|
Status |
Public on Apr 14, 2011 |
Title |
Chromatin accessibility assay of Fetal Intestine, Large; DS17313 |
Sample type |
SRA |
|
|
Source name |
Fetal primary tissue, day 108; DS17313
|
Organism |
Homo sapiens |
Characteristics |
sample alias: fIntestine_Large.H-23769d108 sample common name: Fetal Intestine, Large molecule: genomic DNA disease: None biomaterial_provider: University of Washington, Congenital Defects Lab. Ian Glass biomaterial_type: Primary Tissue tissue_type: Fetal Intestine, Large tissue_depot: UW collection_method: fetal donor_id: H-23769 donor_age: day 108 donor_health_status: NA donor_sex: Male 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_0000059 assay_term_id: OBI_0001853 nucleic_acid_term_id: SO_0000352 Design description: Chromatin accessibility determination via DNase-seq Library name: DS17313 EDACC Genboree Experiment Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.7042 EDACC Genboree Sample Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.7041 **************** 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: GSM701495_UW.Fetal_Intestine_Large.ChromatinAccessibility.H-23769.DS17313.bed ANALYSIS CENTER: EDACC ANALYSIS ALIAS: DS17313.hg19.level.1.release.4 ANALYSIS TITLE: Mapping of Fetal Intestine Large Chromatin Accessibility Data ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fetal Intestine Large, Donor H-23769, Library DS17313 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.7718 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 4
QUALITY SCORES: NUMBER_OF_MAPPED_READS: 28,629,835 NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 54 FINDPEAKS_SCORE: 0.3897 FINDPEAKS_PERCENTILE: 54 HOTSPOT_SCORE: 0.3869 HOTSPOT_PERCENTILE: 54 IROC_SCORE: 0.9973 IROC_PERCENTILE: 93 POISSON_SCORE: 0.4345 POISSON_PERCENTILE: 52 MAXIMUM_REPLICATE_CORRELATION: 0.96
**********************************************************************
ANALYSIS FILE NAME: GSM701495_UW.Fetal_Intestine_Large.ChromatinAccessibility.H-23769.DS17313.wig ANALYSIS CENTER: EDACC ANALYSIS ALIAS: DS17313.hg19.level.2.release.4 ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Intestine Large Chromatin Accessibility Data ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from Fetal Intestine Large, Donor H-23769, Library DS17313 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.7772 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 4 BROWSER_TRACK_NAME: FIL DNase 69 13 BROWSER_TRACK_DESCRIPTION: UW Fetal Intestine Large DNase Hypersensitivity Donor H-23769 Library DS17313 EA Release 4
QUALITY SCORES: NUMBER_OF_MAPPED_READS: 28,629,835 NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 52 FINDPEAKS_SCORE: 0.3897 FINDPEAKS_PERCENTILE: 54 HOTSPOT_SCORE: 0.3869 HOTSPOT_PERCENTILE: 54 IROC_SCORE: 0.9973 IROC_PERCENTILE: 93 POISSON_SCORE: 0.4345 POISSON_PERCENTILE: 52 MAXIMUM_REPLICATE_CORRELATION: 0.96
**********************************************************************
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|
|
Submission date |
Apr 04, 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 |
SRX055159 |
BioSample |
SAMN00254261 |
Named Annotation |
GSM701495_UW.Fetal_Intestine_Large.ChromatinAccessibility.H-23769.DS17313.wig.gz |