|
| Status |
Public on Jul 16, 2014 |
| Title |
Control (siControl-1) |
| Sample type |
RNA |
| |
|
| Source name |
MDA-LM2 cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: MDA-LM2
genotype/variation: Control
|
| Treatment protocol |
Cells were transfected with siTARBP2 and siControl using Lipofectamin 2000 per manufacturer guidelines.
|
| 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 |
48hr post-transfection, 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
siControl
|
| 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 siTARBP2 relative to siControl. (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) |
| GSE49611 |
Regulatory consequences of TARBP2 knock-down in MDA-LM2 cell-line |
| GSE49649 |
Metastasis-suppressor transcript destabilization through TARBP2 binding of mRNA hairpins |
|
