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Status |
Public on Jul 12, 2012 |
Title |
Reference Epigenome: ChIP-Seq Analysis of H3K27ac in Human Gastric Tissue; renlab.H3K27ac.STL003GA.01.01 |
Sample type |
SRA |
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Source name |
Gastric tissue; renlab.H3K27ac.STL003GA.01.01
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Organism |
Homo sapiens |
Characteristics |
sample alias: STL003GA-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: STL003 donor_age: 34 donor_health_status: polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer) donor_sex: Male donor_ethnicity: Caucasian experiment_type: Histone H3K27ac extraction_protocol: See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf extraction_protocol_type_of_sonicator: Biorupter extraction_protocol_sonication_cycles: 80 chip_protocol: See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf chip_protocol_chromatin_amount: 500 micrograms chip_protocol_bead_type: magnetic anti-rabbit chip_protocol_bead_amount: 33,500,000 chip_protocol_antibody_amount: 5 micrograms chip_antibody: H3K27ac chip_antibody_provider: Active Motif chip_antibody_catalog: 39133 chip_antibody_lot: 19208002
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Extracted molecule |
genomic DNA |
Extraction protocol |
Library construction protocol: See http://bioinformatics-renlab.ucsd.edu/RenLabLibraryProtocolV1.pdf
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Library strategy |
ChIP-Seq |
Library source |
genomic |
Library selection |
ChIP |
Instrument model |
Illumina HiSeq 2000 |
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Description |
sample_term_id: UBERON_0000945 assay_term_id: OBI_0000716 nucleic_acid_term_id: SO_0000352 Design description: ChIP-Seq Analysis of H3K27ac in Human Gastric Tissue. Sequencing was done on the Illumina HiSeq 2000 platform. Library name: AK339 EDACC Genboree Experiment Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.12181 EDACC Genboree Sample Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.12180 **************** 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: GSM910555_UCSD.Gastric.H3K27ac.STL003.bed ANALYSIS CENTER: EDACC ANALYSIS ALIAS: renlab.H3K27ac.STL003GA.01.01.hg19.level.1.release.8 ANALYSIS TITLE: Mapping of Gastric H3K27ac ChIP-Seq Data ANALYSIS DESCRIPTION: Illumina reads produced by H3K27ac ChIP-Seq on Gastric, Donor STL003, 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.13546 DATA_ANALYSIS_LEVEL: 1 EXPERIMENT_TYPE: ChIP-Seq 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: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained. ALIGNMENT_POSTPROCESSING: None READ_EXTENSION: 200bp RELEASE_NUMBER: Human Epigenome Atlas 8
QUALITY SCORES: NUMBER_OF_MAPPED_READS: 16,834,677 NUMBER_OF_H3K27ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 21 FINDPEAKS_SCORE: 0.2213 FINDPEAKS_PERCENTILE: 29 HOTSPOT_SCORE: 0.2992 HOTSPOT_PERCENTILE: 29 IROC_SCORE: 0.9943 IROC_PERCENTILE: 29 POISSON_SCORE: 0.338 POISSON_PERCENTILE: 24 MAXIMUM_REPLICATE_CORRELATION: NA
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ANALYSIS FILE NAME: GSM910555_UCSD.Gastric.H3K27ac.STL003.wig ANALYSIS CENTER: EDACC ANALYSIS ALIAS: renlab.H3K27ac.STL003GA.01.01.hg19.level.2.release.8 ANALYSIS TITLE: Raw Signal Density Graphs of Gastric H3K27ac ChIP-Seq Data ANALYSIS DESCRIPTION: Illumina H3K27ac ChIP-Seq read mappings from Gastric, Donor STL003, 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.13666 DATA_ANALYSIS_LEVEL: 2 EXPERIMENT_TYPE: ChIP-Seq GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19 SOFTWARE: In house programs and scripts SOFTWARE_VERSION: NA READ_EXTENSION: 200bp TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained. GENOMIC_WINDOW: 20bp TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None RELEASE_NUMBER: Human Epigenome Atlas 8 BROWSER_TRACK_NAME: Gastric H3K27ac 03 39 BROWSER_TRACK_DESCRIPTION: UCSD Gastric Histone H3K27ac Donor STL003 Library AK339 EA Release 8
QUALITY SCORES: NUMBER_OF_MAPPED_READS: 16,834,677 NUMBER_OF_H3K27ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 21 FINDPEAKS_SCORE: 0.2213 FINDPEAKS_PERCENTILE: 29 HOTSPOT_SCORE: 0.2992 HOTSPOT_PERCENTILE: 29 IROC_SCORE: 0.9943 IROC_PERCENTILE: 29 POISSON_SCORE: 0.338 POISSON_PERCENTILE: 24 MAXIMUM_REPLICATE_CORRELATION: NA
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Submission date |
Apr 06, 2012 |
Last update date |
May 15, 2019 |
Contact name |
UCSD AND SALK |
Organization name |
University of California, San Diego
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Street address |
Health Sciences Drive
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City |
La Jolla |
State/province |
CA |
ZIP/Postal code |
92092 |
Country |
USA |
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Platform ID |
GPL11154 |
Series (1) |
GSE16256 |
UCSD Human Reference Epigenome Mapping Project |
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Relations |
SRA |
SRX136946 |
BioSample |
SAMN00849927 |
Named Annotation |
GSM910555_UCSD.Gastric.H3K27ac.STL003.wig.gz |
Supplementary file |
Size |
Download |
File type/resource |
GSM910555_UCSD.Gastric.H3K27ac.STL003.bed.gz |
255.1 Mb |
(ftp)(http) |
BED |
GSM910555_UCSD.Gastric.H3K27ac.STL003.wig.gz |
35.5 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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