|
| Status |
Public on Jul 16, 2014 |
| Title |
TARBP2 knock-down (siTARBP2-1)_0hrs |
| Sample type |
RNA |
| |
|
| Source name |
MDA-LM2 cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: MDA-LM2
genotype/variation: TARBP2 knock-down
agent: untreated
time-point: 0 hr
|
| Treatment protocol |
Cells were transfected with siTARBP2 and siControl using Lipofectamin 2000 per manufacturer guidelines. 48 hr post-transfection, cells were treated with alpha-amanitine at 10uM for 0 and 18 hours.
|
| Growth protocol |
Cells were grown in DMEM-based media supplemented with 10% FBS, 1% L-glutamine, 1% Sodium Pyruvate, and 1% Pen/Strep
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted and on-column Dnase treated using Norgen Biotek total RNA extraction kit (per manufacturer instructions).
|
| Label |
biotin
|
| Label protocol |
Samples were biotin-labeled using the TargetAmp-Nano Labeling Kit for Ilumina Expression BeadChip
|
| |
|
| Hybridization protocol |
Per manufacturer's instruction
|
| Scan protocol |
Per manufacturer's instruction
|
| Description |
replicate 1
siTARBP2-1 (0 hr)
|
| Data processing |
Data were quantile-normalized and processed using the Lumi package.
Non-normalized values indicate the average probe hybridization signal (supplementary file linked to Series record).
Normalized values are quantile-normalized.
Final processed values are logFC of average stability measurements in siTARBP2 relative to siControl. The stability measurements are calculated as the 18 hr to 0 hr processed signal ratio, further corrected based on the amount of input total and labeled RNA for each sample (supplementary file linked to Series record).
|
| |
|
| Submission date |
Aug 07, 2013 |
| Last update date |
Jul 16, 2014 |
| Contact name |
Hani Goodarzi |
| Organization name |
UCSF
|
| Department |
Biochemistry and Biophysics
|
| Street address |
600 16th St, GH S312D
|
| City |
San Francisco |
| State/province |
CA |
| ZIP/Postal code |
94158 |
| Country |
USA |
| |
|
| Platform ID |
GPL10558 |
| Series (2) |
| GSE49612 |
Regulatory consequences of TARBP2 knock-down in MDA-LM2 cell-line [stability experiment] |
| GSE49649 |
Metastasis-suppressor transcript destabilization through TARBP2 binding of mRNA hairpins |
|
