|
| Status |
Public on Sep 13, 2009 |
| Title |
Control-KD mRNA-Seq |
| Sample type |
SRA |
| |
|
| Source name |
293T cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell l ine: 293T
|
| Treatment protocol |
Day 0: plate cells in 10cm dishes. Day 1: transfect 20nM siRNA using Dharmafect 1 (Dharmacon) as transfection reagent. Day 2: transfect 50nM siRNA using Dharmafect 1 (Dharmacon) as transfection reagent. Day 4: harvest cells. Transfections were conducted using protocols suggested by the manufacturer of the transfection reagent.
|
| Growth protocol |
293T cells were cultured with D-MEM medium supplemented with 10% fetal bovine serum.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
mRNA is purified from total RNA with oligo-dT magnetic beads. cDNA is synthesized with random primer priming. ds-cDNA is sequenced using Illumina Genome Analyzers as recommended by the manufacturer.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer |
| |
|
| Description |
n/a
|
| Data processing |
short reads mapping to human genome hg18 using Eland
|
| |
|
| Submission date |
Jun 16, 2009 |
| Last update date |
May 15, 2019 |
| Contact name |
Xinshu Xiao |
| E-mail(s) |
gxxiao@ucla.edu
|
| Organization name |
MIT
|
| Department |
Biology
|
| Lab |
Chris Burge Lab
|
| Street address |
77 Mass Ave. MIT, 68-211
|
| City |
Cambridge |
| State/province |
MA |
| ZIP/Postal code |
02139 |
| Country |
USA |
| |
|
| Platform ID |
GPL9052 |
| Series (1) |
| GSE16642 |
Illumina mRNA-Seq of control and hnRNP H knockdown in 293T cells |
|
| Relations |
| SRA |
SRX012335 |
| BioSample |
SAMN00004611 |
