|
| Status |
Public on Jul 01, 2014 |
| Title |
ccRCC tumor 2.01 |
| Sample type |
genomic |
| |
|
| Source name |
clear cell renal cell carcinoma
|
| Organism |
Homo sapiens |
| Characteristics |
tumor stage: un-metastasized tumor
gender: Female
tissue: Kidney
disease state: carcinoma
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Extraction of genomic DNA was done using a BioRobot M48 Workstation with MagAttract technology (Qiagen)
|
| Label |
A-DNP, C-Bio
|
| Label protocol |
200 ng of genomic DNA was whole-genome amplified in an overnight reaction at 37¡C using amplification master mix (WG-MSM). After incubation the amplified DNA was fragmented with fragmentation mix (WG-FMS), precipitated with isopropanol and precipitation mix (PM1) and resuspended in hybridization buffer (RA1).
|
| |
|
| Hybridization protocol |
RA1 resuspended DNA was loaded onto BeadChips arrays. After overnight incubation at 48¡C, single-base extension and allele-specific staining was performed on a Teflow chamber rack system (Tecan, Maennedorf, Switzerland).
|
| Scan protocol |
After allele-specific staining BeadChip arrays were coated with XC4/ethanol , dried for 1 hour and scanned on a BeadArray Reader (Illumina).
|
| Description |
Genomic DNA extracted from clear cell renal cell carcinoma tumors was genotyped using Infinium HumanCytoSNP-12 v2.1 BeadChips (Illumina).
|
| Data processing |
Genomic DNA extracted from clear cell renal cell carcinoma was genotyped using Infinium HumanCytoSNP-12 v2.1 BeadChips (Illumina).
|
| |
|
| Submission date |
Jul 06, 2011 |
| Last update date |
Jul 01, 2014 |
| Contact name |
Linda Köhn |
| E-mail(s) |
linda.kohn@medbio.umu.se
|
| Phone |
+46907852873
|
| Organization name |
Umeå University
|
| Department |
Medical Biosciences/pathology
|
| Street address |
Building 6M
|
| City |
Umeå |
| ZIP/Postal code |
90185 |
| Country |
Sweden |
| |
|
| Platform ID |
GPL13829 |
| Series (1) |
| GSE30460 |
Genomic aberrations predicts survival in clear cell renal cell carcinoma |
|
