|
| Status |
Public on May 20, 2014 |
| Title |
A375 cells 24h Control rep3 |
| Sample type |
RNA |
| |
|
| Source name |
A375 melanoma cells treated with vehicle (0.1% DMSO)
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: Melanoma cell line
cell line: A375
|
| Treatment protocol |
Cells were seeded in dup[licate 10cm dishes at 1,000,000 cells per dish and incubated for 24h then cells were treated with vehicle (0.1% DMSO) or Vemurafenib (Vem; PLX4032) for a further 24h.
|
| Growth protocol |
A375 human melanoma cells grown in a monolayer in a 37°C humidified 5%CO2 incubator. Cells were grown in RPMI 1640 + HEPES containing 10% FBS, 2 mM L-alanyl-L-glutamine, 1% penicillin/streptomycin and 250 ng/ml amphotericin B
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using a Qiagen miRNeasy Mini kit according to the manufacturer's protocol.
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNA was prepared from an input of 250ng RNA using an Ambion WT kit followed by the Affymetrix terminal labelling kit according to the manufacturer's instructions.
|
| |
|
| Hybridization protocol |
5μg of fragmented, labeled cRNA was hybridized at 45°C for 16h onto GeneChip® 1.0 ST human gene arrays then washed and stained using the Affymetrix GeneChip Fluidics Station 450
|
| Scan protocol |
GeneChips were scanned using an Affymetrix 3000 7G scanner
|
| Description |
Gene expression data from A375 melanoma cells treated with vehicle control (0.1% DMSO)
|
| Data processing |
Raw data were RMA normalized after which differentially expressed genes were detected using a 2-way ANOVA using Partek software. The batch date of the different replicates was controlled for and the log fold change between control and Vem-treated samples was estimated. Normalized data was also subjected to gene set enrichment analysis (provided online by the Broad Institute) using c2 curated gene sets (Molecular signatures database v3.1) to identify enrichment of entire gene sets in either the control of Vem-treated samples
|
| |
|
| Submission date |
Dec 12, 2012 |
| Last update date |
May 20, 2014 |
| Contact name |
Tiffany Joy Parmenter |
| E-mail(s) |
tiffanyparmenter@gmail.com
|
| Organization name |
Peter MacCallum Cancer Centre
|
| Street address |
1 St Andrews Pl
|
| City |
East Melbourne |
| ZIP/Postal code |
3002 |
| Country |
Australia |
| |
|
| Platform ID |
GPL6244 |
| Series (1) |
| GSE42872 |
Expression data from BRAFV600E A375 melanoma cells treated with vehicle or vemurafenib |
|
