|
Status |
Public on Feb 02, 2011 |
Title |
Chromatin accessibility assay of CD8+ Primary cells; DS17203 |
Sample type |
SRA |
|
|
Source name |
flow sorted CD8+ Cells,year 21; DS17203
|
Organism |
Homo sapiens |
Characteristics |
sample alias: CD8.RO_01721 sample common name: CD8 Primary Cells molecule: genomic DNA disease: None biomaterial_provider: FHCRC HEIMFELD biomaterial_type: Primary Cell cell_type: CD8 Primary Cells markers: CD8+ donor_id: RO 01679 donor_age: year 21 donor_health_status: NA donor_sex: Male donor_ethnicity: Caucasian passage_if_expanded: 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: CL_0000625 assay_term_id: OBI_0001853 nucleic_acid_term_id: SO_0000352 Design description: Chromatin accessibility determination via DNase-seq Library name: DS17203 EDACC Genboree Experiment Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.5353 EDACC Genboree Sample Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.5352 **************** 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: GSM665838_UW.CD8_Primary_Cells.ChromatinAccessibility.RO_01679.DS17203.bed ANALYSIS CENTER: EDACC ANALYSIS ALIAS: DS17203.hg19.level.1.release.3 ANALYSIS TITLE: Mapping of CD8 Primary Cells Chromatin Accessibility Data ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on CD8 Primary Cells, Donor RO 01679, Library DS17203 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.6404 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: 0.6535 FINDPEAKS_PERCENTILE: 100 HOTSPOT_SCORE: 0.6695 HOTSPOT_PERCENTILE: 100 IROC_SCORE: 0.9962 IROC_PERCENTILE: 79 POISSON_SCORE: 0.626 POISSON_PERCENTILE: 95
**********************************************************************
ANALYSIS FILE NAME: GSM665838_UW.CD8_Primary_Cells.ChromatinAccessibility.RO_01679.DS17203.wig ANALYSIS CENTER: EDACC ANALYSIS ALIAS: DS17203.hg19.level.2 ANALYSIS TITLE: Raw Signal Density Graphs of CD8 Primary Cells Chromatin Accessibility Data ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from CD8 Primary Cells, Donor RO 01679, Library DS17203 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.6443 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: CD8 DNase 21 03 BROWSER_TRACK_DESCRIPTION: UW CD8 Primary Cells DNase Hypersensitivity Donor RO 01679 Library DS17203 EA Release 3
QUALITY SCORES: NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 39 FINDPEAKS_SCORE: 0.6535 FINDPEAKS_PERCENTILE: 100 HOTSPOT_SCORE: 0.6695 HOTSPOT_PERCENTILE: 100 IROC_SCORE: 0.9962 IROC_PERCENTILE: 79 POISSON_SCORE: 0.626 POISSON_PERCENTILE: 95
|
|
|
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 |
SRX040414 |
BioSample |
SAMN00204020 |
Named Annotation |
GSM665838_UW.CD8_Primary_Cells.ChromatinAccessibility.RO_01679.DS17203.wig.gz |