|
| Status |
Public on Aug 03, 2023 |
| Title |
WM9_LacZ_DMSO |
| Sample type |
RNA |
| |
|
| Source name |
WM9 melanoma cell line; LacZ + DMSO
|
| Organism |
Homo sapiens |
| Characteristics |
gender: male
group: LacZ + DMSO
cell line: WM9 melanoma cell line
|
| Treatment protocol |
ARoe and LacZ melanoma cells were treated with 500nM Dabrafenib or with a vehicle control (DMSO) 48h prior to RNA extraction.
|
| Growth protocol |
Human melanoma A375, M14 and WM9 cell lines were cultured in RPMI (RPMI1640 with L-glutamine; Corning) supplemented with 10% fetal bovine serum (FBS; Sigma Aldrich). For transduction, cells were treated with ARoe or LacZ lentiviruses overnight. Transduced cells were selected using blasticidin.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using Direct-zol RNA MiniPrep kit (Zymo Research) coupled with DNase treatment. RNA quality was verified by Bioanalyzer (Agilent Technologies).
|
| Label |
biotin
|
| Label protocol |
Affymetrix protocol
|
| |
|
| Hybridization protocol |
Affymetrix protocol
|
| Scan protocol |
Arrays were scanned on GS300 scanner (Thermo Fisher Scientific) with AGCC Scan Control Software.
|
| Data processing |
.CEL files were summarized using RMA function in the R package oligo with background correction and quantile normalization. Gene IDs were mapped using the Chip-annotation package clariomdhumantranscriptcluster.db and differential expression analysis was performed with limma, using the formula ~treatment + cell_line . The cutoffs for the new signatures (BRAF and “extended”) were FC > 1.5, and adj-p < 0.1
|
| |
|
| Submission date |
Mar 25, 2022 |
| Last update date |
Aug 03, 2023 |
| Contact name |
Paola Ostano |
| Organization name |
Fondazione Edo ed Elvo Tempia
|
| Street address |
via Malta 3
|
| City |
Biella |
| ZIP/Postal code |
13900 |
| Country |
Italy |
| |
|
| Platform ID |
GPL23126 |
| Series (2) |
| GSE199405 |
Androgen Receptor is a Determinant of Melanoma BRAFi/MEKi Resistance [Clariom_1] |
| GSE232697 |
Androgen Receptor is a Determinant of Melanoma BRAFi/MEKi Resistance |
|
