|
| Status |
Public on Dec 01, 2011 |
| Title |
IgR3 replicate 2 |
| Sample type |
RNA |
| |
|
| Source name |
melanoma
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: IgR3
|
| Treatment protocol |
To generate p53 silenced stable cell lines, Mel-RM, IgR3 and melanocytes were transduced at an MOI of 10 with either a virus encoding p53 shRNA or control shRNA. Cells were transduced twice with three days in between each transduction.
|
| Growth protocol |
All melanoma cell lines were cultured in DMEM containing 5% FCS (Commonwealth Serum Laboratories, VIC, Australia) and maintained in exponential growth at 37oC and 5% CO2. Melanocytes were cultured in Medium 154 (Cascade Biologics). FLOW2000 and HDF1314 fibroblasts were cultured in DMEM containing 10% FCS (Commonwealth Serum Laboratories).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using the SV Total RNA Isolation System Kit according to the manufacturers’ instructions (Promega, NSW, Australia)
|
| Label |
Biotin
|
| Label protocol |
Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays
|
| |
|
| Hybridization protocol |
Standard Illumina hybridization protocol
|
| Scan protocol |
Standard Illumina scanning protocol
|
| Data processing |
All samples were cubic spline normalised and background subtracted using BeadStudio version 3.2.7 software (Illumina). Two-hundred and ninety probes, representing 247 unique transcripts and 181 unique target genes, identified through literature and database searches to either be regulated by p53 or known to regulate p53 activity, were used for further analysis.
|
| |
|
| Submission date |
May 17, 2011 |
| Last update date |
Dec 01, 2011 |
| Contact name |
Kelly Kiejda |
| E-mail(s) |
[email protected]
|
| Organization name |
University of Newcastle
|
| Street address |
HMRI
|
| City |
New Lambton Heights |
| State/province |
NSW |
| ZIP/Postal code |
2305 |
| Country |
Australia |
| |
|
| Platform ID |
GPL6883 |
| Series (2) |
| GSE29361 |
Analysis of p53 target genes in melanoma part 2 |
| GSE29377 |
Analysis of p53 target genes in melanoma |
|
