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Status |
Public on Oct 15, 2011 |
Title |
Chromatin accessibility assay of Penis Foreskin Keratinocytes Primary Cells; DS18695 |
Sample type |
SRA |
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Source name |
Penis, Foreskin, Keratinocyte Primary Cells skin01; DS18695
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Organism |
Homo sapiens |
Characteristics |
sample alias: Penis, Foreskin, Keratinocyte skin01 sample common name: Penis, Foreskin, Keratinocyte Primary Cells molecule: genomic DNA disease: None biomaterial_provider: SFVAMC Dermatology biomaterial_type: Primary Cell Culture cell_type: Keratinocyte markers: NA culture_conditions: Invitrogen 154CF + HKGS + .07mM Ca donor_id: skin01 donor_age: Neonate donor_health_status: Disease Free donor_sex: Male donor_ethnicity: NA passage_if_expanded: 2 karyotype: 46, XY parity: NA experiment_type: Chromatin Accessibility extraction_protocol: Qiagen minElut dnase_protocol: Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)
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Extracted molecule |
genomic DNA |
Extraction protocol |
Library construction protocol: Single read - Illumina
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Library strategy |
DNase-Hypersensitivity |
Library source |
genomic |
Library selection |
DNAse |
Instrument model |
Illumina Genome Analyzer IIx |
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Description |
Design description: Chromatin accessibility determination via DNase-seq Library name: DS18695 EDACC Genboree Experiment Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.9790 EDACC Genboree Sample Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSF-UBC%2FSAMPLE%2FEDACC.5490 **************** For data usage terms and conditions, please refer to: http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies ****************
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Data processing |
**********************************************************************
ANALYSIS FILE NAME: GSM817195_UW.Penis_Foreskin_Keratinocyte_Primary_Cells.ChromatinAccessibility.skin01.DS18695.bed ANALYSIS CENTER: EDACC ANALYSIS ALIAS: DS18695.hg19.level.1.release.6 ANALYSIS TITLE: Mapping of Penis Foreskin Keratinocyte Primary Cells Chromatin Accessibility Data ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Penis Foreskin Keratinocyte Primary Cells, Donor skin01, Library DS18695 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.12615 DATA_ANALYSIS_LEVEL: 1 EXPERIMENT_TYPE: Chromatin Accessibility GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19 SOFTWARE: Pash SOFTWARE_VERSION: 3.0 MAXIMUM_ALIGNMENT_LENGTH: Read length MISMATCHES_ALLOWED: 10% of read length ALIGNMENTS_ALLOWED: 1 TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration. TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None ALIGNMENT_POSTPROCESSING: None RELEASE_NUMBER: Human Epigenome Atlas 6
QUALITY SCORES: NUMBER_OF_MAPPED_READS: 34,521,027 NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 63 FINDPEAKS_SCORE: 0.455 FINDPEAKS_PERCENTILE: 71 HOTSPOT_SCORE: 0.4944 HOTSPOT_PERCENTILE: 87 IROC_SCORE: 0.9963 IROC_PERCENTILE: 89 POISSON_SCORE: 0.5389 POISSON_PERCENTILE: 83 MAXIMUM_REPLICATE_CORRELATION: 1.0
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ANALYSIS FILE NAME: GSM817195_UW.Penis_Foreskin_Keratinocyte_Primary_Cells.ChromatinAccessibility.skin01.DS18695.wig ANALYSIS CENTER: EDACC ANALYSIS ALIAS: DS18695.hg19.level.2.release.6 ANALYSIS TITLE: Raw Signal Density Graphs of Penis Foreskin Keratinocyte Primary Cells Chromatin Accessibility Data ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from Penis Foreskin Keratinocyte Primary Cells, Donor skin01, Library DS18695 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.12678 DATA_ANALYSIS_LEVEL: 2 EXPERIMENT_TYPE: Chromatin Accessibility GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19 SOFTWARE: In house programs and scripts SOFTWARE_VERSION: NA READ_EXTENSION: 0bp GENOMIC_WINDOW: 150bp TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None RELEASE_NUMBER: Human Epigenome Atlas 6 BROWSER_TRACK_NAME: PFK DNase 01 95 BROWSER_TRACK_DESCRIPTION: UW Penis Foreskin Keratinocyte Primary Cells DNase Hypersensitivity Donor skin01 Library DS18695 EA Release 6
QUALITY SCORES: NUMBER_OF_MAPPED_READS: 34,521,027 NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 63 FINDPEAKS_SCORE: 0.455 FINDPEAKS_PERCENTILE: 71 HOTSPOT_SCORE: 0.4944 HOTSPOT_PERCENTILE: 87 IROC_SCORE: 0.9963 IROC_PERCENTILE: 89 POISSON_SCORE: 0.5389 POISSON_PERCENTILE: 83 MAXIMUM_REPLICATE_CORRELATION: 1.0
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Submission date |
Oct 14, 2011 |
Last update date |
May 15, 2019 |
Contact name |
Northwest REMC |
E-mail(s) |
rharris1@bcm.tmc.edu
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Organization name |
University of Washington
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Street address |
-
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City |
Seattle |
State/province |
WA |
ZIP/Postal code |
98195 |
Country |
USA |
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Platform ID |
GPL10999 |
Series (1) |
GSE18927 |
University of Washington Human Reference Epigenome Mapping Project |
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Relations |
SRA |
SRX100991 |
BioSample |
SAMN00205631 |
Named Annotation |
GSM817195_UW.Penis_Foreskin_Keratinocyte_Primary_Cells.ChromatinAccessibility.skin01.DS18695.wig.gz |
Supplementary file |
Size |
Download |
File type/resource |
GSM817195_UW.Penis_Foreskin_Keratinocyte_Primary_Cells.ChromatinAccessibility.skin01.DS18695.bed.gz |
478.5 Mb |
(ftp)(http) |
BED |
GSM817195_UW.Penis_Foreskin_Keratinocyte_Primary_Cells.ChromatinAccessibility.skin01.DS18695.wig.gz |
185.1 Mb |
(ftp)(http) |
WIG |
SRA Run Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |
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