title: Chromatin accessibility assay of Fetal Heart; DS19427

description:
sample_term_id: UBERON_0000948
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Chromatin accessibility determination via DNase-seq
Library name: DS19427
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.11600
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.11599
****************
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: GSM878630_UW.Fetal_Heart.ChromatinAccessibility.H-24042.DS19427.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS19427.hg19.level.1.release.7
ANALYSIS TITLE: Mapping of Fetal Heart Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fetal Heart, Donor H-24042, Library DS19427 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.12758
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 7

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 42,860,392
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 58
FINDPEAKS_SCORE: 0.5865
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.5773
HOTSPOT_PERCENTILE: 81
IROC_SCORE: 0.9958
IROC_PERCENTILE: 66
POISSON_SCORE: 0.6355
POISSON_PERCENTILE: 95
MAXIMUM_REPLICATE_CORRELATION: 1.0

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

ANALYSIS FILE NAME: GSM878630_UW.Fetal_Heart.ChromatinAccessibility.H-24042.DS19427.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS19427.hg19.level.2.release.7
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Heart Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from  Fetal Heart, Donor H-24042, Library DS19427 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.12816
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 7
BROWSER_TRACK_NAME: FH DNase 42 27
BROWSER_TRACK_DESCRIPTION: UW Fetal Heart DNase Hypersensitivity Donor H-24042 Library DS19427 EA Release 7

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 42,860,392
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 58
FINDPEAKS_SCORE: 0.5865
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.5773
HOTSPOT_PERCENTILE: 81
IROC_SCORE: 0.9958
IROC_PERCENTILE: 66
POISSON_SCORE: 0.6355
POISSON_PERCENTILE: 95
MAXIMUM_REPLICATE_CORRELATION: 1.0

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

source_name: Fetal Heart primary tissue, day 120; DS19427

value: Fetal Heart

value: UW

value: fetal

value: day 120

value: Chromatin Accessibility


title: Chromatin accessibility assay of Fibroblasts, Fetal Skin, Biceps, Left; DS19857

status: Public on Feb 22 2012

type: SRA

city: Seattle

first: Northwest

last: REMC

state: WA

country: USA

institute: University of Washington

description:
sample_term_id: CL_0002620
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Chromatin accessibility determination via DNase-seq
Library name: DS19857
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.11400
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.11406
****************
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: GSM878644_UW.Fibroblasts_Fetal_Skin_Biceps_Left.ChromatinAccessibility.H-24259.DS19857.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS19857.hg19.level.1.release.7
ANALYSIS TITLE: Mapping of Fibroblasts Fetal Skin Biceps Left Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fibroblasts Fetal Skin Biceps Left, Donor H-24259, Library DS19857 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.12738
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 7

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 39,399,311
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 58
FINDPEAKS_SCORE: 0.4987
FINDPEAKS_PERCENTILE: 72
HOTSPOT_SCORE: 0.5916
HOTSPOT_PERCENTILE: 83
IROC_SCORE: 0.9961
IROC_PERCENTILE: 69
POISSON_SCORE: 0.5904
POISSON_PERCENTILE: 78
MAXIMUM_REPLICATE_CORRELATION: 1.0

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

ANALYSIS FILE NAME: GSM878644_UW.Fibroblasts_Fetal_Skin_Biceps_Left.ChromatinAccessibility.H-24259.DS19857.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS19857.hg19.level.2.release.7
ANALYSIS TITLE: Raw Signal Density Graphs of Fibroblasts Fetal Skin Biceps Left Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from  Fibroblasts Fetal Skin Biceps Left, Donor H-24259, Library DS19857 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.12796
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 7
BROWSER_TRACK_NAME: FFSBL DNase 59 57
BROWSER_TRACK_DESCRIPTION: UW Fibroblasts Fetal Skin Biceps Left DNase Hypersensitivity Donor H-24259 Library DS19857 EA Release 7

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 39,399,311
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 58
FINDPEAKS_SCORE: 0.4987
FINDPEAKS_PERCENTILE: 72
HOTSPOT_SCORE: 0.5916
HOTSPOT_PERCENTILE: 83
IROC_SCORE: 0.9961
IROC_PERCENTILE: 69
POISSON_SCORE: 0.5904
POISSON_PERCENTILE: 78
MAXIMUM_REPLICATE_CORRELATION: 1.0

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

molecule: genomic DNA

organism: Homo sapiens

source_name: Fibroblasts, Fetal Skin, Biceps, Left, day 97 donor; DS19857

extract_protocol: Library construction protocol: Single read - Illumina

tag: sample alias

tag: sample common name

value: Fibroblasts, Fetal Skin, Biceps, Left

tag: molecule

value: genomic DNA

tag: disease

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

value: Primary Cell Culture

tag: markers

value: day 97

value: Male

value: short term

value: Qiagen minElut


title: Chromatin accessibility assay of H1 Cell Line; DS19100

description:
Design description: Chromatin accessibility determination via DNase-seq
Library name: DS19100
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.11258
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.3425
****************
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: GSM878621_UW.H1.ChromatinAccessibility.DS19100.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS19100.hg19.level.1.release.7
ANALYSIS TITLE: Mapping of H1 Cell Line Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on the H1 Cell Line, Library DS19100 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.12766
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 7

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 27,768,186
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 58
FINDPEAKS_SCORE: 0.1781
FINDPEAKS_PERCENTILE: 3
HOTSPOT_SCORE: 0.1873
HOTSPOT_PERCENTILE: 3
IROC_SCORE: 0.993
IROC_PERCENTILE: 33
POISSON_SCORE: 0.2347
POISSON_PERCENTILE: 3
MAXIMUM_REPLICATE_CORRELATION: 1.0

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

ANALYSIS FILE NAME: GSM878621_UW.H1.ChromatinAccessibility.DS19100.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS19100.hg19.level.2.release.7
ANALYSIS TITLE: Raw Signal Density Graphs of H1 Cell Line Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from  the H1 Cell Line, Library DS19100 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.12824
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 7
BROWSER_TRACK_NAME: H1 DNase 00
BROWSER_TRACK_DESCRIPTION: UW H1 Cell Line DNase Hypersensitivity Library DS19100 EA Release 7

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 27,768,186
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 58
FINDPEAKS_SCORE: 0.1781
FINDPEAKS_PERCENTILE: 3
HOTSPOT_SCORE: 0.1873
HOTSPOT_PERCENTILE: 3
IROC_SCORE: 0.993
IROC_PERCENTILE: 33
POISSON_SCORE: 0.2347
POISSON_PERCENTILE: 3
MAXIMUM_REPLICATE_CORRELATION: 1.0

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

source_name: Human embryonic stem cells received from the James Thompson laboratory.  Cells are from the H1 line.; DS19100

value: H1 Cell Line

value: James Thompson Laboratory

value: Cell Line

tag: line

tag: lineage

value: Embryonic Stem Cell

tag: passage

value: Between 20 and 40

tag: medium

value: mTeSER

tag: Sex

tag: batch


title: Chromatin accessibility assay of Fetal Muscle, Leg; DS19158

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: DS19158
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.11487
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.11486
****************
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: GSM878622_UW.Fetal_Muscle_Leg.ChromatinAccessibility.H-24198.DS19158.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS19158.hg19.level.1.release.7
ANALYSIS TITLE: Mapping of Fetal Muscle Leg Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fetal Muscle Leg, Donor H-24198, Library DS19158 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.12780
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 7

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 47,737,407
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 58
FINDPEAKS_SCORE: 0.3643
FINDPEAKS_PERCENTILE: 33
HOTSPOT_SCORE: 0.3417
HOTSPOT_PERCENTILE: 22
IROC_SCORE: 0.9914
IROC_PERCENTILE: 19
POISSON_SCORE: 0.4444
POISSON_PERCENTILE: 40
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

ANALYSIS FILE NAME: GSM878622_UW.Fetal_Muscle_Leg.ChromatinAccessibility.H-24198.DS19158.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS19158.hg19.level.2.release.7
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-24198, Library DS19158 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.12838
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 7
BROWSER_TRACK_NAME: FML DNase 98 58
BROWSER_TRACK_DESCRIPTION: UW Fetal Muscle Leg DNase Hypersensitivity Donor H-24198 Library DS19158 EA Release 7

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 47,737,407
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 58
FINDPEAKS_SCORE: 0.3643
FINDPEAKS_PERCENTILE: 33
HOTSPOT_SCORE: 0.3417
HOTSPOT_PERCENTILE: 22
IROC_SCORE: 0.9914
IROC_PERCENTILE: 19
POISSON_SCORE: 0.4444
POISSON_PERCENTILE: 40
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

source_name: Fetal Muscle, Leg primary tissue, day 113; DS19158

value: Fetal Muscle, Leg

value: Primary Tissue

value: UW

value: fetal

value: day 113


title: Chromatin accessibility assay of Fetal Muscle, Arm; DS19270

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: DS19270
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.11532
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.11531
****************
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: GSM878625_UW.Fetal_Muscle_Arm.ChromatinAccessibility.H-24244.DS19270.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS19270.hg19.level.1.release.7
ANALYSIS TITLE: Mapping of Fetal Muscle Arm Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fetal Muscle Arm, Donor H-24244, Library DS19270 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.12757
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 7

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 33,987,181
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 58
FINDPEAKS_SCORE: 0.4402
FINDPEAKS_PERCENTILE: 52
HOTSPOT_SCORE: 0.4265
HOTSPOT_PERCENTILE: 52
IROC_SCORE: 0.9928
IROC_PERCENTILE: 29
POISSON_SCORE: 0.4874
POISSON_PERCENTILE: 52
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

ANALYSIS FILE NAME: GSM878625_UW.Fetal_Muscle_Arm.ChromatinAccessibility.H-24244.DS19270.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS19270.hg19.level.2.release.7
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-24244, Library DS19270 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.12815
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 7
BROWSER_TRACK_NAME: FMA DNase 44 70
BROWSER_TRACK_DESCRIPTION: UW Fetal Muscle Arm DNase Hypersensitivity Donor H-24244 Library DS19270 EA Release 7

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 33,987,181
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 58
FINDPEAKS_SCORE: 0.4402
FINDPEAKS_PERCENTILE: 52
HOTSPOT_SCORE: 0.4265
HOTSPOT_PERCENTILE: 52
IROC_SCORE: 0.9928
IROC_PERCENTILE: 29
POISSON_SCORE: 0.4874
POISSON_PERCENTILE: 52
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

source_name: Fetal Muscle, Arm primary tissue, day 96; DS19270

value: Fetal Muscle, Arm

value: genomic DNA

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

value: day 96

value: Chromatin Accessibility


title: Chromatin accessibility assay of Fibroblasts, Fetal Skin, Back; DS19233

description:
sample_term_id: CL_0002620
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Chromatin accessibility determination via DNase-seq
Library name: DS19233
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.11360
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.11359
****************
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: GSM878624_UW.Fibroblasts_Fetal_Skin_Back.ChromatinAccessibility.H-24218.DS19233.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS19233.hg19.level.1.release.7
ANALYSIS TITLE: Mapping of Fibroblasts Fetal Skin Back Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fibroblasts Fetal Skin Back, Donor H-24218, Library DS19233 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.12761
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 7

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 37,039,229
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 58
FINDPEAKS_SCORE: 0.5327
FINDPEAKS_PERCENTILE: 84
HOTSPOT_SCORE: 0.6378
HOTSPOT_PERCENTILE: 93
IROC_SCORE: 0.9976
IROC_PERCENTILE: 90
POISSON_SCORE: 0.6285
POISSON_PERCENTILE: 90
MAXIMUM_REPLICATE_CORRELATION: 1.0

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

ANALYSIS FILE NAME: GSM878624_UW.Fibroblasts_Fetal_Skin_Back.ChromatinAccessibility.H-24218.DS19233.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS19233.hg19.level.2.release.7
ANALYSIS TITLE: Raw Signal Density Graphs of Fibroblasts Fetal Skin Back Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from  Fibroblasts Fetal Skin Back, Donor H-24218, Library DS19233 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.12819
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 7
BROWSER_TRACK_NAME: FFSB DNase 59 33
BROWSER_TRACK_DESCRIPTION: UW Fibroblasts Fetal Skin Back DNase Hypersensitivity Donor H-24218 Library DS19233 EA Release 7

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 37,039,229
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 58
FINDPEAKS_SCORE: 0.5327
FINDPEAKS_PERCENTILE: 84
HOTSPOT_SCORE: 0.6378
HOTSPOT_PERCENTILE: 93
IROC_SCORE: 0.9976
IROC_PERCENTILE: 90
POISSON_SCORE: 0.6285
POISSON_PERCENTILE: 90
MAXIMUM_REPLICATE_CORRELATION: 1.0

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

source_name: Fibroblasts, Fetal Skin, Back, day 96 donor; DS19233

value: Fibroblasts, Fetal Skin, Back

value: Primary Cell Culture

value: Male

value: short term

value: Qiagen minElut


title: Chromatin accessibility assay of Fetal Muscle, Arm; DS19051

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: DS19051
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.11555
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.11554
****************
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: GSM878619_UW.Fetal_Muscle_Arm.ChromatinAccessibility.H-24198.DS19051.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS19051.hg19.level.1.release.7
ANALYSIS TITLE: Mapping of Fetal Muscle Arm Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fetal Muscle Arm, Donor H-24198, Library DS19051 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.12788
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 7

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 26,364,804
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 58
FINDPEAKS_SCORE: 0.2921
FINDPEAKS_PERCENTILE: 14
HOTSPOT_SCORE: 0.2918
HOTSPOT_PERCENTILE: 14
IROC_SCORE: 0.9912
IROC_PERCENTILE: 14
POISSON_SCORE: 0.3859
POISSON_PERCENTILE: 16
MAXIMUM_REPLICATE_CORRELATION: 0.99

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

ANALYSIS FILE NAME: GSM878619_UW.Fetal_Muscle_Arm.ChromatinAccessibility.H-24198.DS19051.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS19051.hg19.level.2.release.7
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-24198, Library DS19051 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.12846
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 7
BROWSER_TRACK_NAME: FMA DNase 98 51
BROWSER_TRACK_DESCRIPTION: UW Fetal Muscle Arm DNase Hypersensitivity Donor H-24198 Library DS19051 EA Release 7

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 26,364,804
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 58
FINDPEAKS_SCORE: 0.2921
FINDPEAKS_PERCENTILE: 14
HOTSPOT_SCORE: 0.2918
HOTSPOT_PERCENTILE: 14
IROC_SCORE: 0.9912
IROC_PERCENTILE: 14
POISSON_SCORE: 0.3859
POISSON_PERCENTILE: 16
MAXIMUM_REPLICATE_CORRELATION: 0.99

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

source_name: Fetal Muscle, Arm primary tissue, day 113; DS19051


title: Chromatin accessibility assay of Fetal Muscle, Arm; DS18992

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: DS18992
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.11564
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.11563
****************
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: GSM878618_UW.Fetal_Muscle_Arm.ChromatinAccessibility.H-24143.DS18992.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS18992.hg19.level.1.release.7
ANALYSIS TITLE: Mapping of Fetal Muscle Arm Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fetal Muscle Arm, Donor H-24143, Library DS18992 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.12746
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 7

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 23,598,036
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 58
FINDPEAKS_SCORE: 0.3221
FINDPEAKS_PERCENTILE: 17
HOTSPOT_SCORE: 0.3155
HOTSPOT_PERCENTILE: 17
IROC_SCORE: 0.9917
IROC_PERCENTILE: 22
POISSON_SCORE: 0.4049
POISSON_PERCENTILE: 19
MAXIMUM_REPLICATE_CORRELATION: 0.99

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

ANALYSIS FILE NAME: GSM878618_UW.Fetal_Muscle_Arm.ChromatinAccessibility.H-24143.DS18992.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS18992.hg19.level.2.release.7
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-24143, Library DS18992 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.12804
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 7
BROWSER_TRACK_NAME: FMA DNase 43 92
BROWSER_TRACK_DESCRIPTION: UW Fetal Muscle Arm DNase Hypersensitivity Donor H-24143 Library DS18992 EA Release 7

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 23,598,036
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 58
FINDPEAKS_SCORE: 0.3221
FINDPEAKS_PERCENTILE: 17
HOTSPOT_SCORE: 0.3155
HOTSPOT_PERCENTILE: 17
IROC_SCORE: 0.9917
IROC_PERCENTILE: 22
POISSON_SCORE: 0.4049
POISSON_PERCENTILE: 19
MAXIMUM_REPLICATE_CORRELATION: 0.99

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

source_name: Fetal Muscle, Arm primary tissue, day 115; DS18992

value: day 115

value: Female


title: Chromatin accessibility assay of Fetal Muscle, Arm; DS19053

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: DS19053
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.11543
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.11542
****************
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: GSM878620_UW.Fetal_Muscle_Arm.ChromatinAccessibility.H-24218.DS19053.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS19053.hg19.level.1.release.7
ANALYSIS TITLE: Mapping of Fetal Muscle Arm Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fetal Muscle Arm, Donor H-24218, Library DS19053 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.12756
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 7

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 33,972,894
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 58
FINDPEAKS_SCORE: 0.3036
FINDPEAKS_PERCENTILE: 16
HOTSPOT_SCORE: 0.2968
HOTSPOT_PERCENTILE: 16
IROC_SCORE: 0.9907
IROC_PERCENTILE: 9
POISSON_SCORE: 0.4004
POISSON_PERCENTILE: 17
MAXIMUM_REPLICATE_CORRELATION: 0.99

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

ANALYSIS FILE NAME: GSM878620_UW.Fetal_Muscle_Arm.ChromatinAccessibility.H-24218.DS19053.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS19053.hg19.level.2.release.7
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-24218, Library DS19053 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.12814
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 7
BROWSER_TRACK_NAME: FMA DNase 18 53
BROWSER_TRACK_DESCRIPTION: UW Fetal Muscle Arm DNase Hypersensitivity Donor H-24218 Library DS19053 EA Release 7

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 33,972,894
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 58
FINDPEAKS_SCORE: 0.3036
FINDPEAKS_PERCENTILE: 16
HOTSPOT_SCORE: 0.2968
HOTSPOT_PERCENTILE: 16
IROC_SCORE: 0.9907
IROC_PERCENTILE: 9
POISSON_SCORE: 0.4004
POISSON_PERCENTILE: 17
MAXIMUM_REPLICATE_CORRELATION: 0.99

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

source_name: Fetal Muscle, Arm primary tissue, day 96; DS19053


title: Chromatin accessibility assay of H9 Cell Line; DS18522

description:
Design description: Chromatin accessibility determination via DNase-seq
Library name: DS18522
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.11249
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: GSM878613_UW.H9.ChromatinAccessibility.DS18522.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS18522.hg19.level.1.release.7
ANALYSIS TITLE: Mapping of H9 Cell Line Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on the H9 Cell Line, Library DS18522 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.12786
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 7

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 30,147,140
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 58
FINDPEAKS_SCORE: 0.2019
FINDPEAKS_PERCENTILE: 9
HOTSPOT_SCORE: 0.2112
HOTSPOT_PERCENTILE: 7
IROC_SCORE: 0.9889
IROC_PERCENTILE: 3
POISSON_SCORE: 0.3168
POISSON_PERCENTILE: 10
MAXIMUM_REPLICATE_CORRELATION: 0.99

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

ANALYSIS FILE NAME: GSM878613_UW.H9.ChromatinAccessibility.DS18522.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS18522.hg19.level.2.release.7
ANALYSIS TITLE: Raw Signal Density Graphs of H9 Cell Line Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from  the H9 Cell Line, Library DS18522 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.12844
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 7
BROWSER_TRACK_NAME: H9 DNase 22
BROWSER_TRACK_DESCRIPTION: UW H9 Cell Line DNase Hypersensitivity Library DS18522 EA Release 7

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 30,147,140
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 58
FINDPEAKS_SCORE: 0.2019
FINDPEAKS_PERCENTILE: 9
HOTSPOT_SCORE: 0.2112
HOTSPOT_PERCENTILE: 7
IROC_SCORE: 0.9889
IROC_PERCENTILE: 3
POISSON_SCORE: 0.3168
POISSON_PERCENTILE: 10
MAXIMUM_REPLICATE_CORRELATION: 0.99

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

source_name: Human embryonic stem cells received from the James Thompson laboratory.  Cells are from the H9 line.; DS18522

value: H9 Cell Line

value: James Thompson Laboratory

value: Cell Line

value: Embryonic Stem Cell

value: mTeSER


title: Fibroblast Epi OSKM D6 H3K27me3

city: Boston

first: Amit

last: Sinha

state: MA

address: 44 Binney St

department: Pediatric Oncology

institute: Dana-Farber Cancer Institute

description: Chromatin IP against H3K27me3

data_processing:
Sequence reads were aligned to human genome assembly hg18 using Bowtie. ChIP-Seq signal was quantified as total number of reads per million in the region of interest. An empirical background distribution model of reads was constructed to find the significance level of signal in a given region.
Genome Build:
Fibr_Epi_OSKM_D6.H3K27me3.n_1_l_28_e_70_a_m_1_best_strata.hg18.wig: hg18

source_name: Fibroblasts differentiated from H1 ES cells (dH1f)

growth_protocol: alpha-MEM with 10% IFS

extract_protocol: ChIP DNA libraries were made following Illumina ChIP-seq library preparation kit

treatment_protocol: Cells were subjected to ChIP-Seq using an antibody specific for  H3K27me3 or H3K79me2.

tag: cell line

value: fibroblast derived from H1

tag: treatment

value: Cells were treated with 10uM Dot1L inhibitor (EPZ004777) for 5 days and then infected with Oct4, Sox2, Klf4 and c-Myc followed by 6 days of incubation

tag: chip antibody

tag: chip antibody manufacturer

value: Millipore

tag: chip antibody catalog#

tag: chip antibody lot#


title: Fibroblast Epi H3K27me3

description: Chromatin IP against H3K27me3

data_processing:
Sequence reads were aligned to human genome assembly hg18 using Bowtie. ChIP-Seq signal was quantified as total number of reads per million in the region of interest. An empirical background distribution model of reads was constructed to find the significance level of signal in a given region.
Genome Build:
Fibr_Epi.H3K27me3.n_1_l_28_e_70_a_m_1_best_strata.hg18.wig: hg18

value: Cells were treated with 10uM Dot1L inhibitor (EPZ004777)  for 5 days


title: Fibroblast Epi H3K79me2

description: Chromatin IP against H3K79me2

data_processing:
Sequence reads were aligned to human genome assembly hg18 using Bowtie. ChIP-Seq signal was quantified as total number of reads per million in the region of interest. An empirical background distribution model of reads was constructed to find the significance level of signal in a given region.
Genome Build:
Fibr_Epi.H3K79me2.n_1_l_28_e_70_a_m_1_best_strata.hg18.wig: hg18

value: Cells were treated with 10uM Dot1L inhibitor (EPZ004777) for 5 days

value: Abcam


title: ES H3K27me3

description: Chromatin IP against H3K27me3

data_processing:
Sequence reads were aligned to human genome assembly hg18 using Bowtie. ChIP-Seq signal was quantified as total number of reads per million in the region of interest. An empirical background distribution model of reads was constructed to find the significance level of signal in a given region.
Genome Build:
ES.H3K27me3.n_1_l_28_e_70_a_m_1_best_strata.hg18.wig: hg18

source_name: H1 human Embryonic stem cells

growth_protocol: hESC medium containing 20% KOSR and 10ng/ml bFGF on irradiated MEFs

value: diagnostic sample (pre-treatment)


title: Fibroblast OSKM D6 H3K27me3

description: Chromatin IP against H3K27me3

data_processing:
Sequence reads were aligned to human genome assembly hg18 using Bowtie. ChIP-Seq signal was quantified as total number of reads per million in the region of interest. An empirical background distribution model of reads was constructed to find the significance level of signal in a given region.
Genome Build:
Fibr_OSKM_D6.H3K27me3.n_1_l_28_e_70_a_m_1_best_strata.hg18.wig: hg18

value: Cells were infected with Oct4, Sox2, Klf4 and c-Myc retroviruses followed by 6 days of incubation


title: Chromatin accessibility assay of H1 BMP4 Derived Trophoblast Cultured Cells; DS18736

description:
sample_term_id: UBERON_0000088
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Chromatin accessibility determination via DNase-seq
Library name: DS18736
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.11239
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.7847
****************
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: GSM878614_UW.H1_BMP4_Derived_Trophoblast_Cultured_Cells.ChromatinAccessibility.DS18736.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS18736.hg19.level.1.release.7
ANALYSIS TITLE: Mapping of H1 BMP4 Derived Trophoblast Cultured Cells Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on the H1 BMP4 Derived Trophoblast Cultured Cells, Library DS18736 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.12764
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 7

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 42,958,137
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 58
FINDPEAKS_SCORE: 0.1405
FINDPEAKS_PERCENTILE: 2
HOTSPOT_SCORE: 0.1513
HOTSPOT_PERCENTILE: 2
IROC_SCORE: 0.9913
IROC_PERCENTILE: 16
POISSON_SCORE: 0.2033
POISSON_PERCENTILE: 2
MAXIMUM_REPLICATE_CORRELATION: 0.99

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

ANALYSIS FILE NAME: GSM878614_UW.H1_BMP4_Derived_Trophoblast_Cultured_Cells.ChromatinAccessibility.DS18736.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS18736.hg19.level.2.release.7
ANALYSIS TITLE: Raw Signal Density Graphs of H1 BMP4 Derived Trophoblast Cultured Cells Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from  the H1 BMP4 Derived Trophoblast Cultured Cells, Library DS18736 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.12822
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 7
BROWSER_TRACK_NAME: HBDT DNase 36
BROWSER_TRACK_DESCRIPTION: UW H1 BMP4 Derived Trophoblast Cultured Cells DNase Hypersensitivity Library DS18736 EA Release 7

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 42,958,137
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 58
FINDPEAKS_SCORE: 0.1405
FINDPEAKS_PERCENTILE: 2
HOTSPOT_SCORE: 0.1513
HOTSPOT_PERCENTILE: 2
IROC_SCORE: 0.9913
IROC_PERCENTILE: 16
POISSON_SCORE: 0.2033
POISSON_PERCENTILE: 2
MAXIMUM_REPLICATE_CORRELATION: 0.99

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

source_name: Human embryonic stem cells received from the James Thomson laboratory.  Cells are from the H1 line and are differentiated into trophoblast by treatment with BMP4.; DS18736

tag: sample alias

value: genomic DNA

value: James Thomson Laboratory

value: Embryonic stem cell differentiated into trophoblast by treatment with BMP4

value: H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days

value: Male

value: Chromatin Accessibility


title: Fibroblast OSKM D6 H3K79me2

description: Chromatin IP against H3K79me2

data_processing:
Sequence reads were aligned to human genome assembly hg18 using Bowtie. ChIP-Seq signal was quantified as total number of reads per million in the region of interest. An empirical background distribution model of reads was constructed to find the significance level of signal in a given region.
Genome Build:
Fibr_OSKM_D6.H3K79me2.n_1_l_28_e_70_a_m_1_best_strata.hg18.wig: hg18


title: ES H3K79me2

description: Chromatin IP against H3K79me2

data_processing:
Sequence reads were aligned to human genome assembly hg18 using Bowtie. ChIP-Seq signal was quantified as total number of reads per million in the region of interest. An empirical background distribution model of reads was constructed to find the significance level of signal in a given region.
Genome Build:
ES.H3K79me2.n_1_l_28_e_70_a_m_1_best_strata.hg18.wig: hg18

source_name: H1 human Embryonic stem cell


title: H3K27me3_2'AML_WT

description:
H3K27me3_2'AML_WT
Chromatin IP against H3K27me3.

data_processing: Sequence reads were aligned to mouse genome assembly mm8 using Bowtie. The ChIP-Seq signal was quantified as total number of reads per million in the region of interest. An empirical background distribution model of reads was constructed to find the significance level of signal in a given region.

organism: Mus musculus

source_name: leukemic spleen cells, secondary, WT, H3K27me3 ChIP

extract_protocol: ChIP DNA libraries were made following the Illumina ChIP-seq library preparation kit.

treatment_protocol:
GFP/YFP double-positive cells were isolated by flow sorting from spleens of leukemic mice.
Cells were subjected to ChIP using an antibody specific for H3K27me3.

tag: background strain

tag: disease state

value: MLL-AF9-induced acute myeloid leukemia (AML)

tag: cell type

value: leukemic spleen cells

tag: cell origin

value: WT MLL-AF9 leukemic cell from 2' recipient, sorted for GFP and YFP expression


title: Chromatin accessibility assay of Testes; DS18942

description:
sample_term_id: UBERON_0000473
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Chromatin accessibility determination via DNase-seq
Library name: DS18942
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.11290
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.11289
****************
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: GSM878617_UW.Fetal_Testes.ChromatinAccessibility.H24198_H23640_H24042.DS18942.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS18942.hg19.level.1.release.7
ANALYSIS TITLE: Mapping of Fetal Testes Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fetal Testes, Donor H24198_H23640_H24042, Library DS18942 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.12762
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 7

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 26,759,157
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 58
FINDPEAKS_SCORE: 0.3839
FINDPEAKS_PERCENTILE: 41
HOTSPOT_SCORE: 0.3769
HOTSPOT_PERCENTILE: 40
IROC_SCORE: 0.9945
IROC_PERCENTILE: 59
POISSON_SCORE: 0.4491
POISSON_PERCENTILE: 45
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

ANALYSIS FILE NAME: GSM878617_UW.Fetal_Testes.ChromatinAccessibility.H24198_H23640_H24042.DS18942.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS18942.hg19.level.2.release.7
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Testes Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from  Fetal Testes, Donor H24198_H23640_H24042, Library DS18942 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.12820
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 7
BROWSER_TRACK_NAME: FT DNase 42 42
BROWSER_TRACK_DESCRIPTION: UW Fetal Testes DNase Hypersensitivity Donor H24198_H23640_H24042 Library DS18942 EA Release 7

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 26,759,157
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 58
FINDPEAKS_SCORE: 0.3839
FINDPEAKS_PERCENTILE: 41
HOTSPOT_SCORE: 0.3769
HOTSPOT_PERCENTILE: 40
IROC_SCORE: 0.9945
IROC_PERCENTILE: 59
POISSON_SCORE: 0.4491
POISSON_PERCENTILE: 45
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

source_name: Fetal Testes primary tissue, pool; DS18942

tag: sample common name

value: Fetal Testes

tag: molecule

tag: disease

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

value: Primary Tissue

value: UW

value: fetal

value: pool

value: Qiagen minElut


title: H3K27me3_1'AML_Ezh2-null

description:
H3K27me3_1'AML_Ezh2-null
Chromatin IP against H3K27me3.

source_name: leukemic spleen cells, primary, Ezh2-null, H3K27me3 ChIP

value: Ezh2-null MLL-AF9 leukemic cell from 1' recipient, sorted for GFP and YFP expression


title: Fibroblast H3K27me3

description: Chromatin IP against H3K27me3

data_processing:
Sequence reads were aligned to human genome assembly hg18 using Bowtie. ChIP-Seq signal was quantified as total number of reads per million in the region of interest. An empirical background distribution model of reads was constructed to find the significance level of signal in a given region.
Genome Build:
Fibr.H3K27me3.n_1_l_28_e_70_a_m_1_best_strata.hg18.wig: hg18

value: fibroblast derived from H1

value: diagnostic sample (pre-treatment)

value: Millipore


title: Fibroblast H3K79me2

description: Chromatin IP against H3K79me2

data_processing:
Sequence reads were aligned to human genome assembly hg18 using Bowtie. ChIP-Seq signal was quantified as total number of reads per million in the region of interest. An empirical background distribution model of reads was constructed to find the significance level of signal in a given region.
Genome Build:
Fibr.H3K79me2.n_1_l_28_e_70_a_m_1_best_strata.hg18.wig: hg18

value: Abcam


title: Chromatin accessibility assay of H9 Cell Line; DS18517

description:
sample_term_id: NTR_0000838
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Chromatin accessibility determination via DNase-seq
Library name: DS18517
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.11253
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: GSM878612_UW.H9.ChromatinAccessibility.DS18517.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS18517.hg19.level.1.release.7
ANALYSIS TITLE: Mapping of H9 Cell Line Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on the H9 Cell Line, Library DS18517 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.12754
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 7

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 44,584,825
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 58
FINDPEAKS_SCORE: 0.2015
FINDPEAKS_PERCENTILE: 7
HOTSPOT_SCORE: 0.2056
HOTSPOT_PERCENTILE: 5
IROC_SCORE: 0.99
IROC_PERCENTILE: 5
POISSON_SCORE: 0.2908
POISSON_PERCENTILE: 7
MAXIMUM_REPLICATE_CORRELATION: 0.99

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

ANALYSIS FILE NAME: GSM878612_UW.H9.ChromatinAccessibility.DS18517.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS18517.hg19.level.2.release.7
ANALYSIS TITLE: Raw Signal Density Graphs of H9 Cell Line Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from  the H9 Cell Line, Library DS18517 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.12812
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 7
BROWSER_TRACK_NAME: H9 DNase 17
BROWSER_TRACK_DESCRIPTION: UW H9 Cell Line DNase Hypersensitivity Library DS18517 EA Release 7

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 44,584,825
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 58
FINDPEAKS_SCORE: 0.2015
FINDPEAKS_PERCENTILE: 7
HOTSPOT_SCORE: 0.2056
HOTSPOT_PERCENTILE: 5
IROC_SCORE: 0.99
IROC_PERCENTILE: 5
POISSON_SCORE: 0.2908
POISSON_PERCENTILE: 7
MAXIMUM_REPLICATE_CORRELATION: 0.99

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

source_name: Human embryonic stem cells received from the James Thompson laboratory.  Cells are from the H9 line.; DS18517

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

value: Female


title: MLL1_mouse_ChIPSeq

description: Chromatin IP using anti-MLL1 antibody

data_processing: Sequence reads were aligned to mouse genome assembly mm8 using Bowtie. ChIP-Seq signal was quantified as total number of reads per million in the region of interest. An empirical background distribution model of reads was constructed to find the significance level of signal in a given region.

source_name: MLL-AF9 transfromed blasts

growth_protocol: Murine bone marrow cells were  transformed with Flag-tagged MLL-AF9 , harvested after two rounds of replating.

treatment_protocol: Cells were subjected to ChIP-Seq using an antibody for MLL1

tag: strain

value: 5-FU treated BM cells transduced with Flag-tagged MLL-AF9


title: Fibroblast Epi OSKM D6 H3K79me2

description: Chromatin IP against H3K79me2

data_processing:
Sequence reads were aligned to human genome assembly hg18 using Bowtie. ChIP-Seq signal was quantified as total number of reads per million in the region of interest. An empirical background distribution model of reads was constructed to find the significance level of signal in a given region.
Genome Build:
Fibr_Epi_OSKM_D6.H3K79me2.n_1_l_28_e_70_a_m_1_best_strata.hg18.wig: hg18

tag: cell line

tag: treatment

value: Cells were treated with 10uM Dot1L inhibitor (EPZ004777)  for 5 days and then infected with Oct4, Sox2, Klf4 and c-Myc followed by 6 days of incubation

tag: chip antibody


title: Chromatin accessibility assay of Fibroblasts, Fetal Skin, Abdomen; DS19561

description:
sample_term_id: CL_0002620
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Chromatin accessibility determination via DNase-seq
Library name: DS19561
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.11371
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.11370
****************
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: GSM878636_UW.Fibroblasts_Fetal_Skin_Abdomen.ChromatinAccessibility.H-24259.DS19561.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS19561.hg19.level.1.release.7
ANALYSIS TITLE: Mapping of Fibroblasts Fetal Skin Abdomen Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fibroblasts Fetal Skin Abdomen, Donor H-24259, Library DS19561 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.12745
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 7

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 45,280,788
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 58
FINDPEAKS_SCORE: 0.4991
FINDPEAKS_PERCENTILE: 74
HOTSPOT_SCORE: 0.5749
HOTSPOT_PERCENTILE: 79
IROC_SCORE: 0.9968
IROC_PERCENTILE: 76
POISSON_SCORE: 0.5667
POISSON_PERCENTILE: 74
MAXIMUM_REPLICATE_CORRELATION: 1.0

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

ANALYSIS FILE NAME: GSM878636_UW.Fibroblasts_Fetal_Skin_Abdomen.ChromatinAccessibility.H-24259.DS19561.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS19561.hg19.level.2.release.7
ANALYSIS TITLE: Raw Signal Density Graphs of Fibroblasts Fetal Skin Abdomen Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from  Fibroblasts Fetal Skin Abdomen, Donor H-24259, Library DS19561 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.12803
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 7
BROWSER_TRACK_NAME: FFSA DNase 59 61
BROWSER_TRACK_DESCRIPTION: UW Fibroblasts Fetal Skin Abdomen DNase Hypersensitivity Donor H-24259 Library DS19561 EA Release 7

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 45,280,788
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 58
FINDPEAKS_SCORE: 0.4991
FINDPEAKS_PERCENTILE: 74
HOTSPOT_SCORE: 0.5749
HOTSPOT_PERCENTILE: 79
IROC_SCORE: 0.9968
IROC_PERCENTILE: 76
POISSON_SCORE: 0.5667
POISSON_PERCENTILE: 74
MAXIMUM_REPLICATE_CORRELATION: 1.0

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

source_name: Fibroblasts, Fetal Skin, Abdomen, day 97 donor; DS19561

value: Fibroblasts, Fetal Skin, Abdomen

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

value: Primary Cell Culture

tag: markers

value: day 97

value: Male

value: short term

value: Chromatin Accessibility


title: Chromatin accessibility assay of Fetal Muscle, Arm; DS18379

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: DS18379
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.11572
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.11571
****************
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: GSM878610_UW.Fetal_Muscle_Arm.ChromatinAccessibility.H-24078.DS18379.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS18379.hg19.level.1.release.7
ANALYSIS TITLE: Mapping of Fetal Muscle Arm Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fetal Muscle Arm, Donor H-24078, Library DS18379 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.12755
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 7

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 19,619,237
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 58
FINDPEAKS_SCORE: 0.3489
FINDPEAKS_PERCENTILE: 24
HOTSPOT_SCORE: 0.3491
HOTSPOT_PERCENTILE: 29
IROC_SCORE: 0.9921
IROC_PERCENTILE: 26
POISSON_SCORE: 0.4355
POISSON_PERCENTILE: 38
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

ANALYSIS FILE NAME: GSM878610_UW.Fetal_Muscle_Arm.ChromatinAccessibility.H-24078.DS18379.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS18379.hg19.level.2.release.7
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-24078, Library DS18379 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.12813
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 7
BROWSER_TRACK_NAME: FMA DNase 78 79
BROWSER_TRACK_DESCRIPTION: UW Fetal Muscle Arm DNase Hypersensitivity Donor H-24078 Library DS18379 EA Release 7

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 19,619,237
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 58
FINDPEAKS_SCORE: 0.3489
FINDPEAKS_PERCENTILE: 24
HOTSPOT_SCORE: 0.3491
HOTSPOT_PERCENTILE: 29
IROC_SCORE: 0.9921
IROC_PERCENTILE: 26
POISSON_SCORE: 0.4355
POISSON_PERCENTILE: 38
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

source_name: Fetal Muscle, Arm primary tissue, day 127; DS18379

tag: sample alias

value: Fetal Muscle, Arm

value: Primary Tissue

value: UW

value: fetal

value: day 127

value: Qiagen minElut


title: Chromatin accessibility assay of Fetal Muscle, Back; DS18454

description:
sample_term_id: UBERON_0002324
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Chromatin accessibility determination via DNase-seq
Library name: DS18454
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.11521
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.11520
****************
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: GSM878611_UW.Fetal_Muscle_Back.ChromatinAccessibility.H-24089.DS18454.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS18454.hg19.level.1.release.7
ANALYSIS TITLE: Mapping of Fetal Muscle Back Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fetal Muscle Back, Donor H-24089, Library DS18454 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.12775
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 7

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 32,000,595
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 58
FINDPEAKS_SCORE: 0.4145
FINDPEAKS_PERCENTILE: 47
HOTSPOT_SCORE: 0.4036
HOTSPOT_PERCENTILE: 45
IROC_SCORE: 0.9941
IROC_PERCENTILE: 52
POISSON_SCORE: 0.474
POISSON_PERCENTILE: 48
MAXIMUM_REPLICATE_CORRELATION: 0.99

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

ANALYSIS FILE NAME: GSM878611_UW.Fetal_Muscle_Back.ChromatinAccessibility.H-24089.DS18454.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS18454.hg19.level.2.release.7
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Muscle Back Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from  Fetal Muscle Back, Donor H-24089, Library DS18454 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.12833
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 7
BROWSER_TRACK_NAME: FMB DNase 89 54
BROWSER_TRACK_DESCRIPTION: UW Fetal Muscle Back DNase Hypersensitivity Donor H-24089 Library DS18454 EA Release 7

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 32,000,595
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 58
FINDPEAKS_SCORE: 0.4145
FINDPEAKS_PERCENTILE: 47
HOTSPOT_SCORE: 0.4036
HOTSPOT_PERCENTILE: 45
IROC_SCORE: 0.9941
IROC_PERCENTILE: 52
POISSON_SCORE: 0.474
POISSON_PERCENTILE: 48
MAXIMUM_REPLICATE_CORRELATION: 0.99

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

source_name: Fetal Muscle, Back primary tissue, day 96; DS18454

value: Fetal Muscle, Back

value: genomic DNA

value: day 96


title: H3K27me3_1'AML_WT

description:
H3K27me3_1'AML_WT
Chromatin IP against H3K27me3.

source_name: leukemic spleen cells, primary, WT, H3K27me3 ChIP

tag: background strain

value: MLL-AF9-induced acute myeloid leukemia (AML)

value: leukemic spleen cells

value: WT MLL-AF9 leukemic cell from 1' recipient, sorted for GFP and YFP expression


title: Chromatin accessibility assay of H1 Cell Line; DS18873

description:
sample_term_id: EFO_0003042
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Chromatin accessibility determination via DNase-seq
Library name: DS18873
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.11262
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.3425
****************
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: GSM878616_UW.H1.ChromatinAccessibility.DS18873.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS18873.hg19.level.1.release.7
ANALYSIS TITLE: Mapping of H1 Cell Line Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on the H1 Cell Line, Library DS18873 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.12777
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 7

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 48,286,828
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 58
FINDPEAKS_SCORE: 0.2768
FINDPEAKS_PERCENTILE: 12
HOTSPOT_SCORE: 0.277
HOTSPOT_PERCENTILE: 12
IROC_SCORE: 0.9942
IROC_PERCENTILE: 55
POISSON_SCORE: 0.3556
POISSON_PERCENTILE: 12
MAXIMUM_REPLICATE_CORRELATION: 1.0

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

ANALYSIS FILE NAME: GSM878616_UW.H1.ChromatinAccessibility.DS18873.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS18873.hg19.level.2.release.7
ANALYSIS TITLE: Raw Signal Density Graphs of H1 Cell Line Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from  the H1 Cell Line, Library DS18873 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.12835
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 7
BROWSER_TRACK_NAME: H1 DNase 73
BROWSER_TRACK_DESCRIPTION: UW H1 Cell Line DNase Hypersensitivity Library DS18873 EA Release 7

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 48,286,828
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 58
FINDPEAKS_SCORE: 0.2768
FINDPEAKS_PERCENTILE: 12
HOTSPOT_SCORE: 0.277
HOTSPOT_PERCENTILE: 12
IROC_SCORE: 0.9942
IROC_PERCENTILE: 55
POISSON_SCORE: 0.3556
POISSON_PERCENTILE: 12
MAXIMUM_REPLICATE_CORRELATION: 1.0

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

source_name: Human embryonic stem cells received from the James Thompson laboratory.  Cells are from the H1 line.; DS18873

value: H1 Cell Line

value: James Thompson Laboratory

value: Cell Line

value: Embryonic Stem Cell

value: Between 20 and 40

value: mTeSER

tag: Sex

tag: batch


title: Chromatin accessibility assay of H1 Derived Neuronal Progenitor Cultured Cells; DS18739

description:
sample_term_id: CL_0000047
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Chromatin accessibility determination via DNase-seq
Library name: DS18739
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.11244
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.7871
****************
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: GSM878615_UW.H1_Derived_Neuronal_Progenitor_Cultured_Cells.ChromatinAccessibility.DS18739.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS18739.hg19.level.1.release.7
ANALYSIS TITLE: Mapping of H1 Derived Neuronal Progenitor Cultured Cells Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on the H1 Derived Neuronal Progenitor Cultured Cells, Library DS18739 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.12787
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 7

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 37,408,936
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 58
FINDPEAKS_SCORE: 0.1997
FINDPEAKS_PERCENTILE: 5
HOTSPOT_SCORE: 0.2234
HOTSPOT_PERCENTILE: 9
IROC_SCORE: 0.9927
IROC_PERCENTILE: 28
POISSON_SCORE: 0.2784
POISSON_PERCENTILE: 5
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM878615_UW.H1_Derived_Neuronal_Progenitor_Cultured_Cells.ChromatinAccessibility.DS18739.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS18739.hg19.level.2.release.7
ANALYSIS TITLE: Raw Signal Density Graphs of H1 Derived Neuronal Progenitor Cultured Cells Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from  the H1 Derived Neuronal Progenitor Cultured Cells, Library DS18739 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.12845
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 7
BROWSER_TRACK_NAME: HDNP DNase 39
BROWSER_TRACK_DESCRIPTION: UW H1 Derived Neuronal Progenitor Cultured Cells DNase Hypersensitivity Library DS18739 EA Release 7

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 37,408,936
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 58
FINDPEAKS_SCORE: 0.1997
FINDPEAKS_PERCENTILE: 5
HOTSPOT_SCORE: 0.2234
HOTSPOT_PERCENTILE: 9
IROC_SCORE: 0.9927
IROC_PERCENTILE: 28
POISSON_SCORE: 0.2784
POISSON_PERCENTILE: 5
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: Human embryonic stem cells received from the James Thomson laboratory.  Cells are from the H1 line and are differentiated into neural progenitor cells.; DS18739

value: James Thomson Laboratory

value: Embryonic stem cell differentiated into neural progenitor cells

value: Publication in progress

value: Between 20 and 30

value: Male

value: Chromatin Accessibility


title: H3K27me3_2'AML_Ezh2-null

description:
H3K27me3_2'AML_Ezh2-null
Chromatin IP against H3K27me3.

source_name: leukemic spleen cells, secondary, Ezh2-null, H3K27me3 ChIP

tag: disease state

tag: cell type

tag: cell origin

value: Ezh2-null MLL-AF9 leukemic cell from 2' recipient, sorted for GFP and YFP expression


title: PR1

city: Wooster

first: Asela

middle: J

last: Wijeratne

state: Ohio

address: 1680 Madison Av

department: Molecular and Cellular Imaging Center

institute: Ohio State University

description: mRNA-seq

library_source: transcriptomic

data_processing: Reads were mapped to unigenes using BWA (Version: 0.5.9-r16), allowing only two mismatches and output files were further formatted using samtools (Version: 0.1.12a (r862)).

molecule: total RNA

organism: Cimex lectularius

source_name: collected from Columbus

extract_protocol:
Total RNA was extracted from each individual (8 individuals per population) using TRIzol (Invitrogen) separately and were pooled before assessing quality check (Nanodrop, Thermo Scientific Nanodrop 2000 andAgilent Bioanalyzer, Ohio State University, Columbus).
Samples were prepared for Illumina GA sequencing using the PE library preparation kit (Catalogue Number PE-102-1001, Illumina, San Diego, CA, USA) and TruSeq RNA Sample Prep Kits (Catalogue Number FC-122-1001, Illumina, San Diego, CA, USA) as instructed by manufacturer
Fragment size (including the adapters) and standard deviation: pesticide-resistant sample 1: 275 ± 50;  pesticide-resistant sample 2 300 ± 50; pesticide-susceptible sample1: 350 ± 50; pesticide-susceptible sample 2: 350 ± 50

value: collected from Columbus

tag: resistance status

value: pesticide-resistant


title: PR2

description: mRNA-seq


title: PS2

description: mRNA-seq

source_name: NPMA Harlan1

value: NPMA Harlan1

value: pesticide-susceptible


title: PS1

description: mRNA-seq


title: DMC1 KE

status: Public on Feb 21 2012

city: Bethesda

first: Pavel

middle: P

last: Khil

state: MD

address: 5 Memorial Dr.

institute: NIDDK

description: Kinetic Enrichment (KE) protocol. Samples were denatured and quickly renatured before adapter ligation.

data_processing:
DMC1_KE.sorted.ssDNA_type1.bed; genome build: mm9
DMC1_KE.sorted.ssDNA_type2.bed; genome build: mm9
DMC1_KE.sorted.dsDNA.bed; genome build: mm9
DMC1_KE.sorted.1K_100.wig; genome build: mm9
BED: Quality-filtered sequencing reads were mapped to mm9 version of mouse genome assembly using BWA (first end) (http://bio-bwa.sourceforge.net/) or BWA-RA (second end). BWA-RA is modification of BWA that iteratevily seeks longest aligning suffux of the query. Obtained alignments were further processed to generate ssDNA type 1, ssDNA type 2 and dsDNA subsets of fragments. Fourths field in the BED file is (ITR_length)_(microhomology_lenght) and fifth field is BWA-calculated alignment quality. PHRED alignment qualities for both ends (0-30) were added and then re-scaled to 0-1000.
WIG: type1 ssDNA, type2 ssDNA and dsDNA subsets were combined and read coverage was calculated in sliding windows of 1Kb with 100 bp step. Counts were normalized to total numer of reads in the dataset and are given in reads per million.

source_name: adult testis

growth_protocol: Cells were extracted from testis of euthanized mice and subjected to immunoprecipitation.

extract_protocol: Lysates from mouse testis cells were crosslinked, sonicated and immunoprecipitated with anti-DMC1 or anti-RAD51 antibodies. Library construction was done using enzymes from New England Biolabs or Illumina and standard Illumina protocol. Size selection of library fragments of 150~250 bp was performed after PCR amplification. “Klenow exo(-)” sample was prepared by substituting Klenow fragment and T4 DNA polymerase from the end repair step of the standard protocol with Klenow exo(-) enzyme and performing end repair at 37 °C for 1h. “Klenow exo(-), 12 °C“ sample was prepared the same way followed by incubation at 20 °C for 2h and at 12 °C overnight. "Kinetic enrichment" samples were denatured and quickly renatured before adapter ligation.

tag: age

value: adult

tag: gender

value: male

tag: genetic background

value: 9R female x 13R male F1

tag: chip antibody catalog number

tag: chip antibody lot

tag: chip antibody vendor

value: Santa Cruz


title: IgG control KE

data_processing:
IgG_KE.sorted.ssDNA_type1.bed; genome build: mm9
IgG_KE.sorted.ssDNA_type2.bed; genome build: mm9
IgG_KE.sorted.dsDNA.bed; genome build: mm9
IgG_KE.sorted.1K_100.wig; genome build: mm9
BED: Quality-filtered sequencing reads were mapped to mm9 version of mouse genome assembly using BWA (first end) (http://bio-bwa.sourceforge.net/) or BWA-RA (second end). BWA-RA is modification of BWA that iteratevily seeks longest aligning suffux of the query. Obtained alignments were further processed to generate ssDNA type 1, ssDNA type 2 and dsDNA subsets of fragments. Fourths field in the BED file is (ITR_length)_(microhomology_lenght) and fifth field is BWA-calculated alignment quality. PHRED alignment qualities for both ends (0-30) were added and then re-scaled to 0-1000.
WIG: type1 ssDNA, type2 ssDNA and dsDNA subsets were combined and read coverage was calculated in sliding windows of 1Kb with 100 bp step. Counts were normalized to total numer of reads in the dataset and are given in reads per million.

value: IgG


title: DMC1 Hop2-/- Klenow (exo-)

description: Modified ChIP-Seq. End-repair step was performed using only Klenow (exo-) for 1h @ 37C.

data_processing:
DMC1_hop2_no_exo1.sorted.ssDNA_type1.bed; genome build: mm9
DMC1_hop2_no_exo1.sorted.ssDNA_type2.bed; genome build: mm9
DMC1_hop2_no_exo1.sorted.dsDNA.bed; genome build: mm9
DMC1_hop2_no_exo1.sorted.1K_100.wig; genome build: mm9
BED: Quality-filtered sequencing reads were mapped to mm9 version of mouse genome assembly using BWA (first end) (http://bio-bwa.sourceforge.net/) or BWA-RA (second end). BWA-RA is modification of BWA that iteratevily seeks longest aligning suffux of the query. Obtained alignments were further processed to generate ssDNA type 1, ssDNA type 2 and dsDNA subsets of fragments. Fourths field in the BED file is (ITR_length)_(microhomology_lenght) and fifth field is BWA-calculated alignment quality. PHRED alignment qualities for both ends (0-30) were added and then re-scaled to 0-1000.
WIG: type1 ssDNA, type2 ssDNA and dsDNA subsets were combined and read coverage was calculated in sliding windows of 1Kb with 100 bp step. Counts were normalized to total numer of reads in the dataset and are given in reads per million.

tag: genotype


title: IgG control rep2

description: Standard ChIP-Seq.

data_processing:
IgG2.sorted.ssDNA_type1.bed; genome build: mm9
IgG2.sorted.ssDNA_type2.bed; genome build: mm9
IgG2.sorted.dsDNA.bed; genome build: mm9
IgG2.sorted.1K_100.wig; genome build: mm9
BED: Quality-filtered sequencing reads were mapped to mm9 version of mouse genome assembly using BWA (first end) (http://bio-bwa.sourceforge.net/) or BWA-RA (second end). BWA-RA is modification of BWA that iteratevily seeks longest aligning suffux of the query. Obtained alignments were further processed to generate ssDNA type 1, ssDNA type 2 and dsDNA subsets of fragments. Fourths field in the BED file is (ITR_length)_(microhomology_lenght) and fifth field is BWA-calculated alignment quality. PHRED alignment qualities for both ends (0-30) were added and then re-scaled to 0-1000.
WIG: type1 ssDNA, type2 ssDNA and dsDNA subsets were combined and read coverage was calculated in sliding windows of 1Kb with 100 bp step. Counts were normalized to total numer of reads in the dataset and are given in reads per million.

value: 13R female x 9R male F1

tag: chip antibody


title: DMC1 Hop2-/- Klenow (exo-) 12C

description: Modified ChIP-Seq. End-repair step was performed using only Klenow (exo-) and incubations @ 37C, 1h followed by 20C, 2h and o/n @ 12C.

data_processing:
DMC1_hop2_no_exo2.sorted.ssDNA_type1.bed; genome build: mm9
DMC1_hop2_no_exo2.sorted.ssDNA_type2.bed; genome build: mm9
DMC1_hop2_no_exo2.sorted.dsDNA.bed; genome build: mm9
DMC1_hop2_no_exo2.sorted.1K_100.wig; genome build: mm9
BED: Quality-filtered sequencing reads were mapped to mm9 version of mouse genome assembly using BWA (first end) (http://bio-bwa.sourceforge.net/) or BWA-RA (second end). BWA-RA is modification of BWA that iteratevily seeks longest aligning suffux of the query. Obtained alignments were further processed to generate ssDNA type 1, ssDNA type 2 and dsDNA subsets of fragments. Fourths field in the BED file is (ITR_length)_(microhomology_lenght) and fifth field is BWA-calculated alignment quality. PHRED alignment qualities for both ends (0-30) were added and then re-scaled to 0-1000.
WIG: type1 ssDNA, type2 ssDNA and dsDNA subsets were combined and read coverage was calculated in sliding windows of 1Kb with 100 bp step. Counts were normalized to total numer of reads in the dataset and are given in reads per million.


title: DMC1 Hop2-/- KE

data_processing:
DMC1_hop2_KE.sorted.ssDNA_type1.bed; genome build: mm9
DMC1_hop2_KE.sorted.ssDNA_type2.bed; genome build: mm9
DMC1_hop2_KE.sorted.dsDNA.bed; genome build: mm9
DMC1_hop2_KE.sorted.1K_100.wig; genome build: mm9
BED: Quality-filtered sequencing reads were mapped to mm9 version of mouse genome assembly using BWA (first end) (http://bio-bwa.sourceforge.net/) or BWA-RA (second end). BWA-RA is modification of BWA that iteratevily seeks longest aligning suffux of the query. Obtained alignments were further processed to generate ssDNA type 1, ssDNA type 2 and dsDNA subsets of fragments. Fourths field in the BED file is (ITR_length)_(microhomology_lenght) and fifth field is BWA-calculated alignment quality. PHRED alignment qualities for both ends (0-30) were added and then re-scaled to 0-1000.
WIG: type1 ssDNA, type2 ssDNA and dsDNA subsets were combined and read coverage was calculated in sliding windows of 1Kb with 100 bp step. Counts were normalized to total numer of reads in the dataset and are given in reads per million.


title: RNA Pol II WCE

city: St Louis

first: Tiandao

last: Li

state: MO

address: 4444 Forest Park Ave

institute: Washington University

data_processing: Raw sequences generated from Illumina/Solexa sequencer were aligned using ELAND software to NCBI Build 36.1 (UCSC hg18) of the human genome. Only sequences that mapped uniquely to the genome with zero or one mismatch were used for further analysis. When multiple sequences mapped to the same genomic position, a maximum of two reads mapping to the same position were used. The sequenced reads represent only the ends of each immunoprecipitated fragments instead of the precise protein-DNA binding sites. To illustrate the entire DNA fragment, the 3’ end of each read was extended 200 bp. The reference genome was partitioned into 25 bp bins and the total reads (including partial reads) in each bin were summed and used to generate the visualization file in wiggle (WIG) format. The complete set of RefSeq genes was downloaded from the UCSC table browser on December 1, 2010. A custom annotated RefSeq gene list was generated by merging the all TSSs for each gene that were within 500 bases of each other. Then TSSs within 1000 bp of each other (6% of the total number) were removed from the list. This list was used for further analyses. A genomic coordinate file was compiled by extending the 3’ end of each original sequence to a total of 200 bp. The number of reads within 10,000 bases of the TSS of each gene in the custom gene list was tabulated. Similar analysis was applied to the location of center of peaks generated from the peak finding algorithm for the region within 500 bp relative to the TSS. Heat maps were generated using the program R. Genes were rank ordered based on the sequence density for RNAP II from -2K to +2K from the TSS. Using this order, basepair resolution sequence density for RNAP II and Gdown1 for the top 20,000 genes was displayed without binning. A peak finding algorithm (ChIP-Seq Peak) was designed to examine the data within individual WIG files and determine precise position and height of each significant peak. This algorithm assumes that each 200 bp immunoprecipitated DNA fragment is sequenced randomly from either end and that typical peaks would be approximately 400 bases wide at the base. Peaks less than 250 bp wide were eliminated and the center of each remaining peak was determined using Gaussian curve fitting. The height was determined by the area under each peak.

source_name: RNA Pol II WCE

growth_protocol: HeLa cells were maintained at 5% CO2 and 37°C in DMEM plus 10% FBS (Hyclone). Cells were grown in T-150 flasks to 90% confluence and treated for 5 or 60 minutes with Flavopiridol (final concentration 1 μM with 0.1% DMSO) or 0.1% DMSO alone for control.

extract_protocol: DNA from whole cell extracts

tag: cell line

value: HeLa

tag: sample type

value: whole cell extract

tag: treatment


title: RAD51 Hop2-/- rep1

description: Standard ChIP-Seq.

data_processing:
RAD51_hop2.sorted.ssDNA_type1.bed; genome build: mm9
RAD51_hop2.sorted.ssDNA_type2.bed; genome build: mm9
RAD51_hop2.sorted.dsDNA.bed; genome build: mm9
RAD51_hop2.sorted.1K_100.wig; genome build: mm9
BED: Quality-filtered sequencing reads were mapped to mm9 version of mouse genome assembly using BWA (first end) (http://bio-bwa.sourceforge.net/) or BWA-RA (second end). BWA-RA is modification of BWA that iteratevily seeks longest aligning suffux of the query. Obtained alignments were further processed to generate ssDNA type 1, ssDNA type 2 and dsDNA subsets of fragments. Fourths field in the BED file is (ITR_length)_(microhomology_lenght) and fifth field is BWA-calculated alignment quality. PHRED alignment qualities for both ends (0-30) were added and then re-scaled to 0-1000.
WIG: type1 ssDNA, type2 ssDNA and dsDNA subsets were combined and read coverage was calculated in sliding windows of 1Kb with 100 bp step. Counts were normalized to total numer of reads in the dataset and are given in reads per million.


title: RAD51 Hop2-/- rep2

description: Standard ChIP-Seq.

data_processing:
RAD51_hop2_LE.sorted.ssDNA_type1.bed; genome build: mm9
RAD51_hop2_LE.sorted.ssDNA_type2.bed; genome build: mm9
RAD51_hop2_LE.sorted.dsDNA.bed; genome build: mm9
RAD51_hop2_LE.sorted.1K_100.wig; genome build: mm9
BED: Quality-filtered sequencing reads were mapped to mm9 version of mouse genome assembly using BWA (first end) (http://bio-bwa.sourceforge.net/) or BWA-RA (second end). BWA-RA is modification of BWA that iteratevily seeks longest aligning suffux of the query. Obtained alignments were further processed to generate ssDNA type 1, ssDNA type 2 and dsDNA subsets of fragments. Fourths field in the BED file is (ITR_length)_(microhomology_lenght) and fifth field is BWA-calculated alignment quality. PHRED alignment qualities for both ends (0-30) were added and then re-scaled to 0-1000.
WIG: type1 ssDNA, type2 ssDNA and dsDNA subsets were combined and read coverage was calculated in sliding windows of 1Kb with 100 bp step. Counts were normalized to total numer of reads in the dataset and are given in reads per million.


title: DMC1 Hop2-/-

description: Standard ChIP-Seq.

data_processing:
DMC1_hop2.sorted.ssDNA_type1.bed; genome build: mm9
DMC1_hop2.sorted.ssDNA_type2.bed; genome build: mm9
DMC1_hop2.sorted.dsDNA.bed; genome build: mm9
DMC1_hop2.sorted.1K_100.wig; genome build: mm9
BED: Quality-filtered sequencing reads were mapped to mm9 version of mouse genome assembly using BWA (first end) (http://bio-bwa.sourceforge.net/) or BWA-RA (second end). BWA-RA is modification of BWA that iteratevily seeks longest aligning suffux of the query. Obtained alignments were further processed to generate ssDNA type 1, ssDNA type 2 and dsDNA subsets of fragments. Fourths field in the BED file is (ITR_length)_(microhomology_lenght) and fifth field is BWA-calculated alignment quality. PHRED alignment qualities for both ends (0-30) were added and then re-scaled to 0-1000.
WIG: type1 ssDNA, type2 ssDNA and dsDNA subsets were combined and read coverage was calculated in sliding windows of 1Kb with 100 bp step. Counts were normalized to total numer of reads in the dataset and are given in reads per million.


title: IgG control rep1

description: Standard ChIP-Seq.

data_processing:
IgG1.sorted.ssDNA_type1.bed; genome build: mm9
IgG1.sorted.ssDNA_type2.bed; genome build: mm9
IgG1.sorted.dsDNA.bed; genome build: mm9
IgG1.sorted.1K_100.wig; genome build: mm9
BED: Quality-filtered sequencing reads were mapped to mm9 version of mouse genome assembly using BWA (first end) (http://bio-bwa.sourceforge.net/) or BWA-RA (second end). BWA-RA is modification of BWA that iteratevily seeks longest aligning suffux of the query. Obtained alignments were further processed to generate ssDNA type 1, ssDNA type 2 and dsDNA subsets of fragments. Fourths field in the BED file is (ITR_length)_(microhomology_lenght) and fifth field is BWA-calculated alignment quality. PHRED alignment qualities for both ends (0-30) were added and then re-scaled to 0-1000.
WIG: type1 ssDNA, type2 ssDNA and dsDNA subsets were combined and read coverage was calculated in sliding windows of 1Kb with 100 bp step. Counts were normalized to total numer of reads in the dataset and are given in reads per million.