|
Status |
Public on Apr 28, 2010 |
Title |
Chromatin accessibility assay of Fetal Heart Primary Tissue; DS12531 |
Sample type |
SRA |
|
|
Source name |
Fetal Heart primary tissue, day 96; DS12531
|
Organism |
Homo sapiens |
Characteristics |
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-22662 donor_age: 96 days donor_health_status: NA donor_sex: Unknown donor_ethnicity: 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: UBERON_0000948 assay_term_id: OBI_0001853 nucleic_acid_term_id: SO_0000352 Design description: Chromatin accessibility determination via DNase-seq Library name: DS12531 EDACC Genboree Experiment Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.2453 EDACC Genboree Sample Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.2452 **************** 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: GSM530654_UW.FetalHeart.ChromatinAccessibility.fHeart-DS12531.wig ANALYSIS ALIAS: UW.FetalHeart.ChromatinAccessibility.DS12531 ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Heart Chromatin Accessibility Data ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from Fetal Heart 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.2636 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: GSM530654_UW.Fetal_Heart.ChromatinAccessibility.H-22662.DS12531.bed ANALYSIS ALIAS: DS12531.hg19.level.1 ANALYSIS TITLE: Mapping of Fetal Heart Chromatin Accessibility Data ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fetal Heart, Donor H-22662, Library DS12531 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.4118 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: 0.6641 FINDPEAKS_PERCENTILE: 77 HOTSPOT_SCORE: 0.5319 HOTSPOT_PERCENTILE: 72 IROC_SCORE: 0.9959 IROC_PERCENTILE: 30 POISSON_SCORE: 0.5904 POISSON_PERCENTILE: 85
**********************************************************************
ANALYSIS FILE NAME: GSM530654_UW.Fetal_Heart.ChromatinAccessibility.H-22662.DS12531.wig ANALYSIS ALIAS: DS12531.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-22662, Library DS12531 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.4078 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: FH DNase 62 31 BROWSER_TRACK_DESCRIPTION: UW Fetal Heart DNase Hypersensitivity Donor H-22662 Library DS12531 EA Release 2
QUALITY SCORES: NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED: 40 FINDPEAKS_SCORE: 0.6641 FINDPEAKS_PERCENTILE: 77 HOTSPOT_SCORE: 0.5319 HOTSPOT_PERCENTILE: 72 IROC_SCORE: 0.9959 IROC_PERCENTILE: 30 POISSON_SCORE: 0.5904 POISSON_PERCENTILE: 85
|
|
|
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 (2) |
GSE18927 |
University of Washington Human Reference Epigenome Mapping Project |
GSE51336 |
Mouse regulatory DNA landscapes reveal global principles of cis-regulatory evolution |
|
Relations |
SRA |
SRX026917 |
BioSample |
SAMN00113445 |
Named Annotation |
GSM530654_UW.FetalHeart.ChromatinAccessibility.fHeart-DS12531.wig.gz |
Named Annotation |
GSM530654_UW.Fetal_Heart.ChromatinAccessibility.H-22662.DS12531.wig.gz |