_PERCENTILE: 13
MAXIMUM_REPLICATE_CORRELATION: 0.97

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

ANALYSIS FILE NAME: GSM701514_UW.Fetal_Intestine_Large.ChromatinAccessibility.H-23855.DS17502.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS17502.hg19.level.2.release.4
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-23855, Library DS17502 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.7754
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 4
BROWSER_TRACK_NAME: FIL DNase 55 02
BROWSER_TRACK_DESCRIPTION: UW Fetal Intestine Large DNase Hypersensitivity Donor H-23855 Library DS17502 EA Release 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 31,196,282
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 52
FINDPEAKS_SCORE: 0.3462
FINDPEAKS_PERCENTILE: 30
HOTSPOT_SCORE: 0.3448
HOTSPOT_PERCENTILE: 33
IROC_SCORE: 0.9965
IROC_PERCENTILE: 74
POISSON_SCORE: 0.3361
POISSON_PERCENTILE: 13
MAXIMUM_REPLICATE_CORRELATION: 0.97

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

source_name: Fetal  primary tissue, day 85; DS17502

value: Fetal Intestine, Large

value: genomic DNA


title: Chromatin accessibility assay of Fetal Renal Cortex; DS17455

description:
sample_term_id: UBERON_0001225
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Chromatin accessibility determination via DNase-seq
Library name: DS17455
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.7078
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.7077
****************
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: GSM701511_UW.Fetal_Renal_Cortex.ChromatinAccessibility.H-23833.DS17455.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS17455.hg19.level.1.release.4
ANALYSIS TITLE: Mapping of Fetal Renal Cortex Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fetal Renal Cortex, Donor H-23833, Library DS17455 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.7722
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 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 32,119,051
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 54
FINDPEAKS_SCORE: 0.5962
FINDPEAKS_PERCENTILE: 98
HOTSPOT_SCORE: 0.5839
HOTSPOT_PERCENTILE: 94
IROC_SCORE: 0.997
IROC_PERCENTILE: 87
POISSON_SCORE: 0.6235
POISSON_PERCENTILE: 100
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

ANALYSIS FILE NAME: GSM701511_UW.Fetal_Renal_Cortex.ChromatinAccessibility.H-23833.DS17455.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS17455.hg19.level.2.release.4
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Renal Cortex Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from  Fetal Renal Cortex, Donor H-23833, Library DS17455 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.7776
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 4
BROWSER_TRACK_NAME: FRC DNase 33 55
BROWSER_TRACK_DESCRIPTION: UW Fetal Renal Cortex DNase Hypersensitivity Donor H-23833 Library DS17455 EA Release 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 32,119,051
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 52
FINDPEAKS_SCORE: 0.5962
FINDPEAKS_PERCENTILE: 98
HOTSPOT_SCORE: 0.5839
HOTSPOT_PERCENTILE: 94
IROC_SCORE: 0.997
IROC_PERCENTILE: 87
POISSON_SCORE: 0.6235
POISSON_PERCENTILE: 100
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

source_name: Fetal  primary tissue, day 113; DS17455

value: Fetal Renal Cortex

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


title: Chromatin accessibility assay of CD19 Primary Cells; DS17440

description:
sample_term_id: CL_0000236
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Chromatin accessibility determination via DNase-seq
Library name: DS17440
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.6974
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.6973
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

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

ANALYSIS FILE NAME: GSM701507_UW.CD19_Primary_Cells.ChromatinAccessibility.RO_01701.DS17440.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS17440.hg19.level.1.release.4
ANALYSIS TITLE: Mapping of CD19 Primary Cells Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on CD19 Primary Cells, Donor RO 01701, Library DS17440 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.7716
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 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 27,628,541
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 54
FINDPEAKS_SCORE: 0.3076
FINDPEAKS_PERCENTILE: 19
HOTSPOT_SCORE: 0.3082
HOTSPOT_PERCENTILE: 19
IROC_SCORE: 0.9936
IROC_PERCENTILE: 46
POISSON_SCORE: 0.3718
POISSON_PERCENTILE: 20
MAXIMUM_REPLICATE_CORRELATION: 0.99

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

ANALYSIS FILE NAME: GSM701507_UW.CD19_Primary_Cells.ChromatinAccessibility.RO_01701.DS17440.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS17440.hg19.level.2.release.4
ANALYSIS TITLE: Raw Signal Density Graphs of CD19 Primary Cells Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from  CD19 Primary Cells, Donor RO 01701, Library DS17440 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.7770
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 4
BROWSER_TRACK_NAME: CD19 DNase 36 40
BROWSER_TRACK_DESCRIPTION: UW CD19 Primary Cells DNase Hypersensitivity Donor RO 01701 Library DS17440 EA Release 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 27,628,541
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 52
FINDPEAKS_SCORE: 0.3076
FINDPEAKS_PERCENTILE: 19
HOTSPOT_SCORE: 0.3082
HOTSPOT_PERCENTILE: 19
IROC_SCORE: 0.9936
IROC_PERCENTILE: 46
POISSON_SCORE: 0.3718
POISSON_PERCENTILE: 20
MAXIMUM_REPLICATE_CORRELATION: 0.99

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

source_name: flow sorted CD19+ Cells, year 37; DS17440

value: CD19 Primary Cells

value: FHCRC HEIMFELD

value: Primary Cell

value: year 37

value: Hispanic


title: Chromatin accessibility assay of Fetal Lung, Left; DS17464

description:
sample_term_id: UBERON_0002168
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Chromatin accessibility determination via DNase-seq
Library name: DS17464
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.7276
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.7275
****************
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: GSM701512_UW.Fetal_Lung_Left.ChromatinAccessibility.H-23833.DS17464.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS17464.hg19.level.1.release.4
ANALYSIS TITLE: Mapping of Fetal Lung Left Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fetal Lung Left, Donor H-23833, Library DS17464 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.7724
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 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 40,673,123
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 54
FINDPEAKS_SCORE: 0.471
FINDPEAKS_PERCENTILE: 78
HOTSPOT_SCORE: 0.4592
HOTSPOT_PERCENTILE: 74
IROC_SCORE: 0.9935
IROC_PERCENTILE: 43
POISSON_SCORE: 0.5137
POISSON_PERCENTILE: 76
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

ANALYSIS FILE NAME: GSM701512_UW.Fetal_Lung_Left.ChromatinAccessibility.H-23833.DS17464.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS17464.hg19.level.2.release.4
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Lung Left Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from  Fetal Lung Left, Donor H-23833, Library DS17464 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.7778
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 4
BROWSER_TRACK_NAME: FLL DNase 33 64
BROWSER_TRACK_DESCRIPTION: UW Fetal Lung Left DNase Hypersensitivity Donor H-23833 Library DS17464 EA Release 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 40,673,123
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 52
FINDPEAKS_SCORE: 0.471
FINDPEAKS_PERCENTILE: 78
HOTSPOT_SCORE: 0.4592
HOTSPOT_PERCENTILE: 74
IROC_SCORE: 0.9935
IROC_PERCENTILE: 43
POISSON_SCORE: 0.5137
POISSON_PERCENTILE: 76
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

source_name: Fetal  primary tissue, day 113; DS17464

value: Fetal Lung, Left

value: Primary Tissue

value: UW

value: fetal


title: Chromatin accessibility assay of Fetal Intestine, Small; DS17425

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: DS17425
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.7060
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.7059
****************
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: GSM701504_UW.Fetal_Intestine_Small.ChromatinAccessibility.H-23808.DS17425.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS17425.hg19.level.1.release.4
ANALYSIS TITLE: Mapping of Fetal Intestine Small Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fetal Intestine Small, Donor H-23808, Library DS17425 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.7712
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 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 30,474,532
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 54
FINDPEAKS_SCORE: 0.3907
FINDPEAKS_PERCENTILE: 56
HOTSPOT_SCORE: 0.3824
HOTSPOT_PERCENTILE: 48
IROC_SCORE: 0.9669
IROC_PERCENTILE: 2
POISSON_SCORE: 0.428
POISSON_PERCENTILE: 43
MAXIMUM_REPLICATE_CORRELATION: 0.99

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

ANALYSIS FILE NAME: GSM701504_UW.Fetal_Intestine_Small.ChromatinAccessibility.H-23808.DS17425.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS17425.hg19.level.2.release.4
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-23808, Library DS17425 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.7766
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 4
BROWSER_TRACK_NAME: FIS DNase 08 25
BROWSER_TRACK_DESCRIPTION: UW Fetal Intestine Small DNase Hypersensitivity Donor H-23808 Library DS17425 EA Release 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 30,474,532
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 52
FINDPEAKS_SCORE: 0.3907
FINDPEAKS_PERCENTILE: 56
HOTSPOT_SCORE: 0.3824
HOTSPOT_PERCENTILE: 48
IROC_SCORE: 0.9669
IROC_PERCENTILE: 2
POISSON_SCORE: 0.428
POISSON_PERCENTILE: 43
MAXIMUM_REPLICATE_CORRELATION: 0.99

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

source_name: Fetal  primary tissue, day 115; DS17425

value: Fetal Intestine, Small

value: day 115

value: Chromatin Accessibility

value: Qiagen minElut

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


title: Chromatin accessibility assay of Fetal Renal Cortex; DS17387

description:
sample_term_id: UBERON_0001225
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Chromatin accessibility determination via DNase-seq
Library name: DS17387
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.7075
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.7074
****************
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: GSM701502_UW.Fetal_Renal_Cortex.ChromatinAccessibility.H-23790.DS17387.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS17387.hg19.level.1.release.4
ANALYSIS TITLE: Mapping of Fetal Renal Cortex Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fetal Renal Cortex, Donor H-23790, Library DS17387 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.7679
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 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 27,523,931
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 54
FINDPEAKS_SCORE: 0.5648
FINDPEAKS_PERCENTILE: 93
HOTSPOT_SCORE: 0.5543
HOTSPOT_PERCENTILE: 93
IROC_SCORE: 0.9952
IROC_PERCENTILE: 61
POISSON_SCORE: 0.595
POISSON_PERCENTILE: 98
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

ANALYSIS FILE NAME: GSM701502_UW.Fetal_Renal_Cortex.ChromatinAccessibility.H-23790.DS17387.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS17387.hg19.level.2.release.4
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Renal Cortex Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from  Fetal Renal Cortex, Donor H-23790, Library DS17387 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.7733
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 4
BROWSER_TRACK_NAME: FRC DNase 90 87
BROWSER_TRACK_DESCRIPTION: UW Fetal Renal Cortex DNase Hypersensitivity Donor H-23790 Library DS17387 EA Release 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 27,523,931
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 52
FINDPEAKS_SCORE: 0.5648
FINDPEAKS_PERCENTILE: 93
HOTSPOT_SCORE: 0.5543
HOTSPOT_PERCENTILE: 93
IROC_SCORE: 0.9952
IROC_PERCENTILE: 61
POISSON_SCORE: 0.595
POISSON_PERCENTILE: 98
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

source_name: Fetal  primary tissue, day 108; DS17387

value: genomic DNA

value: day 108

value: Male


title: Chromatin accessibility assay of CD20 Primary Cells; DS17371

description:
sample_term_id: CL_0000236
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Chromatin accessibility determination via DNase-seq
Library name: DS17371
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.6978
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.6977
****************
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: GSM701500_UW.CD20_Primary_Cells.ChromatinAccessibility.RO_01778.DS17371.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS17371.hg19.level.1.release.4
ANALYSIS TITLE: Mapping of CD20 Primary Cells Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on CD20 Primary Cells, Donor RO 01778, Library DS17371 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.7676
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 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 31,194,258
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 54
FINDPEAKS_SCORE: 0.3311
FINDPEAKS_PERCENTILE: 24
HOTSPOT_SCORE: 0.3237
HOTSPOT_PERCENTILE: 20
IROC_SCORE: 0.9957
IROC_PERCENTILE: 67
POISSON_SCORE: 0.3846
POISSON_PERCENTILE: 26
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM701500_UW.CD20_Primary_Cells.ChromatinAccessibility.RO_01778.DS17371.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS17371.hg19.level.2.release.4
ANALYSIS TITLE: Raw Signal Density Graphs of CD20 Primary Cells Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from  CD20 Primary Cells, Donor RO 01778, Library DS17371 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.7730
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 4
BROWSER_TRACK_NAME: CD20 DNase 78 71
BROWSER_TRACK_DESCRIPTION: UW CD20 Primary Cells DNase Hypersensitivity Donor RO 01778 Library DS17371 EA Release 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 31,194,258
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 52
FINDPEAKS_SCORE: 0.3311
FINDPEAKS_PERCENTILE: 24
HOTSPOT_SCORE: 0.3237
HOTSPOT_PERCENTILE: 20
IROC_SCORE: 0.9957
IROC_PERCENTILE: 67
POISSON_SCORE: 0.3846
POISSON_PERCENTILE: 26
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: flow sorted CD20+ Cells, year 43; DS17371

value: CD20 Primary Cells

value: year 43

value: Female

value: Caucasian