|
| Status |
Public on Jan 01, 2012 |
| Title |
2µM-Fluva-treated_LotI_12h_rep4 |
| Sample type |
RNA |
| |
|
| Source name |
MDA-MB-231, 12h, Lot I
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: MDA-MB-231
cell line origin: breast cancer
agent: Fluvastatin
dose: 2µM
time: 12h
|
| Treatment protocol |
Fluvastatin, or Zoledronate, or their solvent for mock-treated cells were added to the standard 10% FCS-DMEM to final concentration of 2 µM for Fluvastatine ( 12h and 24hincubation times), 30 µM for Zoledronate (12h, 24h, or 48h incubation times); or 100 µM for Zoledronate (24h incubation). Mock-treated (control) cells were obtained in parallel for each time point. Four independent replicates were used for each condition.
|
| Growth protocol |
MDA-MB-231 cell line were maintained in DMEM supplemented with 10% fetal bovine serum (FBS), 1% sodium pyruvate and 1% penicillin sodium and 1% streptomycin antibiotics (10% FCS-DMEM) at 37°C in a humidified atmosphere containing 5% carbon dioxide.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using RNeasy mini kit (Qiagen) by direct lyses on the 10cm culture dish with 600 μl RLT Buffer following manufacture’s instructions. cDNA synthesis and amplification was performed using the WT cDNA synthesis and amplification kit (Affymetrix) starting from 300 ng of total RNAs.
|
| Label |
biotin
|
| Label protocol |
Samples were enzymatically fragmented and biotinylated using the WT Terminal Labeling Kit (Affymetrix)
|
| |
|
| Hybridization protocol |
Samples were hybridized using Affymetrix hybridization kit materials • Heat cocktails at 99° for 5 minutes, then 45° for 5 minutes centrifuge at max speed for 1 minute. Transfer 80μl of hyb solution to each array, then tape holes and parafilm. • Hybridize 17 hours at 45° at 60rpm• Fluidics washing is FS450_0007
|
| Scan protocol |
Affymetrix Gene ChIP Scanner 3000 7G
|
| Description |
Lot I
|
| Data processing |
Raw data were processed with the apt-probeset-summarize program from the Affymetrix Power Tools (v1.10.2) for background correction and normalization. RMA algorithm with full quantile normalization was applied using the array design library files V1 release 4 and normalised values expressed on a log base 2 scale. Transcripts and genes were annotated with the Affymetrix release 29 annotation file based on the human genome version 18 assembly. Data analysis was performed with the R Bioconductor LIMMA package. Only genes with FDR<0.05 and fold change≥1.5 in paired comparison between treatment and their corresponding controls were considered as differentially regulated.
|
| |
|
| Submission date |
Nov 08, 2011 |
| Last update date |
Sep 01, 2016 |
| Contact name |
Nadejda Vintonenko |
| E-mail(s) |
nadvinton@hotmail.com
|
| Fax |
33(0)153724027
|
| Organization name |
Inserm
|
| Lab |
INSERM U553
|
| Street address |
1 Avenue Claude Vellefaux
|
| City |
Paris |
| ZIP/Postal code |
75010 |
| Country |
France |
| |
|
| Platform ID |
GPL6244 |
| Series (1) |
| GSE33552 |
Expression data from MDA-MB-231 cell line treated with Zoledronate, or Fluvastatin, or mock-treated control cells. |
|
| Relations |
| Reanalyzed by |
GSE86357 |
