|
| Status |
Public on Jun 27, 2009 |
| Title |
REF subpopulation of MDA-MB-231 cell line, biological rep1 |
| Sample type |
RNA |
| |
|
| Source name |
REF
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: MDA-MB-231
cell line origin: breast cancer
cell line subpopulation: reference
|
| Growth protocol |
INV and REF subpopulations of 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 from 8 cell cultures (i.e., four biological replicates corresponding to four different passages of INV and REF cells) were isolated using RNeasy mini kit (Qiagen) by direct lysis on the 10cm culture dish with 600 μl RLT Buffer following manufacturer’s instructions. cDNA synthesis and amplification was performed using the WT cDNA synthesis and amplification kit (Affymetrix) starting from 300 ng total RNA.
|
| 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 according to manufacturer's instructions (i.e., Heat cocktails at 99°C for 5 minutes, then 45°C for 5 minutes, centrifuge at max speed for 1 minute. Transfer 80ul of hyb solution to each array, then tape holes and parafilm. Hybridize 17 hours at 45°C at 60rpm. Fluidics washing is FS450_0007).
|
| Scan protocol |
Affymetrix Gene ChIP Scanner 3000 7G
|
| Description |
REF_1.CEL
|
| Data processing |
Data were processed using Affymetrix Expression Console software. Gene level expression data were summarized and then normalized using the RMA-Sketch default algorithm.
|
| |
|
| Submission date |
Jun 25, 2009 |
| Last update date |
Jun 26, 2009 |
| Contact name |
Nadejda Vintonenko |
| E-mail(s) |
[email protected]
|
| 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) |
| GSE16838 |
Expression data from MDA-MB-231 reference and in vitro-derived subpopulations with distinct invasive potentials |
|
