NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM595923 Query DataSets for GSM595923
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

Supplementary file Size Download File type/resource
GSM595923_UW.Fetal_Brain.ChromatinAccessibility.H-23266.DS14718.bed.gz 350.2 Mb (ftp)(http) BED
GSM595923_UW.Fetal_Brain.ChromatinAccessibility.H-23266.DS14718.wig.gz 177.2 Mb (ftp)(http) WIG
GSM595923_fBrain-DS14718.75.20.filtered-density.36.hg19.wig.gz 191.5 Mb (ftp)(http) WIG
GSM595923_fBrain-DS14718.hg19.bam 946.4 Mb (ftp)(http) BAM
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