|
| Status |
Public on May 24, 2012 |
| Title |
RNA-Seq_HCT116-WT_TNFa-treatment |
| Sample type |
SRA |
| |
|
| Source name |
human colorectal carcinoma cell line HCT116
|
| Organism |
Homo sapiens |
| Characteristics |
genotype/variation: Wild type
cell line: HCT116
stimulation: TNF-alpha
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 |
total RNA |
| Extraction protocol |
See http://bioinformatics-renlab.ucsd.edu/RenLabLibraryProtocolV1.pdf
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Data processing |
Reads were mapped by bowtie to hg18, keeping only uniquely mapping genes and discarding all but one of clonal reads. RPKM was calculated as the number of reads per kilo base of exon model per million reads mapped. Bedgraph files were generated using bed files as the input files. Only chromosome positions with at least 5 monoclonal reads are retained
|
| |
|
| Submission date |
Mar 30, 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 |
GPL10999 |
| Series (1) |
| GSE28115 |
CBX3 Regulates Efficient RNA Processing Genome Wide |
|
| Relations |
| SRA |
SRX055350 |
| BioSample |
SAMN00255092 |
