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Status |
Public on Jul 12, 2012 |
Title |
Reference Epigenome: ChIP-Seq Input from Human Small Bowel Tissue; renlab.Input.STL001SB.01.01 |
Sample type |
SRA |
|
|
Source name |
Small Intestine tissue; renlab.Input.STL001SB.01.01
|
Organism |
Homo sapiens |
Characteristics |
sample alias: STL001SB-01 sample common name: Small Intestine molecule: genomic DNA disease: None biomaterial_provider: Shin Lin, Stanford University biomaterial_type: Primary Tissue tissue_type: Small Intestine 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: 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
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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 |
RANDOM |
Instrument model |
Illumina Genome Analyzer IIx |
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Description |
sample_term_id: UBERON_0002108 assay_term_id: OBI_0000716 nucleic_acid_term_id: SO_0000352 Design description: ChIP-Seq Input from Human Small Bowel Tissue. Sequencing was done on the Illumina Genome Analyzer IIx platform. Library name: AK225 EDACC Genboree Experiment Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.12263 EDACC Genboree Sample Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.12250 **************** 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: GSM915337_UCSD.Small_Intestine.Input.STL001.bed ANALYSIS CENTER: EDACC ANALYSIS ALIAS: renlab.Input.STL001SB.01.01.hg19.level.1.release.8 ANALYSIS TITLE: Mapping of Small Intestine Input ChIP-Seq Data ANALYSIS DESCRIPTION: Illumina reads produced by Input ChIP-Seq on Small Intestine, Donor STL001, 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.13557 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: 34,464,193 NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 19 FINDPEAKS_SCORE: 0.0071 FINDPEAKS_PERCENTILE: 58 HOTSPOT_SCORE: 0.0517 HOTSPOT_PERCENTILE: 42 IROC_SCORE: NA IROC_PERCENTILE: NA POISSON_SCORE: 0.1564 POISSON_PERCENTILE: 53 MAXIMUM_REPLICATE_CORRELATION: NA
**********************************************************************
ANALYSIS FILE NAME: GSM915337_UCSD.Small_Intestine.Input.STL001.wig ANALYSIS CENTER: EDACC ANALYSIS ALIAS: renlab.Input.STL001SB.01.01.hg19.level.2.release.8 ANALYSIS TITLE: Raw Signal Density Graphs of Small Intestine Input ChIP-Seq Data ANALYSIS DESCRIPTION: Illumina Input ChIP-Seq read mappings from Small Intestine, Donor STL001, 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.13677 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: SI Input 01 25 BROWSER_TRACK_DESCRIPTION: UCSD Small Intestine ChIP-Seq Input Donor STL001 Library AK225 EA Release 8
QUALITY SCORES: NUMBER_OF_MAPPED_READS: 34,464,193 NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 19 FINDPEAKS_SCORE: 0.0071 FINDPEAKS_PERCENTILE: 58 HOTSPOT_SCORE: 0.0517 HOTSPOT_PERCENTILE: 42 IROC_SCORE: NA IROC_PERCENTILE: NA POISSON_SCORE: 0.1564 POISSON_PERCENTILE: 53 MAXIMUM_REPLICATE_CORRELATION: NA
**********************************************************************
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|
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Submission date |
Apr 13, 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 |
GPL10999 |
Series (1) |
GSE16256 |
UCSD Human Reference Epigenome Mapping Project |
|
Relations |
SRA |
SRX142124 |
BioSample |
SAMN00849925 |
Named Annotation |
GSM915337_UCSD.Small_Intestine.Input.STL001.wig.gz |