|
| Status |
Public on Jul 19, 2011 |
| Title |
starved_2_RNAseq |
| Sample type |
SRA |
| |
|
| Source name |
HCT-116
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HCT-116
passages: passage 4-15
treatment: none
|
| Treatment protocol |
For serum stimulation, cells were first starved by washing cells 2x in PBS, then culturing for 40 hours in McCoyâs 5A without serum. Cells were then either left untreated or treated with serum for 30 minutes before harvesting.
|
| Growth protocol |
HCT-116 cells were grown in McCoyâs 5A medium supplemented with 10% FBS.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA was extracted from serum-treated and untreated HCT-116 cells with RNeasy kit following manufacturer's protocol. And 2 ug of total RNA from each sample was used to prepare the libraries with the Illumina mRNA-Seq Sample Prep Kit (RS-100-0801) according to Illumina's instructions and sequenced on the Genome Analyzer IIx following the manufacturer's protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Description |
ctrl mRNA
|
| Data processing |
Alignment: Sequencing reads were acquired through the primary Solexa image analysis pipeline, where bases were called and reads were filtered for quality, according to default Solexa standards. Filtered reads were then aligned to the human genome (UCSC hg19) using the tophat (Trapnell et al. 2009) alignment tool, version 1.2.0, allowing unique matches only, and the full human ENSEMBL 59 GTF.
|
| |
|
| Submission date |
Jul 19, 2011 |
| Last update date |
May 15, 2019 |
| Contact name |
Alexander (Garrett) Garruss |
| E-mail(s) |
asg@stowers.org
|
| Organization name |
Stowers Institute for Medical Research
|
| Lab |
Shilatifard
|
| Street address |
1000 East 50th Street
|
| City |
Kansas CIty |
| State/province |
Missouri |
| ZIP/Postal code |
64110 |
| Country |
USA |
| |
|
| Platform ID |
GPL10999 |
| Series (2) |
| GSE30268 |
Dynamic transcriptional events in embryonic stem cells mediated by the super elongation complex (SEC). |
| GSE30786 |
Determination of transcript abundance before and after serum induction in human HCT-116 colon cancer cell line. |
|
| Relations |
| SRA |
SRX084347 |
| BioSample |
SAMN00672476 |
