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| 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 |
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| Source name |
Esophagus tissue; renlab.H3K4me3.STL003EG.01.01
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| 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
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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_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
****************
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| 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
**********************************************************************
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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
|
| 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 |
| 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 Selector |
| Processed data provided as supplementary file |
| Raw data not provided for this record |
| Raw data are available in SRA |
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