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| Status |
Public on Aug 06, 2013 |
| Title |
Chromatin accessibility assay of Gastric Mucosa; DNase.DS20260 |
| Sample type |
SRA |
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| Source name |
Gastric tissue; DNase.DS20260
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| Organism |
Homo sapiens |
| Characteristics |
sample alias: STL001GA-01
sample common name: Gastric
molecule: genomic DNA
disease: None
biomaterial_provider: Shin Lin, Stanford University
biomaterial_type: Primary Tissue
tissue_type: Gastric
tissue_depot: N/A
collection_method: Autopsy
donor_id: STL001
donor_age: 3
donor_health_status: healthy, no prior medical history (NO diabetes, hypertension, coronary artery disease, cancer)
donor_sex: Male
donor_ethnicity: Caucasian and African American
experiment_type: Chromatin Accessibility
extraction_protocol: Qiagen minElut
dnase_protocol: http://www.roadmapepigenomics.org/protocols/type/experimental/
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Library construction protocol: Single read - Illumina
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| Library strategy |
DNase-Hypersensitivity |
| Library source |
genomic |
| Library selection |
DNAse |
| Instrument model |
Illumina HiSeq 2000 |
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| 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: DNase.DS20260
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.14289
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.13944
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************
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| Data processing |
**********************************************************************
ANALYSIS FILE NAME: GSM1027320_UW.Gastric.ChromatinAccessibility.STL001.DNase.DS20260.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNase.DS20260.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Gastric Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Gastric, Donor STL001, Library DNase.DS20260 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.17596
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: 48,828,861
FINDPEAKS_SCORE: 0.2662
FINDPEAKS_PERCENTILE: 13
HOTSPOT_SCORE: 0.2589
HOTSPOT_PERCENTILE: 4
IROC_SCORE: 0.9918
IROC_PERCENTILE: 37
POISSON_SCORE: 0.3244
POISSON_PERCENTILE: 9
MAXIMUM_REPLICATE_CORRELATION: 0.99
**********************************************************************
ANALYSIS FILE NAME: GSM1027320_UW.Gastric.ChromatinAccessibility.STL001.DNase.DS20260.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNase.DS20260.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Gastric Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from Gastric, Donor STL001, Library DNase.DS20260 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.17550
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: Gastric DNase 01 60
BROWSER_TRACK_DESCRIPTION: UW Gastric DNase Hypersensitivity Donor STL001 Library DNase.DS20260 EA Release 9
QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 48,828,861
FINDPEAKS_SCORE: 0.2662
FINDPEAKS_PERCENTILE: 13
HOTSPOT_SCORE: 0.2589
HOTSPOT_PERCENTILE: 4
IROC_SCORE: 0.9918
IROC_PERCENTILE: 37
POISSON_SCORE: 0.3244
POISSON_PERCENTILE: 9
MAXIMUM_REPLICATE_CORRELATION: 0.99
**********************************************************************
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| 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 |
| |
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| Platform ID |
GPL11154 |
| Series (1) |
| GSE18927 |
University of Washington Human Reference Epigenome Mapping Project |
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| Relations |
| SRA |
SRX201807 |
| BioSample |
SAMN01737661 |
| Named Annotation |
GSM1027320_UW.Gastric.ChromatinAccessibility.STL001.DNase.DS20260.wig.gz |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1027320_UW.Gastric.ChromatinAccessibility.STL001.DNase.DS20260.bed.gz |
729.8 Mb |
(ftp)(http) |
BED |
| GSM1027320_UW.Gastric.ChromatinAccessibility.STL001.DNase.DS20260.wig.gz |
277.1 Mb |
(ftp)(http) |
WIG |
SRA Run Selector |
| Processed data provided as supplementary file |
| Raw data not provided for this record |
| Raw data are available in SRA |
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