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Sample GSM956032 Query DataSets for GSM956032
Status Public on Jun 22, 2013
Title Reference Epigenome: ChIP-Seq Input from Human Gastric Tissue; renlab.Input.STL003GA.01.01
Sample type SRA
 
Source name Gastric tissue; renlab.Input.STL003GA.01.01
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: ChIP-Seq Input
extraction_protocol: See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf
extraction_protocol_type_of_sonicator: Biorupter
extraction_protocol_sonication_cycles: 80
chip_protocol: Input
chip_protocol_chromatin_amount: 500 micrograms
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 RANDOM
Instrument model Illumina HiSeq 2000
 
Description sample_term_id: UBERON_0000945
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Input from Human Gastric Tissue. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: AK341
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.13107
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
****************
Data processing **********************************************************************

ANALYSIS FILE NAME: GSM956032_UCSD.Gastric.Input.STL003.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.Input.STL003GA.01.01.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Gastric Input ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Input 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.16485
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 9


QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 66,891,283
FINDPEAKS_SCORE: 0.0038
FINDPEAKS_PERCENTILE: 20
HOTSPOT_SCORE: 0.003
HOTSPOT_PERCENTILE: 11
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.046
POISSON_PERCENTILE: 41
MAXIMUM_REPLICATE_CORRELATION: 0.96

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

ANALYSIS FILE NAME: GSM956032_UCSD.Gastric.Input.STL003.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.Input.STL003GA.01.01.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Gastric Input ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Input 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.16639
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 9
BROWSER_TRACK_NAME: Gastric Input 03 41
BROWSER_TRACK_DESCRIPTION: UCSD Gastric ChIP-Seq Input Donor STL003 Library AK341 EA Release 9


QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 66,891,283
FINDPEAKS_SCORE: 0.0038
FINDPEAKS_PERCENTILE: 20
HOTSPOT_SCORE: 0.003
HOTSPOT_PERCENTILE: 11
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.046
POISSON_PERCENTILE: 41
MAXIMUM_REPLICATE_CORRELATION: 0.96

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

 
Submission date Jul 03, 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
SRA SRX157650
BioSample SAMN00849927
Named Annotation GSM956032_UCSD.Gastric.Input.STL003.wig.gz

Supplementary file Size Download File type/resource
GSM956032_UCSD.Gastric.Input.STL003.bed.gz 993.5 Mb (ftp)(http) BED
GSM956032_UCSD.Gastric.Input.STL003.wig.gz 66.8 Mb (ftp)(http) WIG
SRA Run SelectorHelp
Raw data not provided for this record
Processed data provided as supplementary file
Raw data are available in SRA

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