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Sample GSM530658 Query DataSets for GSM530658
Status Public on Apr 28, 2010
Title Chromatin accessibility assay of human CD34 Primary Cells; DS12771
Sample type SRA
 
Source name flow sorted CD34+ cells from cord blood; DS12771
Organism Homo sapiens
Characteristics molecule: genomic DNA
disease: None
biomaterial_provider: FHCRC HEIMFELD
biomaterial_type: Primary Cell
cell_type: CD34 Primary Cells
markers: CD34+
donor_id: RO 01480
donor_age: 27 years
donor_health_status: NA
donor_sex: Female
donor_ethnicity: Caucasian
passage_if_expanded: NA
experiment_type: Chromatin Accessibility
extraction_protocol: Qiagen minElut
dnase_protocol: Stamlab DNase Protocol
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 II
 
Description sample_term_id: CL_0000837
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Chromatin accessibility determination via DNase-seq
Library name: DS12771
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.2408
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.2407
****************
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: GSM530658_UW.CD34.ChromatinAccessibility.CD34+-DS12771.wig
ANALYSIS ALIAS: UW.CD34.ChromatinAccessibility.DS12771
ANALYSIS TITLE: Raw Signal Density Graphs of CD34 Primary Cell Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from CD34 Primary Cells 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%2FUniversity%20of%20Washington%2FANALYSIS%2FEDACC.2640
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Chromatin Accessibility
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None

**********************************************************************

ANALYSIS FILE NAME: GSM530658_UW.Mobilized_CD34_Primary_Cells.ChromatinAccessibility.RO_01480.DS12771.bed
ANALYSIS ALIAS: DS12771.hg19.level.1
ANALYSIS TITLE: Mapping of Mobilized CD34 Primary Cells Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Mobilized CD34 Primary Cells, Donor RO 01480, Library DS12771 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.4112
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 2


QUALITY SCORES:
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED: 40
FINDPEAKS_SCORE: 0.6529
FINDPEAKS_PERCENTILE: 75
HOTSPOT_SCORE: 0.5473
HOTSPOT_PERCENTILE: 82
IROC_SCORE: 0.9977
IROC_PERCENTILE: 70
POISSON_SCORE: 0.5362
POISSON_PERCENTILE: 60

**********************************************************************

ANALYSIS FILE NAME: GSM530658_UW.Mobilized_CD34_Primary_Cells.ChromatinAccessibility.RO_01480.DS12771.wig
ANALYSIS ALIAS: DS12771.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Mobilized CD34 Primary Cells Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from Mobilized CD34 Primary Cells, Donor RO 01480, Library DS12771 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.4072
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 2
BROWSER_TRACK_NAME: MCD34 DNase 80 71
BROWSER_TRACK_DESCRIPTION: UW Mobilized CD34 Primary Cells DNase Hypersensitivity Donor RO 01480 Library DS12771 EA Release 2


QUALITY SCORES:
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED: 40
FINDPEAKS_SCORE: 0.6529
FINDPEAKS_PERCENTILE: 75
HOTSPOT_SCORE: 0.5473
HOTSPOT_PERCENTILE: 82
IROC_SCORE: 0.9977
IROC_PERCENTILE: 70
POISSON_SCORE: 0.5362
POISSON_PERCENTILE: 60
 
Submission date Apr 06, 2010
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 GPL9115
Series (1)
GSE18927 University of Washington Human Reference Epigenome Mapping Project
Relations
SRA SRX026921
BioSample SAMN00113437
Named Annotation GSM530658_UW.Mobilized_CD34_Primary_Cells.ChromatinAccessibility.RO_01480.DS12771.wig.gz
Named Annotation GSM530658_UW.CD34.ChromatinAccessibility.CD34+-DS12771.wig.gz

Supplementary file Size Download File type/resource
GSM530658_UW.CD34.ChromatinAccessibility.CD34+-DS12771.wig.gz 20.4 Mb (ftp)(http) WIG
GSM530658_UW.Mobilized_CD34_Primary_Cells.ChromatinAccessibility.RO_01480.DS12771.bed.gz 460.7 Mb (ftp)(http) BED
GSM530658_UW.Mobilized_CD34_Primary_Cells.ChromatinAccessibility.RO_01480.DS12771.wig.gz 180.3 Mb (ftp)(http) WIG
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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