|
| Status |
Public on Apr 17, 2021 |
| Title |
MDAmammos-KO-rep1 |
| Sample type |
RNA |
| |
|
| Source name |
unstimulated breast cancer cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: MDA-MB-231
genotype/variation: KO
|
| Treatment protocol |
no stimulation
|
| Growth protocol |
cultured at 37°C/5% CO2 in DMEM supplemented with 8% heat-inactivated FCS and 2 mM L-glutamine
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were dissociated with trypsin/EDTA (0.05% trypsin; Gibco) for 5 min. Dissociated cells were washed twice in PBS. RNA was extracted using the NucleoSpin RNA XS extraction kit (Macherey–Nagel), according to the manufacturer’s recommendations.
|
| Label |
Biotin
|
| Label protocol |
100 ng of total RNA is reverse transcribed following the GeneChip® WT Plus Reagent Kit (Affymetrix) . Briefly, the resulting double strand cDNA is used for in vitro transcription with T7 RNA polymerase (all these steps are included in the WT cDNA synthesis and amplification kit of Affymetrix). After purification according to Affymetrix protocol, 5.5 ug of Sens Target DNA are fragmented and biotin labelled.
|
| |
|
| Hybridization protocol |
After control of fragmentation using Bioanalyzer 2100, cDNA is then hybridized to GeneChip® ClariomS Mouse or HumanGene2.0ST (LifeTechnologies) at 45°C for 17 hours.
|
| Scan protocol |
Hybridized microarrays were scanned by a GeneChip Scanner 3000 7G (Affymetrix).
|
| Description |
Gene expression data from a human triple negative breast cancer cell line
|
| Data processing |
Probes were normalized by robust multi-array averaging with rma function from oligo R package and mapped using hugene20sttranscriptcluster.db as database.Statistical analyses were performed using the Linear Model for Series of Arrays (lmFit) from limma R package.
|
| |
|
| Submission date |
Apr 16, 2021 |
| Last update date |
Apr 17, 2021 |
| Contact name |
Justine Pollet |
| E-mail(s) |
j.pollet@outlook.com
|
| Organization name |
CBRS
|
| Street address |
2, avenue Martin Luther King
|
| City |
Limoges |
| ZIP/Postal code |
87000 |
| Country |
France |
| |
|
| Platform ID |
GPL16686 |
| Series (2) |
| GSE172214 |
CD95 expression in triple negative breast cancer blocks induction of an inflammatory state through differential regulation of NF-κB Signaling [MDA-MB-231] |
| GSE172215 |
CD95 expression in triple negative breast cancer blocks induction of an inflammatory state through differential regulation of NF-κB Signaling |
|
