|
| Status |
Public on Dec 31, 2022 |
| Title |
Muscle-invasive bladder cancer [C8539T1PTa] |
| Sample type |
RNA |
| |
|
| Source name |
Anonymised
|
| Organism |
Homo sapiens |
| Characteristics |
disease: Muscle-invasive bladder cancer
|
| Treatment protocol |
None
|
| Growth protocol |
None
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Two 10µm sections from FFPE bladder cancer embodied blocks. RNA was extracted from the two 10 µm sections using the Roche High Pure FFPET RNA isolation kit. RNA yield was determined on Qubit fluorometer (Invitrogen, Paisley, UK).
|
| Label |
None
|
| Label protocol |
RNA extracted from both sample cohorts were subject to Clariom S analysis. RNA (8 ng/µl in a 9 µl volume) was prepared for gene expression arrays with the Clariom S pico HT human assay (Thermo Fisher Scientific).
|
| |
|
| Hybridization protocol |
Sample hybridisation on Clariom S arrays was carried out by Yourgene Health (Manchester, UK). Batches of CEL files were GC SST (Signal Space Transformation with probe Guanine Cytosine Count Correction) RNA normalised using Affymetrix Array Power Tools. (https://www.thermofisher.com/uk/en/home/life-science/microarray-analysis/microarray-analysis-partners-programs/affymetrix-developers-network.html)
|
| Scan protocol |
None
|
| Data processing |
The log2-summarised gene level expression values generated were batch-corrected using the ComBat function from the Bioconductor package sva.
|
| |
|
| Submission date |
May 17, 2022 |
| Last update date |
Dec 31, 2022 |
| Contact name |
Tim Smith |
| E-mail(s) |
[email protected]
|
| Organization name |
University of Bangor
|
| Department |
School of Computer Science and Engineering
|
| Lab |
Nuclear Futures Institute
|
| Street address |
Dean Street
|
| City |
Bangor |
| ZIP/Postal code |
LL57 2DG |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL24324 |
| Series (1) |
| GSE203149 |
Gene expression data from muscle-invasive bladder cancer samples |
|
