|
| Status |
Public on Jun 10, 2012 |
| Title |
ccRCC tumor of patient 260 |
| Sample type |
RNA |
| |
|
| Source name |
Gene expression profiling of clear-cell renal cell carcinoma (ccRCC) tumor of patient 260
|
| Organism |
Homo sapiens |
| Characteristics |
patient id: 260
tissue: Clear-cell renal cell carcinoma (ccRCC) tumor
gender: Female
age: n/a
disease state: Clear-cell renal cell carcinoma
pathologic tnm staging: T1N0Mx
Stage: n/a
fuhrman grade: 2
bap1 status: wild type
pbrm1 status: wild type
vhl status: mutant
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Tissues were homogenized with an RNase-free pestle alternating freeze/thaw cycles and subsequently passed through a QIAshredder column (Qiagen). RNA fraction was extracted using mirVana (Ambion) kit.
|
| Label |
Biotin
|
| Label protocol |
RNA was reverse-transcribed and biotin-labeled using Affymetrix one-cycle cDNA synthesis and IVT labeling kits (Affymetrix).
|
| |
|
| Hybridization protocol |
Arrays were washed and hybridized using Affymetrix Fluidics Station 450.
|
| Scan protocol |
Arrays were scanned using Affymetrix GeneChip Scanner 3000 7G.
|
| Data processing |
CEL files were pre-processed and normalized using the RMA algorithm through the Affy package of R/Bioconductor.
|
| |
|
| Submission date |
Mar 28, 2012 |
| Last update date |
Jun 10, 2012 |
| Contact name |
Samuel Peña-Llopis |
| E-mail(s) |
Samuel.Pena-Llopis@UTSouthwestern.edu, James.Brugarolas@UTSouthwestern.edu
|
| Phone |
(01) 214-648-4099
|
| Fax |
(01) 214-648-1960
|
| Organization name |
UT Southwestern Medical Center
|
| Department |
Internal Medicine - Oncology Division
|
| Lab |
Brugarolas Lab
|
| Street address |
6000 Harry Hines Blvd., NB5.102
|
| City |
Dallas |
| State/province |
TX |
| ZIP/Postal code |
75390-9133 |
| Country |
USA |
| |
|
| Platform ID |
GPL570 |
| Series (1) |
| GSE36895 |
Molecular Genetic Classification of clear-cell Renal Cell Carcinoma (ccRCC) based on the Gene Expression Profiling of Tumors and Tumorgrafts deficient for BAP1 or PBRM1 |
|
