|
| Status |
Public on Jun 07, 2024 |
| Title |
DNA methylation data of ccRCC tumor 28 |
| Sample type |
genomic |
| |
|
| Source name |
ccRCC tumor 28
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: ccRCC tumor 28
age: 57
Sex: Male
batch: Batch1
|
| Treatment protocol |
Not applicable.
|
| Growth protocol |
Not applicable.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA was isolated from tumor samples using the Flexigene DNA isolation kit from Qiagen as per manufacturer’s protocol and stored in aliquots at −20 °C.
|
| Label |
Cy5 and Cy3
|
| Label protocol |
Standard Illumina Protocol
|
| |
|
| Hybridization protocol |
The DNA (600 ng) of samples underwent pre-processing steps as follows: bisulfite-conversion, whole-genome amplification, fragmentation, and hybridization with complementary probes sequences on The Infinium MethylationEPIC BeadChip v1 using standard Illumina protocol.
|
| Scan protocol |
iScan system scanner (Ilumina) and probe intensities were obtained by GenomeStudio Software ((Ilumina)
|
| Description |
clear clear renal carcinoma tumor, high-quality sample
206402350127_R04C01
|
| Data processing |
The processing steps of probes were performed using the implemented functions in methylkey R package (https://github.com/IARCbioinfo/methylkey). Version 0.1.1.9000
tab-delimited file with a matrix of 121 samples as cols and 792,697 normalised (Funnorm) average beta values as rows. File named as 'MatrixProcessed.tsv',
Unmethylated and methylated signal intensities uploaded as 'rawdata2Geo.tsv' and unprocessed betas as 'betas2Geo.tsv'
|
| |
|
| Submission date |
Jun 05, 2024 |
| Last update date |
Jun 07, 2024 |
| Contact name |
James Mckay |
| E-mail(s) |
mckay@iarc.fr
|
| Organization name |
IARC - International Agency for Research on Cancer
|
| Street address |
25 Av. Tony Garnier
|
| City |
Lyon |
| ZIP/Postal code |
69007 |
| Country |
France |
| |
|
| Platform ID |
GPL21145 |
| Series (1) |
| GSE269180 |
Understanding the biological processes of clear cell renal carcinoma carcinogenesis: an integrative multi-omics approach. |
|
