|
| Status |
Public on Jun 09, 2017 |
| Title |
ccRCC [G1_142] |
| Sample type |
genomic |
| |
|
| Source name |
clear cell renal cell carcinoma tissue
|
| Organism |
Homo sapiens |
| Characteristics |
tumour grading: G1
|
| Treatment protocol |
None
|
| Growth protocol |
Tissue samples were taken immediately after resection of the kidney and cryoconserved in liquid nitrogen.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
About 30 mg tissue was disrupted using mortar and pestle immersed in liquid nitrogen. Genomic DNA was extracted with the QIAamp® DNA Mini Kit (Qiagen, Hilden) according to the manufacturers protocol.
|
| Label |
Biotin
|
| Label protocol |
As per manufacturer (Affymetrix)
|
| |
|
| Hybridization protocol |
DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.
|
| Scan protocol |
The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000.
|
| Description |
Hybridized to Genome-Wide Human SNP 6.0 Array
|
| Data processing |
The array image was acquired using Affymetrix GeneChip® Operating Software (GCOS version 1.4). Copy number values for individual SNPs were extracted and converted from CEL files into signal intensities using Genotyping Console 4.2.0. and Birdseed algoritm and Affymetrix Copy Number Analysis Tool (CNAT) softwares using default values.
|
| |
|
| Submission date |
Feb 23, 2017 |
| Last update date |
Jun 09, 2017 |
| Contact name |
Dirk Koczan |
| E-mail(s) |
dirk.koczan@med.uni-rostock.de
|
| Phone |
+493814945885
|
| Organization name |
University of Rostock
|
| Department |
Institute for Immunology
|
| Street address |
Schillingallee 70
|
| City |
Rostock |
| ZIP/Postal code |
18057 |
| Country |
Germany |
| |
|
| Platform ID |
GPL6801 |
| Series (1) |
| GSE95239 |
Stratification of clear cell renal cell carcinoma (ccRCC) genomes by gene-directed copy number alteration (CNA) analysis |
|
