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Sample GSM665802 Query DataSets for GSM665802
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)
Extracted molecule genomic DNA
Extraction protocol Library construction protocol: Single read - Illumina
 
Library strategy DNase-Hypersensitivity
Library source genomic
Library selection DNAse
Instrument model Illumina Genome Analyzer IIx
 
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
 
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

Supplementary file Size Download File type/resource
GSM665802_UW.iPS_DF_6.9.ChromatinAccessibility.DS15164.bed.gz 367.1 Mb (ftp)(http) BED
GSM665802_UW.iPS_DF_6.9.ChromatinAccessibility.DS15164.wig.gz 186.8 Mb (ftp)(http) WIG
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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