|
Status |
Public on Sep 21, 2010 |
Title |
Chromatin accessibility assay of Fetal brain tissue; DS14718 |
Sample type |
SRA |
|
|
Source name |
Fetal Brain primary tissue, day 85; DS14718
|
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 brain tissue_depot: UW collection_method: fetal donor_id: H-23266 donor_age: day 85 donor_health_status: NA donor_sex: Female 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_0000955 assay_term_id: OBI_0001853 nucleic_acid_term_id: SO_0000352 Design description: Chromatin accessibility determination via DNase-seq Library name: DS14718 EDACC Genboree Experiment Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.3149 EDACC Genboree Sample Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.3146 **************** 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: GSM595923_fBrain-DS14718.hg19.bam ANALYSIS ALIAS: DS14718-align ANALYSIS TITLE: Alignments DS14718 ANALYSIS DESCRIPTION: Bowtie (v0.12.5) alignments of Chromatin Accessibility Illumina sequencing lane data to the human genome The Genome Reference Consortium GRCh37 (hg19) ANALYSIS TYPE: REFERENCE_ALIGNMENT EDACC Genboree Analysis Page: DATA_ANALYSIS_LEVEL: 1 EXPERIMENT_TYPE: Chromatin Accessibility SOFTWARE: Bowtie SOFTWARE_VERSION: 0.12.5 MAXIMUM_ALIGNMENT_LENGTH: 36 MISMATCHES_ALLOWED: 2 ALIGNMENTS_ALLOWED: 1 TREATMENT_OF_MULTIPLE_ALIGNMENTS: not submitted TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: allowed ALIGNMENT_POSTPROCESSING: none
**********************************************************************
ANALYSIS FILE NAME: GSM595923_fBrain-DS14718.75.20.filtered-density.36.hg19.wig ANALYSIS ALIAS: DS14718-signal ANALYSIS TITLE: Signal DS14718 ANALYSIS DESCRIPTION: Chromatin Accessibility data with a sliding window (+/-75bp) summation at 20 bp steps across the genome ANALYSIS TYPE: ABUNDANCE_MEASUREMENT EDACC Genboree Analysis Page: DATA_ANALYSIS_LEVEL: 2 EXPERIMENT_TYPE: Chromatin Accessibility SOFTWARE: signalmap SOFTWARE_VERSION: 1.0 READ_EXTENSION: 150 GENOMIC_WINDOW: 20bp TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: NA
**********************************************************************
ANALYSIS FILE NAME: GSM595923_UW.Fetal_Brain.ChromatinAccessibility.H-23266.DS14718.bed ANALYSIS ALIAS: DS14718.hg19.level.1 ANALYSIS TITLE: Mapping of Fetal Brain Chromatin Accessibility Data ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fetal Brain, Donor H-23266, Library DS14718 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.4106 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: 0.5215 FINDPEAKS_PERCENTILE: 35 HOTSPOT_SCORE: 0.4083 HOTSPOT_PERCENTILE: 45 IROC_SCORE: 0.9954 IROC_PERCENTILE: 25 POISSON_SCORE: 0.5003 POISSON_PERCENTILE: 47
**********************************************************************
ANALYSIS FILE NAME: GSM595923_UW.Fetal_Brain.ChromatinAccessibility.H-23266.DS14718.wig ANALYSIS ALIAS: DS14718.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-23266, Library DS14718 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.4066 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: FB DNase 66 18 BROWSER_TRACK_DESCRIPTION: UW Fetal Brain DNase Hypersensitivity Donor H-23266 Library DS14718 EA Release 2
QUALITY SCORES: NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED: 40 FINDPEAKS_SCORE: 0.5215 FINDPEAKS_PERCENTILE: 35 HOTSPOT_SCORE: 0.4083 HOTSPOT_PERCENTILE: 45 IROC_SCORE: 0.9954 IROC_PERCENTILE: 25 POISSON_SCORE: 0.5003 POISSON_PERCENTILE: 47
|
|
|
Submission date |
Sep 20, 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 |
SRX027086 |
BioSample |
SAMN00113493 |
Named Annotation |
GSM595923_UW.Fetal_Brain.ChromatinAccessibility.H-23266.DS14718.wig.gz |
Named Annotation |
GSM595923_fBrain-DS14718.75.20.filtered-density.36.hg19.wig.gz |