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| Status |
Public on Jun 22, 2013 |
| Title |
Reference Epigenome: ChIP-Seq Input from Human Thymus Tissue; renlab.Input.STL001TH.01.01 |
| Sample type |
SRA |
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| Source name |
Thymus tissue; renlab.Input.STL001TH.01.01
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| Organism |
Homo sapiens |
| Characteristics |
sample alias: STL001TH-01
sample common name: Thymus
molecule: genomic DNA
disease: None
biomaterial_provider: Shin Lin, Stanford University
biomaterial_type: Primary Tissue
tissue_type: Thymus
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 HiSeq 2000 |
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| Description |
sample_term_id: UBERON_0002370
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Input from Human Thymus Tissue. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: AY295
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.13370
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.13369
****************
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: GSM956030_UCSD.Thymus.Input.STL001.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.Input.STL001TH.01.01.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Thymus Input ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Input ChIP-Seq on Thymus, 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.16411
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: 13,636,668
FINDPEAKS_SCORE: 0.0071
FINDPEAKS_PERCENTILE: 74
HOTSPOT_SCORE: 0.0829
HOTSPOT_PERCENTILE: 83
IROC_SCORE: 0.2395
IROC_PERCENTILE: 23
POISSON_SCORE: 0.1319
POISSON_PERCENTILE: 78
MAXIMUM_REPLICATE_CORRELATION: NA
**********************************************************************
ANALYSIS FILE NAME: GSM956030_UCSD.Thymus.Input.STL001.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.Input.STL001TH.01.01.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Thymus Input ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Input ChIP-Seq read mappings from Thymus, 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.16565
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: Thymus Input 01 95
BROWSER_TRACK_DESCRIPTION: UCSD Thymus ChIP-Seq Input Donor STL001 Library AY295 EA Release 9
QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 13,636,668
FINDPEAKS_SCORE: 0.0071
FINDPEAKS_PERCENTILE: 74
HOTSPOT_SCORE: 0.0829
HOTSPOT_PERCENTILE: 83
IROC_SCORE: 0.2395
IROC_PERCENTILE: 23
POISSON_SCORE: 0.1319
POISSON_PERCENTILE: 78
MAXIMUM_REPLICATE_CORRELATION: NA
**********************************************************************
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| 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 |
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| Platform ID |
GPL11154 |
| Series (1) |
| GSE16256 |
UCSD Human Reference Epigenome Mapping Project |
|
| Relations |
| SRA |
SRX157648 |
| BioSample |
SAMN01085432 |
| Named Annotation |
GSM956030_UCSD.Thymus.Input.STL001.wig.gz |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM956030_UCSD.Thymus.Input.STL001.bed.gz |
209.5 Mb |
(ftp)(http) |
BED |
| GSM956030_UCSD.Thymus.Input.STL001.wig.gz |
34.5 Mb |
(ftp)(http) |
WIG |
SRA Run Selector |
| Raw data not provided for this record |
| Processed data provided as supplementary file |
| Raw data are available in SRA |
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