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| Status |
Public on Nov 01, 2012 |
| Title |
Chromatin accessibility assay of Heart; DNase.DS20383 |
| Sample type |
SRA |
| |
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| Source name |
Adult Heart primary tissue, year 3; DNase.DS20383
|
| Organism |
Homo sapiens |
| Characteristics |
sample alias: Heart.STL001y3
sample common name: Heart
molecule: genomic DNA
disease: None
biomaterial_provider: Lin Laboratory
biomaterial_type: Primary Tissue
tissue_type: Heart
tissue_depot: Washington University, St. Louis
collection_method: After the donor aorta and inferior mesenteric vein (IMV) were cannulated, the aorta was flushed with 5L of 4degC cooled histidine-tryptophan-ketoglutarate solution (HTK) and the IMV was flushed with 3L of HTK which results in the perfusion of all intra-abdominal organs with preservative solution. The abdominal cavity was cooled topically with ice during perfusion. The relevant tissues were then removed and transported to a local laboratory within 1 hour. There, the tissues were minced with a blade and 1gm of tissue was placed into a cryovial with 1mL of freezing solution (freezing solution 50mL: 25mL DMEM, 10mL Normosol-R, 10mL 25% BSA, 5mL DMSO, 1 tablet protease inhibitor) for 15min on ice. The cyrovial was then placed in a 1inch-thick styrofoam container, and then placed into -80C freezer, resulting in a slow freezing to -80C over an 1hour period.
donor_id: STL001
donor_age: year 3
donor_health_status: NA
donor_sex: Male
donor_ethnicity: NA
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_0000948
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Chromatin accessibility determination via DNase-seq
Library name: DNase.DS20383
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.14534
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.14533
****************
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: GSM1027322_UW.Heart.ChromatinAccessibility.STL001.DNase.DS20383.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNase.DS20383.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Heart Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Heart, Donor STL001, Library DNase.DS20383 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.17601
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: 42,520,289
FINDPEAKS_SCORE: 0.2991
FINDPEAKS_PERCENTILE: 24
HOTSPOT_SCORE: 0.2876
HOTSPOT_PERCENTILE: 22
IROC_SCORE: 0.9883
IROC_PERCENTILE: 13
POISSON_SCORE: 0.3792
POISSON_PERCENTILE: 37
MAXIMUM_REPLICATE_CORRELATION: NA
**********************************************************************
ANALYSIS FILE NAME: GSM1027322_UW.Heart.ChromatinAccessibility.STL001.DNase.DS20383.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNase.DS20383.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Heart Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from Heart, Donor STL001, Library DNase.DS20383 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.17555
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: Heart DNase 01 83
BROWSER_TRACK_DESCRIPTION: UW Heart DNase Hypersensitivity Donor STL001 Library DNase.DS20383 EA Release 9
QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 42,520,289
FINDPEAKS_SCORE: 0.2991
FINDPEAKS_PERCENTILE: 24
HOTSPOT_SCORE: 0.2876
HOTSPOT_PERCENTILE: 22
IROC_SCORE: 0.9883
IROC_PERCENTILE: 13
POISSON_SCORE: 0.3792
POISSON_PERCENTILE: 37
MAXIMUM_REPLICATE_CORRELATION: NA
**********************************************************************
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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 |
|
| Relations |
| SRA |
SRX201809 |
| BioSample |
SAMN01797248 |
| Named Annotation |
GSM1027322_UW.Heart.ChromatinAccessibility.STL001.DNase.DS20383.wig.gz |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1027322_UW.Heart.ChromatinAccessibility.STL001.DNase.DS20383.bed.gz |
631.4 Mb |
(ftp)(http) |
BED |
| GSM1027322_UW.Heart.ChromatinAccessibility.STL001.DNase.DS20383.wig.gz |
252.5 Mb |
(ftp)(http) |
WIG |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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