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Sample GSM701537 Query DataSets for GSM701537
Status Public on Apr 14, 2011
Title Chromatin accessibility assay of Fetal Thymus; DS17875
Sample type SRA
 
Source name Fetal primary tissue, day 98; DS17875
Organism Homo sapiens
Characteristics sample alias: fThymus.H-23964d98
sample common name: Fetal Thymus
molecule: genomic DNA
disease: None
biomaterial_provider: University of Washington, Congenital Defects Lab. Ian Glass
biomaterial_type: Primary Tissue
tissue_type: Fetal Thymus
tissue_depot: UW
collection_method: fetal
donor_id: H-23964
donor_age: day 98
donor_health_status: NA
donor_sex: Female
donor_ethnicity: 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: UBERON_0002370
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Chromatin accessibility determination via DNase-seq
Library name: DS17875
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.7181
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.7180
****************
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: GSM701537_UW.Fetal_Thymus.ChromatinAccessibility.H-23964.DS17875.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS17875.hg19.level.1.release.4
ANALYSIS TITLE: Mapping of Fetal Thymus Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fetal Thymus, Donor H-23964, Library DS17875 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.7691
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: 30,577,108
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 54
FINDPEAKS_SCORE: 0.2815
FINDPEAKS_PERCENTILE: 17
HOTSPOT_SCORE: 0.2823
HOTSPOT_PERCENTILE: 17
IROC_SCORE: 0.9969
IROC_PERCENTILE: 85
POISSON_SCORE: 0.318
POISSON_PERCENTILE: 7
MAXIMUM_REPLICATE_CORRELATION: 0.96

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

ANALYSIS FILE NAME: GSM701537_UW.Fetal_Thymus.ChromatinAccessibility.H-23964.DS17875.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS17875.hg19.level.2.release.4
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Thymus Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from Fetal Thymus, Donor H-23964, Library DS17875 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.7745
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: FT DNase 64 75
BROWSER_TRACK_DESCRIPTION: UW Fetal Thymus DNase Hypersensitivity Donor H-23964 Library DS17875 EA Release 4


QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 30,577,108
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 52
FINDPEAKS_SCORE: 0.2815
FINDPEAKS_PERCENTILE: 17
HOTSPOT_SCORE: 0.2823
HOTSPOT_PERCENTILE: 17
IROC_SCORE: 0.9969
IROC_PERCENTILE: 85
POISSON_SCORE: 0.318
POISSON_PERCENTILE: 7
MAXIMUM_REPLICATE_CORRELATION: 0.96

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

 
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 SRX055201
BioSample SAMN00254298
Named Annotation GSM701537_UW.Fetal_Thymus.ChromatinAccessibility.H-23964.DS17875.wig.gz

Supplementary file Size Download File type/resource
GSM701537_UW.Fetal_Thymus.ChromatinAccessibility.H-23964.DS17875.bed.gz 433.9 Mb (ftp)(http) BED
GSM701537_UW.Fetal_Thymus.ChromatinAccessibility.H-23964.DS17875.wig.gz 224.1 Mb (ftp)(http) WIG
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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