|
Status |
Public on Aug 06, 2013 |
Title |
Chromatin accessibility assay of Pancreas; DNase.DS20753 |
Sample type |
SRA |
|
|
Source name |
Pancreas tissue; DNase.DS20753
|
Organism |
Homo sapiens |
Characteristics |
sample alias: STL003PA-01 sample common name: Pancreas molecule: genomic DNA disease: None biomaterial_provider: Shin Lin, Stanford University biomaterial_type: Primary Tissue tissue_type: Pancreas tissue_depot: N/A collection_method: Autopsy donor_id: STL003 donor_age: 34 donor_health_status: polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer) donor_sex: Male donor_ethnicity: Caucasian 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_0001264 assay_term_id: OBI_0001853 nucleic_acid_term_id: SO_0000352 Design description: Chromatin accessibility determination via DNase-seq Library name: DNase.DS20753 EDACC Genboree Experiment Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.14271 EDACC Genboree Sample Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.11847 **************** 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: GSM1027326_UW.Pancreas.ChromatinAccessibility.STL003.DNase.DS20753.bed ANALYSIS CENTER: EDACC ANALYSIS ALIAS: DNase.DS20753.hg19.level.1.release.9 ANALYSIS TITLE: Mapping of Pancreas Chromatin Accessibility Data ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Pancreas, Donor STL003, Library DNase.DS20753 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.17625 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 9
QUALITY SCORES: NUMBER_OF_MAPPED_READS: 43,237,714 FINDPEAKS_SCORE: 0.2597 FINDPEAKS_PERCENTILE: 9 HOTSPOT_SCORE: 0.272 HOTSPOT_PERCENTILE: 11 IROC_SCORE: 0.9918 IROC_PERCENTILE: 37 POISSON_SCORE: 0.3263 POISSON_PERCENTILE: 11 MAXIMUM_REPLICATE_CORRELATION: 0.98
**********************************************************************
ANALYSIS FILE NAME: GSM1027326_UW.Pancreas.ChromatinAccessibility.STL003.DNase.DS20753.wig ANALYSIS CENTER: EDACC ANALYSIS ALIAS: DNase.DS20753.hg19.level.2.release.9 ANALYSIS TITLE: Raw Signal Density Graphs of Pancreas Chromatin Accessibility Data ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from Pancreas, Donor STL003, Library DNase.DS20753 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.17579 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 9 BROWSER_TRACK_NAME: Pancreas DNase 03 53 BROWSER_TRACK_DESCRIPTION: UW Pancreas DNase Hypersensitivity Donor STL003 Library DNase.DS20753 EA Release 9
QUALITY SCORES: NUMBER_OF_MAPPED_READS: 43,237,714 FINDPEAKS_SCORE: 0.2597 FINDPEAKS_PERCENTILE: 9 HOTSPOT_SCORE: 0.272 HOTSPOT_PERCENTILE: 11 IROC_SCORE: 0.9918 IROC_PERCENTILE: 37 POISSON_SCORE: 0.3263 POISSON_PERCENTILE: 11 MAXIMUM_REPLICATE_CORRELATION: 0.98
**********************************************************************
|
|
|
Submission date |
Oct 29, 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 (1) |
GSE18927 |
University of Washington Human Reference Epigenome Mapping Project |
|
Relations |
SRA |
SRX201813 |
BioSample |
SAMN00847539 |
Named Annotation |
GSM1027326_UW.Pancreas.ChromatinAccessibility.STL003.DNase.DS20753.wig.gz |