|
| Status |
Public on Feb 02, 2011 |
| Title |
Chromatin accessibility assay of CD4+ Primary cells; DS17212 |
| Sample type |
SRA |
| |
|
| Source name |
flow sorted CD4+ Cells,year 21; DS17212
|
| Organism |
Homo sapiens |
| Characteristics |
sample alias: CD4.RO_01721
sample common name: CD4 Primary Cells
molecule: genomic DNA
disease: None
biomaterial_provider: FHCRC HEIMFELD
biomaterial_type: Primary Cell
cell_type: CD4 Primary Cells
markers: CD4+
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_0000492
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Chromatin accessibility determination via DNase-seq
Library name: DS17212
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.5346
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.5345
****************
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: GSM665839_UW.CD4_Primary_Cells.ChromatinAccessibility.RO_01679.DS17212.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS17212.hg19.level.1.release.3
ANALYSIS TITLE: Mapping of CD4 Primary Cells Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on CD4 Primary Cells, Donor RO 01679, Library DS17212 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.6369
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: 0.4851
FINDPEAKS_PERCENTILE: 85
HOTSPOT_SCORE: 0.489
HOTSPOT_PERCENTILE: 85
IROC_SCORE: 0.9946
IROC_PERCENTILE: 59
POISSON_SCORE: 0.4804
POISSON_PERCENTILE: 59
**********************************************************************
ANALYSIS FILE NAME: GSM665839_UW.CD4_Primary_Cells.ChromatinAccessibility.RO_01679.DS17212.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS17212.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of CD4 Primary Cells Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from CD4 Primary Cells, Donor RO 01679, Library DS17212 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.6408
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: CD4 DNase 21 12
BROWSER_TRACK_DESCRIPTION: UW CD4 Primary Cells DNase Hypersensitivity Donor RO 01679 Library DS17212 EA Release 3
QUALITY SCORES:
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 39
FINDPEAKS_SCORE: 0.4851
FINDPEAKS_PERCENTILE: 85
HOTSPOT_SCORE: 0.489
HOTSPOT_PERCENTILE: 85
IROC_SCORE: 0.9946
IROC_PERCENTILE: 59
POISSON_SCORE: 0.4804
POISSON_PERCENTILE: 59
**********************************************************************
|
| |
|
| 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 |
SRX040415 |
| BioSample |
SAMN00204016 |
| Named Annotation |
GSM665839_UW.CD4_Primary_Cells.ChromatinAccessibility.RO_01679.DS17212.wig.gz |
