|
| Status |
Public on Sep 30, 2020 |
| Title |
RCC-Chromophobe (chRCC_2) |
| Sample type |
genomic |
| |
|
| Source name |
RCC-Chromophobe
|
| Organism |
Homo sapiens |
| Characteristics |
gender: Male
sample type: renal cell carcinoma-chromophobe
age: 69
race: white
tumor size: 4.1
pathologic stage: pT1b
patient: 2
|
| Treatment protocol |
None
|
| Growth protocol |
None
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA was extracted from fresh frozen tissue samples using the Qiagen DNA Mini kit
|
| Label |
Cy5 and Cy3
|
| Label protocol |
Standard Illumina Protocol
|
| |
|
| Hybridization protocol |
Bisulphite converted DNA was amplified, fragmented and hybridized to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol
|
| Scan protocol |
Illumina HiScan
|
| Description |
RCC-Chromophobe
|
| Data processing |
Raw 450k array data was extracted using GenomeStudio. Methylation data preprocessing was performed using the minfi R package (15). CpGs with missing data in more than ten percent of patient samples (n= 2371 CpG sites) were discarded.
|
| |
|
| Submission date |
Aug 26, 2020 |
| Last update date |
Oct 01, 2020 |
| Contact name |
Caroline Dive |
| E-mail(s) |
caroline.dive@cruk.manchester.ac.uk
|
| Organization name |
Cancer Research UK Manchester Institute
|
| Street address |
Cancer Research UK Manchester Institute, The University of Manchester, Wilmslow Road
|
| City |
Manchester |
| ZIP/Postal code |
M20 4BX |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL13534 |
| Series (1) |
| GSE156932 |
Development of a DNA methylation-based diagnostic signature to distinguish benign oncocytoma from renal cell carcinoma |
|
