|
| Status |
Public on Oct 21, 2009 |
| Title |
AALE-KRAS + shGFP, biological rep3 |
| Sample type |
RNA |
| |
|
| Source name |
KRAS expression/control suppression
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: Immortalized lung epithelial cells
|
| Treatment protocol |
Cells were infected with TBK1- or GFP-specific lentivirally delivered shRNAs for 4 hours, puromycin selection was initiated 24 hours post-infection, then RNA was harvested 48 hours post-infection.
|
| Growth protocol |
AALE cells (Lundberg et al., Oncogene 2002;21:4577) expressing oncogenic KRAS or vector alone were grown in serum free SABM media with supplements using standard culture conditions.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol extraction of total RNA was performed according to the manufacturer's instructions.
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNA was prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
|
| |
|
| Hybridization protocol |
Following fragmentation, 15 ug of cRNA was hybridized for 16 hr at 45C on U133A Human Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
|
| Scan protocol |
The data were scanned using Affymetrix Gene Chip Scanner 3000
|
| Description |
Gene expression data from KRAS expression/control suppression
|
| Data processing |
The data were analyzed with RMA (Gene Pattern's ExpressionFileCreator version 8). Parameters: method RMA quantile normalization yes background correct yes compute present absent calls no normalization method none value to scale to clm file annotate probes yes
|
| |
|
| Submission date |
Aug 14, 2009 |
| Last update date |
Oct 21, 2009 |
| Contact name |
Pablo Tamayo |
| E-mail(s) |
ptamayo@ucsd.edu
|
| Phone |
508-259-0630
|
| Organization name |
UCSD
|
| Department |
Moores Cancer Center
|
| Street address |
3855 Health Sciences Drive MC 0658
|
| City |
La Jolla |
| State/province |
CA |
| ZIP/Postal code |
92093 |
| Country |
USA |
| |
|
| Platform ID |
GPL571 |
| Series (2) |
| GSE17643 |
Profiling of immortalized human lung epithelial cells following oncogenic KRAS expression and TBK1 suppression |
| GSE17672 |
Profiling genes induced by oncogenic KRAS (G12V) and genes regulated by TBK1, a synthetic lethal partner of KRAS |
|
