|
| Status |
Public on Feb 23, 2021 |
| Title |
cell transfected siFra-1-rep2 |
| Sample type |
RNA |
| |
|
| Source name |
MDA-MB-231
|
| Organism |
Homo sapiens |
| Characteristics |
batch: T1- transcriptome 1
cell line: MDA-MB-231
treatment: siFra1
replicate: B
|
| Growth protocol |
MDA-MB-231 cells were cultured in in Dulbecco’s modified Eagle’s medium containing 10% fetal calf serum and penicillin/streptomycin (100µg/ml each)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNAs were extracted using the Qiagen miRNeasy kit according to the supplier's specifications and controlled for purity and integrity using the Agilent Bioanalyser with RNA600 nano LabChipkits (Agilent technologies). On-column DNAse I digestions were performed as described in the user’s guide. RNA with neither signs of contamination nor of degradation (RIN>9) were further processed to generate aplified and biotinylated sense-strand cDNA
|
| Label |
Biotin
|
| Label protocol |
biotinylated sense-strand cDNA were produced using the GeneChip WT PLUS Reagent kit from Affymetrix according to the manufacturer’s specifications
|
| |
|
| Hybridization protocol |
cDNA targets were used to probe Affymetrix GeneChip Human Gene 2.0 ST arrays, which were then washed, stained and scanned according to Affymetrix instructions (user manual P/N 702731 Rev. 3)
|
| Scan protocol |
GeneChips were scanned using GeneChip Scanner 3000
|
| Data processing |
21 CEL (7 conditions, n=3 each) files generated after array scanning were imported into the Partek Genomics Suite 6.6 (Partek) for preprocessing (default Partek options)
|
| |
|
| Submission date |
Mar 11, 2020 |
| Last update date |
Feb 23, 2021 |
| Contact name |
Isabelle Jariel-Encontre |
| E-mail(s) |
[email protected]
|
| Phone |
00 33 (0)4 11 28 31 53
|
| Organization name |
IRCM-U1194- INSERM
|
| Street address |
208 Avenue des Apothicaires
|
| City |
Montpellier |
| State/province |
Montpellier Cedex5 |
| ZIP/Postal code |
34298 |
| Country |
France |
| |
|
| Platform ID |
GPL16686 |
| Series (2) |
| GSE146823 |
Identification of Fra-1 and/or Fra-2 regulated genes in MDA-MB231 cells |
| GSE146825 |
Transcriptional regulation by Fra-1 in triple negative breast cancers |
|
