|
Status |
Public on Feb 22, 2012 |
Title |
Chromatin accessibility assay of Fetal Stomach; DS20349 |
Sample type |
SRA |
|
|
Source name |
Fetal Stomach primary tissue, day 108; DS20349
|
Organism |
Homo sapiens |
Characteristics |
sample alias: fStomach.H-24401d108 sample common name: Fetal Stomach molecule: genomic DNA disease: None biomaterial_provider: University of Washington, Congenital Defects Lab. Ian Glass biomaterial_type: Primary Tissue tissue_type: Fetal Stomach tissue_depot: UW collection_method: fetal donor_id: H-24401 donor_age: day 108 donor_health_status: NA donor_sex: Female donor_ethnicity: NA experiment_type: Chromatin Accessibility extraction_protocol: Qiagen minElut dnase_protocol: http://www.roadmapepigenomics.org/protocols/type/experimental/
|
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 HiSeq 2000 |
|
|
Description |
sample_term_id: UBERON_0000945 assay_term_id: OBI_0001853 nucleic_acid_term_id: SO_0000352 Design description: Chromatin accessibility determination via DNase-seq Library name: DS20349 EDACC Genboree Experiment Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.11300 EDACC Genboree Sample Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.11299 **************** 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: GSM878660_UW.Fetal_Stomach.ChromatinAccessibility.H-24401.DS20349.bed ANALYSIS CENTER: EDACC ANALYSIS ALIAS: DS20349.hg19.level.1.release.7 ANALYSIS TITLE: Mapping of Fetal Stomach Chromatin Accessibility Data ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fetal Stomach, Donor H-24401, Library DS20349 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.12742 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 7
QUALITY SCORES: NUMBER_OF_MAPPED_READS: 34,089,889 NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 58 FINDPEAKS_SCORE: 0.3466 FINDPEAKS_PERCENTILE: 21 HOTSPOT_SCORE: 0.3382 HOTSPOT_PERCENTILE: 19 IROC_SCORE: 0.9908 IROC_PERCENTILE: 12 POISSON_SCORE: 0.4111 POISSON_PERCENTILE: 28 MAXIMUM_REPLICATE_CORRELATION: 0.99
**********************************************************************
ANALYSIS FILE NAME: GSM878660_UW.Fetal_Stomach.ChromatinAccessibility.H-24401.DS20349.wig ANALYSIS CENTER: EDACC ANALYSIS ALIAS: DS20349.hg19.level.2.release.7 ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Stomach Chromatin Accessibility Data ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from Fetal Stomach, Donor H-24401, Library DS20349 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.12800 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 7 BROWSER_TRACK_NAME: FS DNase 01 49 BROWSER_TRACK_DESCRIPTION: UW Fetal Stomach DNase Hypersensitivity Donor H-24401 Library DS20349 EA Release 7
QUALITY SCORES: NUMBER_OF_MAPPED_READS: 34,089,889 NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 58 FINDPEAKS_SCORE: 0.3466 FINDPEAKS_PERCENTILE: 21 HOTSPOT_SCORE: 0.3382 HOTSPOT_PERCENTILE: 19 IROC_SCORE: 0.9908 IROC_PERCENTILE: 12 POISSON_SCORE: 0.4111 POISSON_PERCENTILE: 28 MAXIMUM_REPLICATE_CORRELATION: 0.99
**********************************************************************
|
|
|
Submission date |
Feb 21, 2012 |
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 |
GPL11154 |
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 |
SRX121286 |
BioSample |
SAMN00791544 |
Named Annotation |
GSM878660_UW.Fetal_Stomach.ChromatinAccessibility.H-24401.DS20349.wig.gz |