|
Status |
Public on Feb 02, 2011 |
Title |
Chromatin accessibility assay of Fetal Brain Tissue; DS15453 |
Sample type |
SRA |
|
|
Source name |
Fetal Brain primary tissue, day 112; DS15453
|
Organism |
Homo sapiens |
Characteristics |
sample alias: fBrain.H-23399d112 sample common name: Fetal Brain molecule: genomic DNA disease: None biomaterial_provider: University of Washington, Congenital Defects Lab. Ian Glass biomaterial_type: Primary Tissue tissue_type: Fetal Brain tissue_depot: UW collection_method: fetal donor_id: H-23399 donor_age: day 112 donor_health_status: NA donor_sex: Unknown 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_0000955 assay_term_id: OBI_0001853 nucleic_acid_term_id: SO_0000352 Design description: Chromatin accessibility determination via DNase-seq Library name: DS15453 EDACC Genboree Experiment Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.5296 EDACC Genboree Sample Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.5295 **************** 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: GSM665804_UW.Fetal_Brain.ChromatinAccessibility.H-23399.DS15453.bed ANALYSIS CENTER: EDACC ANALYSIS ALIAS: DS15453.hg19.level.1.release.3 ANALYSIS TITLE: Mapping of Fetal Brain Chromatin Accessibility Data ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fetal Brain, Donor H-23399, Library DS15453 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.6376 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: 0.3342 FINDPEAKS_PERCENTILE: 36 HOTSPOT_SCORE: 0.3261 HOTSPOT_PERCENTILE: 31 IROC_SCORE: 0.9913 IROC_PERCENTILE: 23 POISSON_SCORE: 0.4304 POISSON_PERCENTILE: 41
**********************************************************************
ANALYSIS FILE NAME: GSM665804_UW.Fetal_Brain.ChromatinAccessibility.H-23399.DS15453.wig ANALYSIS CENTER: EDACC ANALYSIS ALIAS: DS15453.hg19.level.2 ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Brain Chromatin Accessibility Data ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from Fetal Brain, Donor H-23399, Library DS15453 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.6415 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: FB DNase 99 53 BROWSER_TRACK_DESCRIPTION: UW Fetal Brain DNase Hypersensitivity Donor H-23399 Library DS15453 EA Release 3
QUALITY SCORES: NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 39 FINDPEAKS_SCORE: 0.3342 FINDPEAKS_PERCENTILE: 36 HOTSPOT_SCORE: 0.3261 HOTSPOT_PERCENTILE: 31 IROC_SCORE: 0.9913 IROC_PERCENTILE: 23 POISSON_SCORE: 0.4304 POISSON_PERCENTILE: 41
|
|
|
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 |
SRX040380 |
BioSample |
SAMN00204022 |
Named Annotation |
GSM665804_UW.Fetal_Brain.ChromatinAccessibility.H-23399.DS15453.wig.gz |