|
Status |
Public on Feb 02, 2011 |
Title |
Chromatin accessibility assay of iPS DF 6.9 Cell line; DS15164 |
Sample type |
SRA |
|
|
Source name |
iPS DF 6.9 Cell Line, Induced pluripotent stem cel, derived from fibroblast. the first set of numbers before the period refer to different clones, the number after the period indicates the sub-clone.; DS15164
|
Organism |
Homo sapiens |
Characteristics |
sample alias: iPS_6_9 sample common name: iPS DF 6.9 Cell Line molecule: genomic DNA disease: None biomaterial_provider: James Thomson, Morgridge Institute for Research, University of Wisconsin-Madison biomaterial_type: Cell Line line: iPS DF 6.9 Cell Line lineage: Derived from newborn foreskin fibroblast: Cat# CRL-2097TM, ATCC differentiation_stage: Induced pluripotent stem cell differentiation_method: http://www.sciencemag.org/cgi/content/full/324/5928/797?rss=1 passage: 32 medium: NA Sex: Unknown batch: 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 |
sample_term_id: NTR_0001172 assay_term_id: OBI_0001853 nucleic_acid_term_id: SO_0000352 Design description: Chromatin accessibility determination via DNase-seq Library name: DS15164 EDACC Genboree Experiment Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.5337 EDACC Genboree Sample Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.5336 **************** 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: GSM665802_UW.iPS_DF_6.9.ChromatinAccessibility.DS15164.bed ANALYSIS CENTER: EDACC ANALYSIS ALIAS: DS15164.hg19.level.1.release.3 ANALYSIS TITLE: Mapping of iPS DF 6.9 Cell Line Chromatin Accessibility Data ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on the iPS DF 6.9 Cell Line, Library DS15164 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.6394 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 3
QUALITY SCORES: NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 39 FINDPEAKS_SCORE: 0.2693 FINDPEAKS_PERCENTILE: 15 HOTSPOT_SCORE: 0.307 HOTSPOT_PERCENTILE: 21 IROC_SCORE: 0.9907 IROC_PERCENTILE: 18 POISSON_SCORE: 0.3938 POISSON_PERCENTILE: 23
**********************************************************************
ANALYSIS FILE NAME: GSM665802_UW.iPS_DF_6.9.ChromatinAccessibility.DS15164.wig ANALYSIS CENTER: EDACC ANALYSIS ALIAS: DS15164.hg19.level.2 ANALYSIS TITLE: Raw Signal Density Graphs of iPS DF 6.9 Cell Line Chromatin Accessibility Data ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from the iPS DF 6.9 Cell Line, Library DS15164 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.6433 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 3 BROWSER_TRACK_NAME: iD6.9 DNase 64 64 BROWSER_TRACK_DESCRIPTION: UW iPS DF 6.9 Cell Line DNase Hypersensitivity Library DS15164 EA Release 3
QUALITY SCORES: NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 39 FINDPEAKS_SCORE: 0.2693 FINDPEAKS_PERCENTILE: 15 HOTSPOT_SCORE: 0.307 HOTSPOT_PERCENTILE: 21 IROC_SCORE: 0.9907 IROC_PERCENTILE: 18 POISSON_SCORE: 0.3938 POISSON_PERCENTILE: 23
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|
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Submission date |
Feb 02, 2011 |
Last update date |
May 15, 2019 |
Contact name |
Northwest REMC |
E-mail(s) |
rharris1@bcm.tmc.edu
|
Organization name |
University of Washington
|
Street address |
-
|
City |
Seattle |
State/province |
WA |
ZIP/Postal code |
98195 |
Country |
USA |
|
|
Platform ID |
GPL10999 |
Series (1) |
GSE18927 |
University of Washington Human Reference Epigenome Mapping Project |
|
Relations |
SRA |
SRX040378 |
BioSample |
SAMN00204011 |
Named Annotation |
GSM665802_UW.iPS_DF_6.9.ChromatinAccessibility.DS15164.wig.gz |