title: Chromatin accessibility assay of Fetal Spleen; DS17448

description:
sample_term_id: UBERON_0002106
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Chromatin accessibility determination via DNase-seq
Library name: DS17448
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.7259
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.7258
****************
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: GSM701509_UW.Fetal_Spleen.ChromatinAccessibility.H-23399.DS17448.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS17448.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of Fetal Spleen Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fetal Spleen, Donor H-23399, Library DS17448 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.10367
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: Chromatin Accessibility
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 28,837,173
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 47
FINDPEAKS_SCORE: 0.311
FINDPEAKS_PERCENTILE: 15
HOTSPOT_SCORE: 0.3063
HOTSPOT_PERCENTILE: 15
IROC_SCORE: 0.9906
IROC_PERCENTILE: 19
POISSON_SCORE: 0.382
POISSON_PERCENTILE: 23
MAXIMUM_REPLICATE_CORRELATION:

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

ANALYSIS FILE NAME: GSM701509_UW.Fetal_Spleen.ChromatinAccessibility.H-23399.DS17448.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS17448.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Spleen Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from  Fetal Spleen, Donor H-23399, Library DS17448 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.10320
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: FSp DNase 99 48
BROWSER_TRACK_DESCRIPTION: UW Fetal Spleen DNase Hypersensitivity Donor H-23399 Library DS17448 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 28,837,173
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 47
FINDPEAKS_SCORE: 0.311
FINDPEAKS_PERCENTILE: 15
HOTSPOT_SCORE: 0.3063
HOTSPOT_PERCENTILE: 15
IROC_SCORE: 0.9906
IROC_PERCENTILE: 19
POISSON_SCORE: 0.382
POISSON_PERCENTILE: 23
MAXIMUM_REPLICATE_CORRELATION:

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

source_name: Fetal  primary tissue, day 112; DS17448

value: Fetal Spleen

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

value: day 112

value: Unknown


title: Chromatin accessibility assay of Fetal Muscle, Leg; DS17429

status: Public on Apr 14 2011

type: SRA

city: Seattle

first: Northwest

last: REMC

state: WA

country: USA

institute: University of Washington

description:
sample_term_id: UBERON_0001383
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Chromatin accessibility determination via DNase-seq
Library name: DS17429
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.7282
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.7281
****************
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: GSM701505_UW.Fetal_Muscle_Leg.ChromatinAccessibility.H-23808.DS17429.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS17429.hg19.level.1.release.4
ANALYSIS TITLE: Mapping of Fetal Muscle Leg Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fetal Muscle Leg, Donor H-23808, Library DS17429 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.7713
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: 27,903,762
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 54
FINDPEAKS_SCORE: 0.3493
FINDPEAKS_PERCENTILE: 31
HOTSPOT_SCORE: 0.3419
HOTSPOT_PERCENTILE: 31
IROC_SCORE: 0.9907
IROC_PERCENTILE: 20
POISSON_SCORE: 0.4305
POISSON_PERCENTILE: 48
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM701505_UW.Fetal_Muscle_Leg.ChromatinAccessibility.H-23808.DS17429.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS17429.hg19.level.2.release.4
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Muscle Leg Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from  Fetal Muscle Leg, Donor H-23808, Library DS17429 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.7767
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: FML DNase 08 29
BROWSER_TRACK_DESCRIPTION: UW Fetal Muscle Leg DNase Hypersensitivity Donor H-23808 Library DS17429 EA Release 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 27,903,762
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 52
FINDPEAKS_SCORE: 0.3493
FINDPEAKS_PERCENTILE: 31
HOTSPOT_SCORE: 0.3419
HOTSPOT_PERCENTILE: 31
IROC_SCORE: 0.9907
IROC_PERCENTILE: 20
POISSON_SCORE: 0.4305
POISSON_PERCENTILE: 48
MAXIMUM_REPLICATE_CORRELATION: NA

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

molecule: genomic DNA

organism: Homo sapiens

source_name: Fetal  primary tissue, day 115; DS17429

extract_protocol: Library construction protocol: Single read - Illumina

tag: sample alias

tag: sample common name

value: Fetal Muscle, Leg

tag: molecule

value: genomic DNA

tag: disease

value: Primary Tissue

value: UW

value: fetal

value: day 115

value: Male

value: Chromatin Accessibility

value: Qiagen minElut

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


title: Chromatin accessibility assay of Fetal Muscle, Arm; DS17432

description:
sample_term_id: UBERON_0001499
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Chromatin accessibility determination via DNase-seq
Library name: DS17432
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.7272
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.7271
****************
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: GSM701506_UW.Fetal_Muscle_Arm.ChromatinAccessibility.H-23808.DS17432.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS17432.hg19.level.1.release.4
ANALYSIS TITLE: Mapping of Fetal Muscle Arm Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fetal Muscle Arm, Donor H-23808, Library DS17432 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.7714
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: 30,970,938
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 54
FINDPEAKS_SCORE: 0.3798
FINDPEAKS_PERCENTILE: 46
HOTSPOT_SCORE: 0.3658
HOTSPOT_PERCENTILE: 44
IROC_SCORE: 0.992
IROC_PERCENTILE: 30
POISSON_SCORE: 0.4468
POISSON_PERCENTILE: 54
MAXIMUM_REPLICATE_CORRELATION: 0.91

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

ANALYSIS FILE NAME: GSM701506_UW.Fetal_Muscle_Arm.ChromatinAccessibility.H-23808.DS17432.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS17432.hg19.level.2.release.4
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Muscle Arm Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from  Fetal Muscle Arm, Donor H-23808, Library DS17432 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.7768
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: FMA DNase 08 32
BROWSER_TRACK_DESCRIPTION: UW Fetal Muscle Arm DNase Hypersensitivity Donor H-23808 Library DS17432 EA Release 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 30,970,938
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 52
FINDPEAKS_SCORE: 0.3798
FINDPEAKS_PERCENTILE: 46
HOTSPOT_SCORE: 0.3658
HOTSPOT_PERCENTILE: 44
IROC_SCORE: 0.992
IROC_PERCENTILE: 30
POISSON_SCORE: 0.4468
POISSON_PERCENTILE: 54
MAXIMUM_REPLICATE_CORRELATION: 0.91

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

source_name: Fetal  primary tissue, day 115; DS17432

value: Fetal Muscle, Arm


title: Chromatin accessibility assay of Fetal Renal Pelvis; DS17451

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: DS17451
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.7120
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.7119
****************
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: GSM701510_UW.Fetal_Renal_Pelvis.ChromatinAccessibility.H-23833.DS17451.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS17451.hg19.level.1.release.4
ANALYSIS TITLE: Mapping of Fetal Renal Pelvis Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fetal Renal Pelvis, Donor H-23833, Library DS17451 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.7720
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: 36,563,105
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 54
FINDPEAKS_SCORE: 0.3838
FINDPEAKS_PERCENTILE: 50
HOTSPOT_SCORE: 0.3726
HOTSPOT_PERCENTILE: 46
IROC_SCORE: 0.9905
IROC_PERCENTILE: 17
POISSON_SCORE: 0.4517
POISSON_PERCENTILE: 57
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

ANALYSIS FILE NAME: GSM701510_UW.Fetal_Renal_Pelvis.ChromatinAccessibility.H-23833.DS17451.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS17451.hg19.level.2.release.4
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Renal Pelvis Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from  Fetal Renal Pelvis, Donor H-23833, Library DS17451 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.7774
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: FRP DNase 33 51
BROWSER_TRACK_DESCRIPTION: UW Fetal Renal Pelvis DNase Hypersensitivity Donor H-23833 Library DS17451 EA Release 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 36,563,105
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 52
FINDPEAKS_SCORE: 0.3838
FINDPEAKS_PERCENTILE: 50
HOTSPOT_SCORE: 0.3726
HOTSPOT_PERCENTILE: 46
IROC_SCORE: 0.9905
IROC_PERCENTILE: 17
POISSON_SCORE: 0.4517
POISSON_PERCENTILE: 57
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

source_name: Fetal  primary tissue, day 113; DS17451

value: Fetal Renal Pelvis

value: day 113


title: Chromatin accessibility assay of CD8 Primary Cells; DS17332

description:
sample_term_id: CL_0000625
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Chromatin accessibility determination via DNase-seq
Library name: DS17332
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.7032
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.7031
****************
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: GSM701499_UW.CD8_Primary_Cells.ChromatinAccessibility.RO_01689.DS17332.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS17332.hg19.level.1.release.4
ANALYSIS TITLE: Mapping of CD8 Primary Cells Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on CD8 Primary Cells, Donor RO 01689, Library DS17332 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.7725
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: 25,588,179
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 54
FINDPEAKS_SCORE: 0.2729
FINDPEAKS_PERCENTILE: 13
HOTSPOT_SCORE: 0.2739
HOTSPOT_PERCENTILE: 11
IROC_SCORE: 0.9955
IROC_PERCENTILE: 63
POISSON_SCORE: 0.3195
POISSON_PERCENTILE: 9
MAXIMUM_REPLICATE_CORRELATION: 0.93

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

ANALYSIS FILE NAME: GSM701499_UW.CD8_Primary_Cells.ChromatinAccessibility.RO_01689.DS17332.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS17332.hg19.level.2.release.4
ANALYSIS TITLE: Raw Signal Density Graphs of CD8 Primary Cells Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from  CD8 Primary Cells, Donor RO 01689, Library DS17332 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.7779
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: CD8 DNase 27 32
BROWSER_TRACK_DESCRIPTION: UW CD8 Primary Cells DNase Hypersensitivity Donor RO 01689 Library DS17332 EA Release 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 25,588,179
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 52
FINDPEAKS_SCORE: 0.2729
FINDPEAKS_PERCENTILE: 13
HOTSPOT_SCORE: 0.2739
HOTSPOT_PERCENTILE: 11
IROC_SCORE: 0.9955
IROC_PERCENTILE: 63
POISSON_SCORE: 0.3195
POISSON_PERCENTILE: 9
MAXIMUM_REPLICATE_CORRELATION: 0.93

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

source_name: flow sorted CD8+ Cells, year 34; DS17332

value: CD8 Primary Cells

value: FHCRC HEIMFELD

value: Primary Cell

tag: markers

value: year 34

value: Female

value: Caucasian


title: Chromatin accessibility assay of Fetal Intestine, Small; DS17317

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: DS17317
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.7056
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.7055
****************
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: GSM701496_UW.Fetal_Intestine_Small.ChromatinAccessibility.H-23769.DS17317.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS17317.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-23769, Library DS17317 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.7719
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: 25,304,735
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 54
FINDPEAKS_SCORE: 0.3319
FINDPEAKS_PERCENTILE: 26
HOTSPOT_SCORE: 0.3255
HOTSPOT_PERCENTILE: 24
IROC_SCORE: 0.9972
IROC_PERCENTILE: 89
POISSON_SCORE: 0.3885
POISSON_PERCENTILE: 30
MAXIMUM_REPLICATE_CORRELATION: 0.99

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

ANALYSIS FILE NAME: GSM701496_UW.Fetal_Intestine_Small.ChromatinAccessibility.H-23769.DS17317.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS17317.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-23769, Library DS17317 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.7773
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 69 17
BROWSER_TRACK_DESCRIPTION: UW Fetal Intestine Small DNase Hypersensitivity Donor H-23769 Library DS17317 EA Release 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 25,304,735
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 52
FINDPEAKS_SCORE: 0.3319
FINDPEAKS_PERCENTILE: 26
HOTSPOT_SCORE: 0.3255
HOTSPOT_PERCENTILE: 24
IROC_SCORE: 0.9972
IROC_PERCENTILE: 89
POISSON_SCORE: 0.3885
POISSON_PERCENTILE: 30
MAXIMUM_REPLICATE_CORRELATION: 0.99

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

source_name: Fetal  primary tissue, day 108; DS17317

value: Fetal Intestine, Small

value: genomic DNA

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

value: Primary Tissue

value: day 108


title: Chromatin accessibility assay of CD14 Primary Cells; DS17391

description:
sample_term_id: CL_0001054
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Chromatin accessibility determination via DNase-seq
Library name: DS17391
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.6960
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.6959
****************
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: GSM701503_UW.CD14_Primary_Cells.ChromatinAccessibility.RO_01689.DS17391.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS17391.hg19.level.1.release.4
ANALYSIS TITLE: Mapping of CD14 Primary Cells Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on CD14 Primary Cells, Donor RO 01689, Library DS17391 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.7680
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: 23,022,907
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 54
FINDPEAKS_SCORE: 0.3921
FINDPEAKS_PERCENTILE: 57
HOTSPOT_SCORE: 0.3947
HOTSPOT_PERCENTILE: 56
IROC_SCORE: 0.9979
IROC_PERCENTILE: 98
POISSON_SCORE: 0.3997
POISSON_PERCENTILE: 37
MAXIMUM_REPLICATE_CORRELATION: 0.97

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

ANALYSIS FILE NAME: GSM701503_UW.CD14_Primary_Cells.ChromatinAccessibility.RO_01689.DS17391.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS17391.hg19.level.2.release.4
ANALYSIS TITLE: Raw Signal Density Graphs of CD14 Primary Cells Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from  CD14 Primary Cells, Donor RO 01689, Library DS17391 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.7734
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: CD14 DNase 27 91
BROWSER_TRACK_DESCRIPTION: UW CD14 Primary Cells DNase Hypersensitivity Donor RO 01689 Library DS17391 EA Release 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 23,022,907
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 52
FINDPEAKS_SCORE: 0.3921
FINDPEAKS_PERCENTILE: 57
HOTSPOT_SCORE: 0.3947
HOTSPOT_PERCENTILE: 56
IROC_SCORE: 0.9979
IROC_PERCENTILE: 98
POISSON_SCORE: 0.3997
POISSON_PERCENTILE: 37
MAXIMUM_REPLICATE_CORRELATION: 0.97

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

source_name: flow sorted CD14+ Cells, year 34; DS17391

value: CD14 Primary Cells

value: Chromatin Accessibility


title: Chromatin accessibility assay of Fetal Renal Cortex; DS17307

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: DS17307
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.7071
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.7070
****************
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: GSM701494_UW.Fetal_Renal_Cortex.ChromatinAccessibility.H-23769.DS17307.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS17307.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-23769, Library DS17307 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.7715
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: 32,880,966
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 54
FINDPEAKS_SCORE: 0.4058
FINDPEAKS_PERCENTILE: 65
HOTSPOT_SCORE: 0.3954
HOTSPOT_PERCENTILE: 57
IROC_SCORE: 0.9919
IROC_PERCENTILE: 28
POISSON_SCORE: 0.4873
POISSON_PERCENTILE: 65
MAXIMUM_REPLICATE_CORRELATION: 0.9

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

ANALYSIS FILE NAME: GSM701494_UW.Fetal_Renal_Cortex.ChromatinAccessibility.H-23769.DS17307.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS17307.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-23769, Library DS17307 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.7769
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 69 07
BROWSER_TRACK_DESCRIPTION: UW Fetal Renal Cortex DNase Hypersensitivity Donor H-23769 Library DS17307 EA Release 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 32,880,966
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 52
FINDPEAKS_SCORE: 0.4058
FINDPEAKS_PERCENTILE: 65
HOTSPOT_SCORE: 0.3954
HOTSPOT_PERCENTILE: 57
IROC_SCORE: 0.9919
IROC_PERCENTILE: 28
POISSON_SCORE: 0.4873
POISSON_PERCENTILE: 65
MAXIMUM_REPLICATE_CORRELATION: 0.9

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

source_name: Fetal  primary tissue, day 108; DS17307

value: Fetal Renal Cortex

value: UW

value: fetal

value: Male

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; DS17381

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: DS17381
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.7117
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.7116
****************
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: GSM701501_UW.Fetal_Renal_Pelvis.ChromatinAccessibility.H-23790.DS17381.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS17381.hg19.level.1.release.4
ANALYSIS TITLE: Mapping of Fetal Renal Pelvis Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fetal Renal Pelvis, Donor H-23790, Library DS17381 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.7677
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: 32,094,923
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 54
FINDPEAKS_SCORE: 0.4876
FINDPEAKS_PERCENTILE: 81
HOTSPOT_SCORE: 0.4824
HOTSPOT_PERCENTILE: 81
IROC_SCORE: 0.994
IROC_PERCENTILE: 48
POISSON_SCORE: 0.5473
POISSON_PERCENTILE: 87
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

ANALYSIS FILE NAME: GSM701501_UW.Fetal_Renal_Pelvis.ChromatinAccessibility.H-23790.DS17381.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS17381.hg19.level.2.release.4
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Renal Pelvis Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from  Fetal Renal Pelvis, Donor H-23790, Library DS17381 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.7731
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: FRP DNase 90 81
BROWSER_TRACK_DESCRIPTION: UW Fetal Renal Pelvis DNase Hypersensitivity Donor H-23790 Library DS17381 EA Release 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 32,094,923
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 52
FINDPEAKS_SCORE: 0.4876
FINDPEAKS_PERCENTILE: 81
HOTSPOT_SCORE: 0.4824
HOTSPOT_PERCENTILE: 81
IROC_SCORE: 0.994
IROC_PERCENTILE: 48
POISSON_SCORE: 0.5473
POISSON_PERCENTILE: 87
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

source_name: Fetal  primary tissue, day 108; DS17381

value: Fetal Renal Pelvis


title: Chromatin accessibility assay of CD19 Primary Cells; DS17281

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: DS17281
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.6970
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.6969
****************
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: GSM701493_UW.CD19_Primary_Cells.ChromatinAccessibility.RO_01689.DS17281.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS17281.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 01689, Library DS17281 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.7683
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: 25,191,144
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 54
FINDPEAKS_SCORE: 0.3926
FINDPEAKS_PERCENTILE: 59
HOTSPOT_SCORE: 0.3992
HOTSPOT_PERCENTILE: 59
IROC_SCORE: 0.9967
IROC_PERCENTILE: 80
POISSON_SCORE: 0.4285
POISSON_PERCENTILE: 44
MAXIMUM_REPLICATE_CORRELATION: 1.0

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

ANALYSIS FILE NAME: GSM701493_UW.CD19_Primary_Cells.ChromatinAccessibility.RO_01689.DS17281.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS17281.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 01689, Library DS17281 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.7737
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 27 81
BROWSER_TRACK_DESCRIPTION: UW CD19 Primary Cells DNase Hypersensitivity Donor RO 01689 Library DS17281 EA Release 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 25,191,144
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 52
FINDPEAKS_SCORE: 0.3926
FINDPEAKS_PERCENTILE: 59
HOTSPOT_SCORE: 0.3992
HOTSPOT_PERCENTILE: 59
IROC_SCORE: 0.9967
IROC_PERCENTILE: 80
POISSON_SCORE: 0.4285
POISSON_PERCENTILE: 44
MAXIMUM_REPLICATE_CORRELATION: 1.0

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

source_name: flow sorted CD19+ Cells, year 34; DS17281

value: CD19 Primary Cells

value: FHCRC HEIMFELD

value: Primary Cell

value: year 34


title: Chromatin accessibility assay of Fetal Stomach; DS17325

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: DS17325
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.7124
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.7123
****************
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: GSM701498_UW.Fetal_Stomach.ChromatinAccessibility.H-23769.DS17325.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS17325.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-23769, Library DS17325 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.7723
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: 22,490,944
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 54
FINDPEAKS_SCORE: 0.2628
FINDPEAKS_PERCENTILE: 9
HOTSPOT_SCORE: 0.2743
HOTSPOT_PERCENTILE: 13
IROC_SCORE: 0.9908
IROC_PERCENTILE: 22
POISSON_SCORE: 0.3366
POISSON_PERCENTILE: 15
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

ANALYSIS FILE NAME: GSM701498_UW.Fetal_Stomach.ChromatinAccessibility.H-23769.DS17325.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS17325.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-23769, Library DS17325 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.7777
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 69 25
BROWSER_TRACK_DESCRIPTION: UW Fetal Stomach DNase Hypersensitivity Donor H-23769 Library DS17325 EA Release 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 22,490,944
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 52
FINDPEAKS_SCORE: 0.2628
FINDPEAKS_PERCENTILE: 9
HOTSPOT_SCORE: 0.2743
HOTSPOT_PERCENTILE: 13
IROC_SCORE: 0.9908
IROC_PERCENTILE: 22
POISSON_SCORE: 0.3366
POISSON_PERCENTILE: 15
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

source_name: Fetal  primary tissue, day 108; DS17325

value: Fetal Stomach

value: genomic DNA


title: Chromatin accessibility assay of CD19 Primary Cells; DS17186

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: DS17186
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.6966
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.6965
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

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

ANALYSIS FILE NAME: GSM701492_UW.CD19_Primary_Cells.ChromatinAccessibility.RO_01679.DS17186.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS17186.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 01679, Library DS17186 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.7690
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: 27,493,357
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 54
FINDPEAKS_SCORE: 0.4227
FINDPEAKS_PERCENTILE: 69
HOTSPOT_SCORE: 0.427
HOTSPOT_PERCENTILE: 67
IROC_SCORE: 0.9951
IROC_PERCENTILE: 57
POISSON_SCORE: 0.457
POISSON_PERCENTILE: 59
MAXIMUM_REPLICATE_CORRELATION: 1.0

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

ANALYSIS FILE NAME: GSM701492_UW.CD19_Primary_Cells.ChromatinAccessibility.RO_01679.DS17186.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS17186.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 01679, Library DS17186 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.7744
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 21 86
BROWSER_TRACK_DESCRIPTION: UW CD19 Primary Cells DNase Hypersensitivity Donor RO 01679 Library DS17186 EA Release 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 27,493,357
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 52
FINDPEAKS_SCORE: 0.4227
FINDPEAKS_PERCENTILE: 69
HOTSPOT_SCORE: 0.427
HOTSPOT_PERCENTILE: 67
IROC_SCORE: 0.9951
IROC_PERCENTILE: 57
POISSON_SCORE: 0.457
POISSON_PERCENTILE: 59
MAXIMUM_REPLICATE_CORRELATION: 1.0

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

source_name: flow sorted CD19+ Cells, year 21; DS17186

value: year 21

value: Caucasian


title: Chromatin accessibility assay of Fetal Thymus; DS17323

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: DS17323
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.7172
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.7171
****************
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: GSM701497_UW.Fetal_Thymus.ChromatinAccessibility.H-23769.DS17323.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS17323.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-23769, Library DS17323 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.7721
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: 29,292,637
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 54
FINDPEAKS_SCORE: 0.273
FINDPEAKS_PERCENTILE: 15
HOTSPOT_SCORE: 0.2705
HOTSPOT_PERCENTILE: 9
IROC_SCORE: 0.9962
IROC_PERCENTILE: 70
POISSON_SCORE: 0.3133
POISSON_PERCENTILE: 6
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

ANALYSIS FILE NAME: GSM701497_UW.Fetal_Thymus.ChromatinAccessibility.H-23769.DS17323.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS17323.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-23769, Library DS17323 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.7775
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 69 23
BROWSER_TRACK_DESCRIPTION: UW Fetal Thymus DNase Hypersensitivity Donor H-23769 Library DS17323 EA Release 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 29,292,637
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 52
FINDPEAKS_SCORE: 0.273
FINDPEAKS_PERCENTILE: 15
HOTSPOT_SCORE: 0.2705
HOTSPOT_PERCENTILE: 9
IROC_SCORE: 0.9962
IROC_PERCENTILE: 70
POISSON_SCORE: 0.3133
POISSON_PERCENTILE: 6
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

source_name: Fetal  primary tissue, day 108; DS17323

value: Fetal Thymus

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

value: Primary Tissue

value: day 108


title: Chromatin accessibility assay of Moblized CD4 Primary Cells; DS16955

description:
sample_term_id: CL_0000492
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Chromatin accessibility determination via DNase-seq
Library name: DS16955
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.7015
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.7014
****************
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: GSM701489_UW.Mobilized_CD4_Primary_Cells.ChromatinAccessibility.RO_01679.DS16955.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS16955.hg19.level.1.release.4
ANALYSIS TITLE: Mapping of Mobilized CD4 Primary Cells Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Mobilized CD4 Primary Cells, Donor RO 01679, Library DS16955 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.7674
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: 39,459,639
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 54
FINDPEAKS_SCORE: 0.371
FINDPEAKS_PERCENTILE: 41
HOTSPOT_SCORE: 0.3595
HOTSPOT_PERCENTILE: 35
IROC_SCORE: 0.9936
IROC_PERCENTILE: 46
POISSON_SCORE: 0.4193
POISSON_PERCENTILE: 41
MAXIMUM_REPLICATE_CORRELATION: 0.99

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

ANALYSIS FILE NAME: GSM701489_UW.Mobilized_CD4_Primary_Cells.ChromatinAccessibility.RO_01679.DS16955.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS16955.hg19.level.2.release.4
ANALYSIS TITLE: Raw Signal Density Graphs of Mobilized CD4 Primary Cells Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from  Mobilized CD4 Primary Cells, Donor RO 01679, Library DS16955 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.7728
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: MCD4 DNase 79 55
BROWSER_TRACK_DESCRIPTION: UW Mobilized CD4 Primary Cells DNase Hypersensitivity Donor RO 01679 Library DS16955 EA Release 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 39,459,639
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 52
FINDPEAKS_SCORE: 0.371
FINDPEAKS_PERCENTILE: 41
HOTSPOT_SCORE: 0.3595
HOTSPOT_PERCENTILE: 35
IROC_SCORE: 0.9936
IROC_PERCENTILE: 46
POISSON_SCORE: 0.4193
POISSON_PERCENTILE: 41
MAXIMUM_REPLICATE_CORRELATION: 0.99

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

source_name: flow sorted CD4+ Primary Cells, Mobilized, year 21; DS16955

value: Mobilized CD4 Primary Cells

value: Chromatin Accessibility


title: Chromatin accessibility assay of Fetal Intestine, Large; DS17313

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: DS17313
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.7042
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.7041
****************
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: GSM701495_UW.Fetal_Intestine_Large.ChromatinAccessibility.H-23769.DS17313.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS17313.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-23769, Library DS17313 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.7718
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: 28,629,835
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 54
FINDPEAKS_SCORE: 0.3897
FINDPEAKS_PERCENTILE: 54
HOTSPOT_SCORE: 0.3869
HOTSPOT_PERCENTILE: 54
IROC_SCORE: 0.9973
IROC_PERCENTILE: 93
POISSON_SCORE: 0.4345
POISSON_PERCENTILE: 52
MAXIMUM_REPLICATE_CORRELATION: 0.96

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

ANALYSIS FILE NAME: GSM701495_UW.Fetal_Intestine_Large.ChromatinAccessibility.H-23769.DS17313.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS17313.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-23769, Library DS17313 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.7772
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 69 13
BROWSER_TRACK_DESCRIPTION: UW Fetal Intestine Large DNase Hypersensitivity Donor H-23769 Library DS17313 EA Release 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 28,629,835
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 52
FINDPEAKS_SCORE: 0.3897
FINDPEAKS_PERCENTILE: 54
HOTSPOT_SCORE: 0.3869
HOTSPOT_PERCENTILE: 54
IROC_SCORE: 0.9973
IROC_PERCENTILE: 93
POISSON_SCORE: 0.4345
POISSON_PERCENTILE: 52
MAXIMUM_REPLICATE_CORRELATION: 0.96

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

source_name: Fetal  primary tissue, day 108; DS17313

value: Fetal Intestine, Large

value: UW

value: fetal

value: Male

value: Qiagen minElut


title: Chromatin accessibility assay of Fetal Intestine, Large; DS17157

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: DS17157
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.7039
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.7038
****************
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: GSM701490_UW.Fetal_Intestine_Large.ChromatinAccessibility.H-23758.DS17157.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS17157.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-23758, Library DS17157 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.7684
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: 23,112,193
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 54
FINDPEAKS_SCORE: 0.3545
FINDPEAKS_PERCENTILE: 35
HOTSPOT_SCORE: 0.3596
HOTSPOT_PERCENTILE: 37
IROC_SCORE: 0.9951
IROC_PERCENTILE: 57
POISSON_SCORE: 0.3955
POISSON_PERCENTILE: 31
MAXIMUM_REPLICATE_CORRELATION: 1.0

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

ANALYSIS FILE NAME: GSM701490_UW.Fetal_Intestine_Large.ChromatinAccessibility.H-23758.DS17157.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS17157.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-23758, Library DS17157 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.7738
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 58 57
BROWSER_TRACK_DESCRIPTION: UW Fetal Intestine Large DNase Hypersensitivity Donor H-23758 Library DS17157 EA Release 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 23,112,193
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 52
FINDPEAKS_SCORE: 0.3545
FINDPEAKS_PERCENTILE: 35
HOTSPOT_SCORE: 0.3596
HOTSPOT_PERCENTILE: 37
IROC_SCORE: 0.9951
IROC_PERCENTILE: 57
POISSON_SCORE: 0.3955
POISSON_PERCENTILE: 31
MAXIMUM_REPLICATE_CORRELATION: 1.0

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

source_name: Fetal  primary tissue, day 107; DS17157

value: day 107

value: Female

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


title: Chromatin accessibility assay of Moblized CD4 Primary Cells; DS17175

description:
sample_term_id: CL_0000492
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Chromatin accessibility determination via DNase-seq
Library name: DS17175
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.6989
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.6988
****************
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: GSM701491_UW.Mobilized_CD4_Primary_Cells.ChromatinAccessibility.RO_01701.DS17175.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS17175.hg19.level.1.release.4
ANALYSIS TITLE: Mapping of Mobilized CD4 Primary Cells Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Mobilized CD4 Primary Cells, Donor RO 01701, Library DS17175 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.7688
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: 27,146,074
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 54
FINDPEAKS_SCORE: 0.3201
FINDPEAKS_PERCENTILE: 22
HOTSPOT_SCORE: 0.3263
HOTSPOT_PERCENTILE: 26
IROC_SCORE: 0.9957
IROC_PERCENTILE: 67
POISSON_SCORE: 0.3671
POISSON_PERCENTILE: 19
MAXIMUM_REPLICATE_CORRELATION: 0.99

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

ANALYSIS FILE NAME: GSM701491_UW.Mobilized_CD4_Primary_Cells.ChromatinAccessibility.RO_01701.DS17175.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS17175.hg19.level.2.release.4
ANALYSIS TITLE: Raw Signal Density Graphs of Mobilized CD4 Primary Cells Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from  Mobilized CD4 Primary Cells, Donor RO 01701, Library DS17175 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.7742
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: MCD4 DNase 01 75
BROWSER_TRACK_DESCRIPTION: UW Mobilized CD4 Primary Cells DNase Hypersensitivity Donor RO 01701 Library DS17175 EA Release 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 27,146,074
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 52
FINDPEAKS_SCORE: 0.3201
FINDPEAKS_PERCENTILE: 22
HOTSPOT_SCORE: 0.3263
HOTSPOT_PERCENTILE: 26
IROC_SCORE: 0.9957
IROC_PERCENTILE: 67
POISSON_SCORE: 0.3671
POISSON_PERCENTILE: 19
MAXIMUM_REPLICATE_CORRELATION: 0.99

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

source_name: flow sorted CD4+ Primary Cells, Mobilized, year 37; DS17175

value: genomic DNA

value: FHCRC HEIMFELD

value: Primary Cell

value: year 37

value: Hispanic


title: Chromatin accessibility assay of Moblized CD3 Primary Cells; DS16834

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: DS16834
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.6981
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.6980
****************
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: GSM701488_UW.Mobilized_CD3_Primary_Cells.ChromatinAccessibility.RO_01679.DS16834.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS16834.hg19.level.1.release.4
ANALYSIS TITLE: Mapping of Mobilized CD3 Primary Cells Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Mobilized CD3 Primary Cells, Donor RO 01679, Library DS16834 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.7675
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: 51,978,386
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 54
FINDPEAKS_SCORE: 0.3591
FINDPEAKS_PERCENTILE: 37
HOTSPOT_SCORE: 0.3413
HOTSPOT_PERCENTILE: 30
IROC_SCORE: 0.9929
IROC_PERCENTILE: 37
POISSON_SCORE: 0.3881
POISSON_PERCENTILE: 28
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM701488_UW.Mobilized_CD3_Primary_Cells.ChromatinAccessibility.RO_01679.DS16834.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS16834.hg19.level.2.release.4
ANALYSIS TITLE: Raw Signal Density Graphs of Mobilized CD3 Primary Cells Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from  Mobilized CD3 Primary Cells, Donor RO 01679, Library DS16834 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.7729
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: MCD3 DNase 79 34
BROWSER_TRACK_DESCRIPTION: UW Mobilized CD3 Primary Cells DNase Hypersensitivity Donor RO 01679 Library DS16834 EA Release 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 51,978,386
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 52
FINDPEAKS_SCORE: 0.3591
FINDPEAKS_PERCENTILE: 37
HOTSPOT_SCORE: 0.3413
HOTSPOT_PERCENTILE: 30
IROC_SCORE: 0.9929
IROC_PERCENTILE: 37
POISSON_SCORE: 0.3881
POISSON_PERCENTILE: 28
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: flow sorted CD3+ Primary Cells, Mobilized, year 21; DS16834

value: Mobilized CD3 Primary Cells

value: year 21

value: Caucasian


title: Chromatin accessibility assay of Fetal Intestine, Small; DS16712

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: DS16712
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.7052
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.7051
****************
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: GSM701487_UW.Fetal_Intestine_Small.ChromatinAccessibility.H-23640.DS16712.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS16712.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-23640, Library DS16712 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.7726
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: 21,730,050
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 54
FINDPEAKS_SCORE: 0.378
FINDPEAKS_PERCENTILE: 43
HOTSPOT_SCORE: 0.3841
HOTSPOT_PERCENTILE: 52
IROC_SCORE: 0.9969
IROC_PERCENTILE: 85
POISSON_SCORE: 0.4294
POISSON_PERCENTILE: 46
MAXIMUM_REPLICATE_CORRELATION: 0.99

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

ANALYSIS FILE NAME: GSM701487_UW.Fetal_Intestine_Small.ChromatinAccessibility.H-23640.DS16712.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS16712.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-23640, Library DS16712 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.7780
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 40 12
BROWSER_TRACK_DESCRIPTION: UW Fetal Intestine Small DNase Hypersensitivity Donor H-23640 Library DS16712 EA Release 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 21,730,050
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 52
FINDPEAKS_SCORE: 0.378
FINDPEAKS_PERCENTILE: 43
HOTSPOT_SCORE: 0.3841
HOTSPOT_PERCENTILE: 52
IROC_SCORE: 0.9969
IROC_PERCENTILE: 85
POISSON_SCORE: 0.4294
POISSON_PERCENTILE: 46
MAXIMUM_REPLICATE_CORRELATION: 0.99

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

source_name: Fetal  primary tissue, day 115; DS16712

value: Fetal Intestine, Small

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

value: Primary Tissue

value: day 115

value: Chromatin Accessibility


title: Mouse villus cell input DNA

status: Public on Apr 13 2011

city: Piscataway

first: Michael

middle: P

last: Verzi

state: NJ

address: 145 Bevier Road

department: Genetics

institute: Rutgers, the State University of New Jersey

description:
input DNA
sonicated input DNA fragments

data_processing: ChIP-Seq: ELAND mapping (mm9) + MACS for CDX2.

organism: Mus musculus

source_name: Mouse villus

growth_protocol: for ChIP-seq experiments,villus epithelium was collected by vortexing in PBS with EDTA, and collecting Villi on top of a 70uM filter.

extract_protocol: Library was constructed using 10 ng each of ChIP and input DNA and processed for deep sequencing according to manufacturer’s instructions (Illumina). Prior to sequencing, qPCR was used to verify that positive and negative control ChIP regions amplified in the linear range.

treatment_protocol: For transcription factor ChIP, cells Villi were fixed in 1% formaldehyde for 15 minutes at 4 degrees, then 35 minutes at 25 degrees, washed with cold PBS and resuspended in ChIP lysis buffer, sonicated and immunoprecipitated and processed as described by Carroll, et al, 2005, PMID: 16009131 and as described in our current work. Antibody was CDX2 (Bethyl BL3194).

tag: strain

value: C57BL/6-129 mixed

tag: cell type

value: intestinal villus cells

tag: chip antibody

value: none (input)


title: CDX2 ChIP-seq in mouse jejunum villus cells

description:
ChIP DNA
chromatin IP against Cdx2 in mouse villus cells

tag: antibody cat#

value: Bethyl Labs BL3194


title: Reference Epigenome: ChIP-Seq Analysis of H3K79me1 in hESC H9 Cells; renlab.H3K79me1.hESC.H9.02.01

city: La Jolla

first: UCSD AND

last: SALK

state: CA

address: Health Sciences Drive

institute: University of California, San Diego

description:
sample_term_id: NTR_0000838
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K79me1 in hESC H9 Cells. Sequencing was done on the Illumina Genome Analyzer IIx platform.
Library name: SK374
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.6941
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.6940
****************
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: GSM706077_UCSD.H9.H3K79me1.SK374.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K79me1.hESC.H9.02.01.hg19.level.1.release.4
ANALYSIS TITLE: Mapping of H9 Cell Line Histone H3K79me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K79me1 ChIP-Seq on the H9 Cell Line, Library SK374 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.8291
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 13,074,740
NUMBER_OF_H3K79me1_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 1
FINDPEAKS_SCORE: 0.1069
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.2344
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.839
IROC_PERCENTILE: 100
POISSON_SCORE: 0.3567
POISSON_PERCENTILE: 100
MAXIMUM_REPLICATE_CORRELATION: 0.92

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

ANALYSIS FILE NAME: GSM706077_UCSD.H9.H3K79me1.SK374.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K79me1.hESC.H9.02.01.hg19.level.2.release.4
ANALYSIS TITLE: Raw Signal Density Graphs of H9 Cell Line Histone H3K79me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K79me1 ChIP-Seq read mappings from the H9 Cell Line, Library SK374 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.8310
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 4
BROWSER_TRACK_NAME: H9 H3K79me1 74
BROWSER_TRACK_DESCRIPTION: UCSD H9 Cell Line Histone H3K79me1 Library SK374 EA Release 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 13,074,740
NUMBER_OF_H3K79me1_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 1
FINDPEAKS_SCORE: 0.1069
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.2344
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.839
IROC_PERCENTILE: 100
POISSON_SCORE: 0.3567
POISSON_PERCENTILE: 100
MAXIMUM_REPLICATE_CORRELATION: 0.92

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

source_name: Human embryonic stem cells received from the James Thompson laboratory.  Cells are from the H9 line.; renlab.H3K79me1.hESC.H9.02.01

extract_protocol: Library construction protocol: See http://bioinformatics-renlab.ucsd.edu/RenLabLibraryProtocolV1.pdf

value: H9 Cell Line

value: genomic DNA

value: James Thompson Laboratory

value: Cell Line

tag: line

tag: lineage

value: Embryonic Stem Cell

tag: passage

tag: medium

value: mTeSER

tag: Sex

value: Female

tag: batch

value: Histone H3K79me1

value: Biorupter

value: 500 micrograms

value: magnetic anti-rabbit

value: 5 micrograms

value: Abcam


title: Reference Epigenome: ChIP-Seq Input from iPS 19.11 Cells; renlab.Input.iPS-19.11_01.01

description:
sample_term_id: NTR_0001173
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Input from iPS 19.11 Cells. Sequencing was done on the Illumina Genome Analyzer IIx platform.
Library name: SKiPS19.11-1
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.6824
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.6813
****************
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: GSM706082_UCSD.iPS_DF_19.11.Input.SKiPS19.11-1.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.Input.iPS-19.11_01.01.hg19.level.1.release.4
ANALYSIS TITLE: Mapping of iPS DF 19.11 Cell Line ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina reads produced by ChIP-Seq Input on the iPS DF 19.11 Cell Line, Library SKiPS19.11-1 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.8286
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 19,331,754
NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 14
FINDPEAKS_SCORE: 0.0039
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.0702
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.943
IROC_PERCENTILE: 100
POISSON_SCORE: 0.1167
POISSON_PERCENTILE: 100
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM706082_UCSD.iPS_DF_19.11.Input.SKiPS19.11-1.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.Input.iPS-19.11_01.01.hg19.level.2.release.4
ANALYSIS TITLE: Raw Signal Density Graphs of iPS DF 19.11 Cell Line ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina ChIP-Seq Input read mappings from the iPS DF 19.11 Cell Line, Library SKiPS19.11-1 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.8305
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 4
BROWSER_TRACK_NAME: iD19.11 Input 1
BROWSER_TRACK_DESCRIPTION: UCSD iPS DF 19.11 Cell Line ChIP-Seq Input Library SKiPS19.11-1 EA Release 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 19,331,754
NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 14
FINDPEAKS_SCORE: 0.0039
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.0702
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.943
IROC_PERCENTILE: 100
POISSON_SCORE: 0.1167
POISSON_PERCENTILE: 100
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: Human induced pluripotent stem cell line derived from foreskin fibroblasts, isolated as described by Yu, J. et al. Human induced pluripotent stem cells free of vector and transgene sequences. Science 324, 797-801 (2009).; renlab.Input.iPS-19.11_01.01

value: iPS DF 19.11 Cell Line

value: Induced pluripotent stem cell line derived from foreskin fibroblasts

value: Induced pluripotent stem cell

value: As described by Yu, J. et al. Human induced pluripotent stem cells free of vector and transgene sequences. Science 324, 797-801 (2009).

value: Between 30 and 40

value: mTeSR

value: Male

value: ChIP-Seq Input

value: Input


title: Reference Epigenome: ChIP-Seq Input from hESC H9 Cells; renlab.Input.hESC.H9.02.01

description:
sample_term_id: NTR_0000838
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Input from hESC H9 Cells. Sequencing was done on the Illumina Genome Analyzer IIx platform.
Library name: AK144
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.6954
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.6947
****************
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: GSM706081_UCSD.H9.Input.AK144.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.Input.hESC.H9.02.01.hg19.level.1.release.4
ANALYSIS TITLE: Mapping of H9 Cell Line ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina reads produced by ChIP-Seq Input on the H9 Cell Line, Library AK144 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.8281
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 30,493,469
NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 14
FINDPEAKS_SCORE: 0.0085
FINDPEAKS_PERCENTILE: 92
HOTSPOT_SCORE: 0.0066
HOTSPOT_PERCENTILE: 33
IROC_SCORE: 0.0
IROC_PERCENTILE: 17
POISSON_SCORE: 0.0319
POISSON_PERCENTILE: 33
MAXIMUM_REPLICATE_CORRELATION: 0.9

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

ANALYSIS FILE NAME: GSM706081_UCSD.H9.Input.AK144.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.Input.hESC.H9.02.01.hg19.level.2.release.4
ANALYSIS TITLE: Raw Signal Density Graphs of H9 Cell Line ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina ChIP-Seq Input read mappings from the H9 Cell Line, Library AK144 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.8300
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 4
BROWSER_TRACK_NAME: H9 Input 44
BROWSER_TRACK_DESCRIPTION: UCSD H9 Cell Line ChIP-Seq Input Library AK144 EA Release 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 30,493,469
NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 14
FINDPEAKS_SCORE: 0.0085
FINDPEAKS_PERCENTILE: 92
HOTSPOT_SCORE: 0.0066
HOTSPOT_PERCENTILE: 33
IROC_SCORE: 0.0
IROC_PERCENTILE: 17
POISSON_SCORE: 0.0319
POISSON_PERCENTILE: 33
MAXIMUM_REPLICATE_CORRELATION: 0.9

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

source_name: Human embryonic stem cells received from the James Thompson laboratory.  Cells are from the H9 line.; renlab.Input.hESC.H9.02.01

value: H9 Cell Line

value: genomic DNA

value: James Thompson Laboratory

value: Cell Line

value: Embryonic Stem Cell

value: Between 30 and 50

value: mTeSER


title: Reference Epigenome: ChIP-Seq Analysis of H3K9me3 in iPS 6.9 Cells; renlab.H3K9me3.iPS-6.9_01.01

description:
sample_term_id: NTR_0001172
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K9me3 in iPS 6.9 Cells. Sequencing was done on the Illumina Genome Analyzer IIx platform.
Library name: SK274
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.6893
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.6880
****************
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: GSM706080_UCSD.iPS_DF_6.9.H3K9me3.SK274.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K9me3.iPS-6.9_01.01.hg19.level.1.release.4
ANALYSIS TITLE: Mapping of iPS DF 6.9 Cell Line Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K9me3 ChIP-Seq on the iPS DF 6.9 Cell Line, Library SK274 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.8293
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 16,709,047
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 6
FINDPEAKS_SCORE: 0.047
FINDPEAKS_PERCENTILE: 17
HOTSPOT_SCORE: 0.1215
HOTSPOT_PERCENTILE: 17
IROC_SCORE: 0.7329
IROC_PERCENTILE: 17
POISSON_SCORE: 0.2325
POISSON_PERCENTILE: 17
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM706080_UCSD.iPS_DF_6.9.H3K9me3.SK274.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K9me3.iPS-6.9_01.01.hg19.level.2.release.4
ANALYSIS TITLE: Raw Signal Density Graphs of iPS DF 6.9 Cell Line Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K9me3 ChIP-Seq read mappings from the iPS DF 6.9 Cell Line, Library SK274 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.8312
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 4
BROWSER_TRACK_NAME: iD6.9 H3K9me3 74
BROWSER_TRACK_DESCRIPTION: UCSD iPS DF 6.9 Cell Line Histone H3K9me3 Library SK274 EA Release 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 16,709,047
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 6
FINDPEAKS_SCORE: 0.047
FINDPEAKS_PERCENTILE: 17
HOTSPOT_SCORE: 0.1215
HOTSPOT_PERCENTILE: 17
IROC_SCORE: 0.7329
IROC_PERCENTILE: 17
POISSON_SCORE: 0.2325
POISSON_PERCENTILE: 17
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: Human induced pluripotent stem cell line derived from foreskin fibroblasts, isolated as described by Yu, J. et al. Human induced pluripotent stem cells free of vector and transgene sequences. Science 324, 797-801 (2009).; renlab.H3K9me3.iPS-6.9_01.01

value: iPS DF 6.9 Cell Line

value: iPS 6.9

value: iPSC 6.9

value: Histone H3K9me3

value: Biorupter

value: 500 micrograms

value: magnetic anti-rabbit

value: 5 micrograms

value: Abcam