|
| Status |
Public on May 07, 2015 |
| Title |
LM2-Hypoxia-shYBX1-2 |
| Sample type |
RNA |
| |
|
| Source name |
MDA-LM2-shYBX1
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: MDA-LM2
genotype/variation: shYBX1 knockdown
treatment: Hypoxia
|
| Treatment protocol |
The hypoxia chamber was flushed with 1% oxygen at a rate of 25L/min for 5 minutes. Cells were then incubated at 37C.
|
| 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
|
| Data processing |
Data were quantile-normalized and processed using the Lumi package. Futher processed values are the difference between the logFC of average normalized signals changes in hypoxic versus normoxic cells relative to YBX1-knockdown cells.
|
| |
|
| Submission date |
Nov 21, 2014 |
| Last update date |
May 07, 2015 |
| 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) |
| GSE63562 |
YBX1-dependent hypoxia-induced modulation of gene expression |
| GSE63605 |
Endogenous tRNA-derived fragments suppress breast cancer progression via YBX1 displacement |
|
