|
Status |
Public on Apr 14, 2011 |
Title |
Chromatin accessibility assay of Moblized CD3 Primary Cells; DS16834 |
Sample type |
SRA |
|
|
Source name |
flow sorted CD3+ Primary Cells, Mobilized, year 21; DS16834
|
Organism |
Homo sapiens |
Characteristics |
sample alias: CD3.RO_01679 sample common name: Mobilized CD3 Primary Cells molecule: genomic DNA disease: None biomaterial_provider: FHCRC HEIMFELD biomaterial_type: Primary Cell cell_type: Mobilized CD3 Primary Cells markers: CD3+ 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_0000084 assay_term_id: OBI_0001853 nucleic_acid_term_id: SO_0000352 Design description: Chromatin accessibility determination via DNase-seq Library name: DS16834 EDACC Genboree Experiment Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.6981 EDACC Genboree Sample Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.6980 **************** 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: GSM701488_UW.Mobilized_CD3_Primary_Cells.ChromatinAccessibility.RO_01679.DS16834.bed ANALYSIS CENTER: EDACC ANALYSIS ALIAS: DS16834.hg19.level.1.release.4 ANALYSIS TITLE: Mapping of Mobilized CD3 Primary Cells Chromatin Accessibility Data ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Mobilized CD3 Primary Cells, Donor RO 01679, Library DS16834 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.7675 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 4
QUALITY SCORES: NUMBER_OF_MAPPED_READS: 51,978,386 NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 54 FINDPEAKS_SCORE: 0.3591 FINDPEAKS_PERCENTILE: 37 HOTSPOT_SCORE: 0.3413 HOTSPOT_PERCENTILE: 30 IROC_SCORE: 0.9929 IROC_PERCENTILE: 37 POISSON_SCORE: 0.3881 POISSON_PERCENTILE: 28 MAXIMUM_REPLICATE_CORRELATION: NA
**********************************************************************
ANALYSIS FILE NAME: GSM701488_UW.Mobilized_CD3_Primary_Cells.ChromatinAccessibility.RO_01679.DS16834.wig ANALYSIS CENTER: EDACC ANALYSIS ALIAS: DS16834.hg19.level.2.release.4 ANALYSIS TITLE: Raw Signal Density Graphs of Mobilized CD3 Primary Cells Chromatin Accessibility Data ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from Mobilized CD3 Primary Cells, Donor RO 01679, Library DS16834 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.7729 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 4 BROWSER_TRACK_NAME: MCD3 DNase 79 34 BROWSER_TRACK_DESCRIPTION: UW Mobilized CD3 Primary Cells DNase Hypersensitivity Donor RO 01679 Library DS16834 EA Release 4
QUALITY SCORES: NUMBER_OF_MAPPED_READS: 51,978,386 NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 52 FINDPEAKS_SCORE: 0.3591 FINDPEAKS_PERCENTILE: 37 HOTSPOT_SCORE: 0.3413 HOTSPOT_PERCENTILE: 30 IROC_SCORE: 0.9929 IROC_PERCENTILE: 37 POISSON_SCORE: 0.3881 POISSON_PERCENTILE: 28 MAXIMUM_REPLICATE_CORRELATION: NA
**********************************************************************
|
|
|
Submission date |
Apr 04, 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 |
SRX055152 |
BioSample |
SAMN00254252 |
Named Annotation |
GSM701488_UW.Mobilized_CD3_Primary_Cells.ChromatinAccessibility.RO_01679.DS16834.wig.gz |