|
Status |
Public on Apr 14, 2011 |
Title |
Chromatin accessibility assay of CD3 Primary Cells, cord blood; DS17706 |
Sample type |
SRA |
|
|
Source name |
flow sorted CD3+ Primary Cells, from cord blood; DS17706
|
Organism |
Homo sapiens |
Characteristics |
sample alias: CD3.CB6_1-4-2011 sample common name: CD3 Cord Blood Primary Cells molecule: genomic DNA disease: None biomaterial_provider: FHCRC HEIMFELD biomaterial_type: Primary Cell cell_type: CD3 Primary Cells markers: CD3+ donor_id: CB6 1-4-2011 donor_age: NA donor_health_status: NA donor_sex: Unknown donor_ethnicity: NA 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: DS17706 EDACC Genboree Experiment Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.7022 EDACC Genboree Sample Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.7021 **************** 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: GSM701526_UW.CD3_Primary_Cells.ChromatinAccessibility.CB6_1-4-2011.DS17706.bed ANALYSIS CENTER: EDACC ANALYSIS ALIAS: DS17706.hg19.level.1.release.5 ANALYSIS TITLE: Mapping of CD3 Primary Cells Chromatin Accessibility Data ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on CD3 Primary Cells, Donor CB6 1-4-2011, Library DS17706 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.10382 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 5
QUALITY SCORES: NUMBER_OF_MAPPED_READS: 21,594,260 NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 47 FINDPEAKS_SCORE: 0.4226 FINDPEAKS_PERCENTILE: 47 HOTSPOT_SCORE: 0.4283 HOTSPOT_PERCENTILE: 49 IROC_SCORE: 0.9954 IROC_PERCENTILE: 70 POISSON_SCORE: 0.4188 POISSON_PERCENTILE: 28 MAXIMUM_REPLICATE_CORRELATION: 0.97
**********************************************************************
ANALYSIS FILE NAME: GSM701526_UW.CD3_Primary_Cells.ChromatinAccessibility.CB6_1-4-2011.DS17706.wig ANALYSIS CENTER: EDACC ANALYSIS ALIAS: DS17706.hg19.level.2.release.5 ANALYSIS TITLE: Raw Signal Density Graphs of CD3 Primary Cells Chromatin Accessibility Data ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from CD3 Primary Cells, Donor CB6 1-4-2011, Library DS17706 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.10335 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 5 BROWSER_TRACK_NAME: CD3 DNase 11 06 BROWSER_TRACK_DESCRIPTION: UW CD3 Primary Cells DNase Hypersensitivity Donor CB6 1-4-2011 Library DS17706 EA Release 5
QUALITY SCORES: NUMBER_OF_MAPPED_READS: 21,594,260 NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 47 FINDPEAKS_SCORE: 0.4226 FINDPEAKS_PERCENTILE: 47 HOTSPOT_SCORE: 0.4283 HOTSPOT_PERCENTILE: 49 IROC_SCORE: 0.9954 IROC_PERCENTILE: 70 POISSON_SCORE: 0.4188 POISSON_PERCENTILE: 28 MAXIMUM_REPLICATE_CORRELATION: 0.97
**********************************************************************
|
|
|
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 |
SRX055190 |
BioSample |
SAMN00254251 |
Named Annotation |
GSM701526_UW.CD3_Primary_Cells.ChromatinAccessibility.CB6_1-4-2011.DS17706.wig.gz |