|
| Status |
Public on Jun 19, 2015 |
| Title |
UM-UC-17 |
| Sample type |
RNA |
| |
|
| Source name |
Bladder Cell Line_UM-UC-17
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: UM-UC-17
cell type: urothelial bladder carcinoma
|
| Growth protocol |
Cells were cultured in RPMI supplemented with 10-20% FBS and were harvested at 70-90% confluence.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated with Trizol according to the manufacturers instructions.
|
| Label |
biotin
|
| Label protocol |
500 ng of biotinylated cRNA were prepared according to the standard Affymetrix protocol.
|
| |
|
| Hybridization protocol |
Following fragmentation, cRNA were hybridized for 16 hr at 45C on the Affymetrix U133 array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
|
| Scan protocol |
GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.
|
| Description |
SAMPLE 16
|
| Data processing |
Raw expression data from these cell lines were normalized using the R library Frozen Robust Multiarray Analysis (fRMA) method [Biostatistics 2010, 11:242-253]. We applied this method as described by the authors for multiple arrays. We read the raw data (CEL files) and used the Random effect model for preprocessing. This model let us combine data from different batches and same microarray platform for analysis. Further, to obtain a matrix of gene-level expression values we used the exprs function with parameters by default.
|
| |
|
| Submission date |
Dec 17, 2014 |
| Last update date |
Jun 19, 2015 |
| Contact name |
Enrique Carrillo de Santa Pau |
| E-mail(s) |
enrique.carrillo@imdea.org
|
| Organization name |
Spanish National Cancer Research Centre (CNIO)
|
| Department |
Cancer Cell Biology Programme
|
| Lab |
Epithelial Carcinogenesis group
|
| Street address |
C/ Melchor Fernández Almagro, 3
|
| City |
Madrid |
| ZIP/Postal code |
28029 |
| Country |
Spain |
| |
|
| Platform ID |
GPL96 |
| Series (2) |
| GSE64279 |
The UBC-40 Urothelial Bladder Cancer Cell Line Index [gene expression] |
| GSE64573 |
The UBC-40 Urothelial Bladder Cancer Cell Line Index |
|
