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Sample GSM910578 Query DataSets for GSM910578
Status Public on Jul 12, 2012
Title Reference Epigenome: ChIP-Seq Analysis of H3K4me3 in Human Esophagus Tissue; renlab.H3K4me3.STL003EG.01.01
Sample type SRA
 
Source name Esophagus tissue; renlab.H3K4me3.STL003EG.01.01
Organism Homo sapiens
Characteristics sample alias: STL003EG-01
sample common name: Esophagus
molecule: genomic DNA
disease: None
biomaterial_provider: Shin Lin, Stanford University
biomaterial_type: Primary Tissue
tissue_type: Esophagus
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 H3K4me3
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: H3K4me3
chip_antibody_provider: Active Motif
chip_antibody_catalog: 39159
chip_antibody_lot: 15808002
Extracted molecule genomic DNA
Extraction protocol Library construction protocol: See http://bioinformatics-renlab.ucsd.edu/RenLabLibraryProtocolV1.pdf
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 2000
 
Description sample_term_id: UBERON_0001043
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K4me3 in Human Esophagus Tissue. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: AY182
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.12193
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.11826
****************
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: GSM910578_UCSD.Esophagus.H3K4me3.STL003.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K4me3.STL003EG.01.01.hg19.level.1.release.8
ANALYSIS TITLE: Mapping of Esophagus H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K4me3 ChIP-Seq on Esophagus, 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.13518
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: 16,576,428
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 14
FINDPEAKS_SCORE: 0.3911
FINDPEAKS_PERCENTILE: 57
HOTSPOT_SCORE: 0.4585
HOTSPOT_PERCENTILE: 64
IROC_SCORE: 0.9998
IROC_PERCENTILE: 67
POISSON_SCORE: 0.4456
POISSON_PERCENTILE: 64
MAXIMUM_REPLICATE_CORRELATION: NA

**********************************************************************

ANALYSIS FILE NAME: GSM910578_UCSD.Esophagus.H3K4me3.STL003.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K4me3.STL003EG.01.01.hg19.level.2.release.8
ANALYSIS TITLE: Raw Signal Density Graphs of Esophagus H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K4me3 ChIP-Seq read mappings from Esophagus, 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.13638
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: Esophagus H3K4me3 03 82
BROWSER_TRACK_DESCRIPTION: UCSD Esophagus Histone H3K4me3 Donor STL003 Library AY182 EA Release 8


QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 16,576,428
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 14
FINDPEAKS_SCORE: 0.3911
FINDPEAKS_PERCENTILE: 57
HOTSPOT_SCORE: 0.4585
HOTSPOT_PERCENTILE: 64
IROC_SCORE: 0.9998
IROC_PERCENTILE: 67
POISSON_SCORE: 0.4456
POISSON_PERCENTILE: 64
MAXIMUM_REPLICATE_CORRELATION: NA

**********************************************************************

 
Submission date Apr 06, 2012
Last update date May 15, 2019
Contact name UCSD AND SALK
Organization name University of California, San Diego
Street address Health Sciences Drive
City La Jolla
State/province CA
ZIP/Postal code 92092
Country USA
 
Platform ID GPL11154
Series (1)
GSE16256 UCSD Human Reference Epigenome Mapping Project
Relations
Reanalyzed by GSE99453
SRA SRX136969
BioSample SAMN00847535
Named Annotation GSM910578_UCSD.Esophagus.H3K4me3.STL003.wig.gz

Supplementary file Size Download File type/resource
GSM910578_UCSD.Esophagus.H3K4me3.STL003.bed.gz 246.8 Mb (ftp)(http) BED
GSM910578_UCSD.Esophagus.H3K4me3.STL003.wig.gz 30.7 Mb (ftp)(http) WIG
SRA Run SelectorHelp
Processed data provided as supplementary file
Raw data not provided for this record
Raw data are available in SRA

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