|
| Status |
Public on May 24, 2012 |
| Title |
RNA-Seq_HCT116-KD_TNF-treatment_rep2 |
| Sample type |
SRA |
| |
|
| Source name |
human colorectal carcinoma cell line HCT116
|
| Organism |
Homo sapiens |
| Characteristics |
celll line: HCT116
genotype/variation: HP1 gamma knock down
stimulation: TNF
chip antibody: none
data processing (alignment) algorithm: 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 HiSeq 2000 |
| |
|
| 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
Genome_build: hg18
Supplementary_files_format_and_content: bed files, BEDGRAPH files: standard UCSC genome browser format
|
| |
|
| Submission date |
Mar 21, 2012 |
| 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 |
SRX130494 |
| BioSample |
SAMN00829244 |
