|
| Status |
Public on Aug 03, 2015 |
| Title |
MDA-MB-231 cells siControl, biological replica C |
| Sample type |
RNA |
| |
|
| Source name |
control cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: MDA-MB-231
cell type: breast cancer
transfection construct: Control siRNA
|
| Treatment protocol |
Cells were transfected on day 2 with siRNA oligonucleotides (final concentration 33nM) by using RNAi MAX (Life Technologies), following a direct transfection protocol as indicated by manifacturer's instructions. On day 3, medium was renewed. On day 4, cells were washed with 1XHBSS and harvested for RNA extraction.
|
| Growth protocol |
Cells were seeded at low confluence on day 1 in standard growth medium (DMEM/F12 with 2mM Glutamine, 17.5mM D-glucose, without antibiotics, 10% Fetal Bovine Serum).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol extraction of total RNA, followed by DNAseI digestion to reduce genomic DNA contaminations, was performed according to the manufacturer's instructions.
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNA were prepared using the 3'IVT Kit ( Affymetrix, Santa Clara, USA, CA) according to manufacturer's intructions.
|
| |
|
| Hybridization protocol |
Following fragmentation, 12.5 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Human Genome U133 Plus 2.0 arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
|
| Scan protocol |
Standard Affymetrix scanning procedures on a GCS3000 7G Affymetrix scanner operated by GeneChip Command Console Software (AGCC)
|
| Description |
Gene expression data from control MDA-MB-231 cells
|
| Data processing |
RMA of .CEL files using affy Bioconductor library and Brainarray HGU133Plus2_Hs_ENTREZG_v17 custom cdf. In RMA, PM values have been background adjusted, normalized using quantile normalization, and expression measure calculated using median polish summarization
|
| |
|
| Submission date |
Feb 19, 2015 |
| Last update date |
Aug 03, 2015 |
| Contact name |
Silvio Bicciato |
| E-mail(s) |
silvio.bicciato@unipd.it
|
| Phone |
+39-049-827-6108
|
| Organization name |
University of Padova
|
| Department |
Molecular Medicine
|
| Street address |
via U. Bassi 59/b
|
| City |
Padova |
| ZIP/Postal code |
35131 |
| Country |
Italy |
| |
|
| Platform ID |
GPL17811 |
| Series (2) |
| GSE66082 |
Widespread association between YAP/TAZ/TEAD and AP-1 at enhancers drives oncogenic growth [gene expression] |
| GSE66083 |
Widespread association between YAP/TAZ/TEAD and AP-1 at enhancers drives oncogenic growth |
|
| Relations |
| Reanalysis of |
GSM1431024 |
