NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM665824 Query DataSets for GSM665824
Status Public on Feb 02, 2011
Title Chromatin accessibility assay of Fetal Heart Tissue; DS16500
Sample type SRA
 
Source name Fetal Heart primary tissue, day 147; DS16500
Organism Homo sapiens
Characteristics sample alias: fHeart.H-23589d147
sample common name: Fetal Heart
molecule: genomic DNA
disease: None
biomaterial_provider: University of Washington, Congenital Defects Lab. Ian Glass
biomaterial_type: Primary Tissue
tissue_type: Fetal Heart
tissue_depot: UW
collection_method: fetal
donor_id: H-23589
donor_age: day 147
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_0000948
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Chromatin accessibility determination via DNase-seq
Library name: DS16500
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.5283
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.5282
****************
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: GSM665824_UW.Fetal_Heart.ChromatinAccessibility.H-23589.DS16500.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS16500.hg19.level.1.release.3
ANALYSIS TITLE: Mapping of Fetal Heart Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fetal Heart, Donor H-23589, Library DS16500 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.6373
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: 0.4152
FINDPEAKS_PERCENTILE: 56
HOTSPOT_SCORE: 0.3977
HOTSPOT_PERCENTILE: 56
IROC_SCORE: 0.9946
IROC_PERCENTILE: 59
POISSON_SCORE: 0.515
POISSON_PERCENTILE: 79

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

ANALYSIS FILE NAME: GSM665824_UW.Fetal_Heart.ChromatinAccessibility.H-23589.DS16500.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS16500.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Heart Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from Fetal Heart, Donor H-23589, Library DS16500 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.6412
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: FH DNase 89 00
BROWSER_TRACK_DESCRIPTION: UW Fetal Heart DNase Hypersensitivity Donor H-23589 Library DS16500 EA Release 3


QUALITY SCORES:
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 39
FINDPEAKS_SCORE: 0.4152
FINDPEAKS_PERCENTILE: 56
HOTSPOT_SCORE: 0.3977
HOTSPOT_PERCENTILE: 56
IROC_SCORE: 0.9946
IROC_PERCENTILE: 59
POISSON_SCORE: 0.515
POISSON_PERCENTILE: 79
 
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 (2)
GSE18927 University of Washington Human Reference Epigenome Mapping Project
GSE51336 Mouse regulatory DNA landscapes reveal global principles of cis-regulatory evolution
Relations
SRA SRX040400
BioSample SAMN00204028
Named Annotation GSM665824_UW.Fetal_Heart.ChromatinAccessibility.H-23589.DS16500.wig.gz

Supplementary file Size Download File type/resource
GSM665824_UW.Fetal_Heart.ChromatinAccessibility.H-23589.DS16500.bed.gz 500.0 Mb (ftp)(http) BED
GSM665824_UW.Fetal_Heart.ChromatinAccessibility.H-23589.DS16500.wig.gz 204.4 Mb (ftp)(http) WIG
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap