|
| Status |
Public on May 24, 2012 |
| Title |
Input_HCT116-WT_no-treatment_rep2 |
| Sample type |
SRA |
| |
|
| Source name |
human colorectal carcinoma cell line HCT116
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HCT116
genotype/variation: Wild type
stimulation: none
chip antibody: none
alignment program: Bowtie
|
| Treatment protocol |
Cells were treated with 10 ng/ml TNF-alpha for 30-60 mins.
|
| Growth protocol |
HCT116 cells were grown in McCoys media, supplemented with 10% FBS and 1% pen-strep.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
See http://bioinformatics-renlab.ucsd.edu/RenLabLibraryProtocolV1.pdf
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
ChIP-Seq reads were mapped by bowtie to hg18, keeping only uniquely mapping reads and discarding all but one of clonal reads. Bedgraph files were generated using bed files as the input files. Only chromosome positions with at least 5 monoclonal reads are retained.
|
| |
|
| Submission date |
Sep 26, 2011 |
| Last update date |
May 15, 2019 |
| Contact name |
Bing Ren |
| E-mail(s) |
biren@ucsd.edu
|
| Organization name |
University of California, San Diego
|
| Street address |
9500 Gilman Drive
|
| City |
La Jolla |
| State/province |
CA |
| ZIP/Postal code |
92093 |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE28115 |
CBX3 Regulates Efficient RNA Processing Genome Wide |
|
| Relations |
| SRA |
SRX098625 |
| BioSample |
SAMN00727671 |
