|
| Status |
Public on Dec 31, 2018 |
| Title |
WM2664-NT-D3a |
| Sample type |
RNA |
| |
|
| Source name |
WM2664-NT-D3a
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: WM266-4
genotype: BRAF V600D
treatment: Doxycycline-NT
time point: 3d
|
| Treatment protocol |
WM266-4 cells were treated with 0.05uM LGX818, 0.003uM trametinib, 0.3uM MEK162, 0.2uM ERK1/2 inhibitor or DMSO for 3hr or 24hr in triplicates. WM266-4 cells carrying inducible shRNAs were treated with 100ng/ml doxycycline for 3 or 7 days in triplicates.
|
| Growth protocol |
WM266-4 cells or WM266-6 carrying inducible shRNAs were seeded on 6-well plates at 300,000 cells per well, 24hr before treatment
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted with RNAeasy Plus kit (Qiagen) according to the manufacturer's instructions.
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, Affymetrix).
|
| |
|
| Hybridization protocol |
Following fragmentation, 15 ug of cRNA were hybridized for 16hr at 45C on GeneChip Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station.
|
| Scan protocol |
GeneChips were scanned using the GeneChip Scanner 3000.
|
| Description |
non-targeting shRNA treatment day 3
|
| Data processing |
The data were analyzed with Bioconductor affy package (http://bioconductor.org) with RMA method and HGU133Plus2_Hs_ENTREZG custom CDF v16 for target gene definition (Dai et al., 2005)
|
| |
|
| Submission date |
May 16, 2014 |
| Last update date |
Dec 31, 2018 |
| Contact name |
Guoying Karen Yu |
| E-mail(s) |
yu.karen@gmail.com
|
| Organization name |
Novartis - NIBR
|
| Department |
bioinformatics
|
| Street address |
4560 Horton St, MS 4.1
|
| City |
Emeryville |
| State/province |
CA |
| ZIP/Postal code |
94608 |
| Country |
USA |
| |
|
| Platform ID |
GPL17810 |
| Series (1) |
| GSE57721 |
Expression profiling of MAPK inhibition in WM266-4 BRAF V600D mutant melanoma cell line |
|
