|
| Status |
Public on Feb 02, 2011 |
| Title |
Chromatin accessibility assay of iPS DF 19.11 Cell line; DS15153 |
| Sample type |
SRA |
| |
|
| Source name |
iPS DF 19.11 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.; DS15153
|
| Organism |
Homo sapiens |
| Characteristics |
sample alias: iPS_19_11
sample common name: iPS DF 19.11 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 19.11 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: 31
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_0001173
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Chromatin accessibility determination via DNase-seq
Library name: DS15153
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.5334
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.5333
****************
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: GSM665801_UW.iPS_DF_19.11.ChromatinAccessibility.DS15153.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS15153.hg19.level.1.release.3
ANALYSIS TITLE: Mapping of iPS DF 19.11 Cell Line Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on the iPS DF 19.11 Cell Line, Library DS15153 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.6392
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: 0.2874
FINDPEAKS_PERCENTILE: 18
HOTSPOT_SCORE: 0.3406
HOTSPOT_PERCENTILE: 33
IROC_SCORE: 0.9933
IROC_PERCENTILE: 41
POISSON_SCORE: 0.394
POISSON_PERCENTILE: 26
**********************************************************************
ANALYSIS FILE NAME: GSM665801_UW.iPS_DF_19.11.ChromatinAccessibility.DS15153.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS15153.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of iPS DF 19.11 Cell Line Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from the iPS DF 19.11 Cell Line, Library DS15153 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.6431
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: iD19.11 DNase 53 53
BROWSER_TRACK_DESCRIPTION: UW iPS DF 19.11 Cell Line DNase Hypersensitivity Library DS15153 EA Release 3
QUALITY SCORES:
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 39
FINDPEAKS_SCORE: 0.2874
FINDPEAKS_PERCENTILE: 18
HOTSPOT_SCORE: 0.3406
HOTSPOT_PERCENTILE: 33
IROC_SCORE: 0.9933
IROC_PERCENTILE: 41
POISSON_SCORE: 0.394
POISSON_PERCENTILE: 26
|
| |
|
| 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 |
SRX040377 |
| BioSample |
SAMN00204008 |
| Named Annotation |
GSM665801_UW.iPS_DF_19.11.ChromatinAccessibility.DS15153.wig.gz |
