|
| Status |
Public on Apr 19, 2017 |
| Title |
Reference Epigenome: ChIP-Seq Analysis of H3K27ac in Human Esophagus Tissue; renlab.H3K27ac.STL003EG.02.01 |
| Sample type |
SRA |
| |
|
| Source name |
Esophagus tissue; renlab.H3K27ac.STL003EG.02.01
|
| Organism |
Homo sapiens |
| Characteristics |
sra sample accession: SRS306616
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
biosamplemodel: Generic
experiment_type: Histone H3K27ac
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: H3K27ac
chip_antibody_provider: Active Motif
chip_antibody_catalog: 39133
chip_antibody_lot: 19208002
|
| 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 H3K27ac in Human Esophagus Tissue. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: AK324
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.19830
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 |
Various levels of processed data files will be made available as this project proceeds.
|
| |
|
| Submission date |
Jan 12, 2015 |
| Last update date |
Apr 19, 2017 |
| 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 |
| BioSample |
SAMN00847535 |
