|
| Status |
Public on Jan 23, 2012 |
| Title |
36_pT3 |
| Sample type |
RNA |
| |
|
| Source name |
Bladder Cancer
|
| Organism |
Homo sapiens |
| Characteristics |
gender: male
preopclinstage: T2
age at rc: 84.48
survival.months: 3.383984
rc_stage: pT3
rc_histology: TCC
plnd result: Nx
rc grade: High
nomogram score: 38.24540238
distant mets: 0
local recurrence: 0
urothelial recurrence: 0
metastasis: 0
last known status: NED
prerc_chemo: No
post rc_chemo: No
smoking: Former
smokingpack-years: 40
recurrence free survival months (distant and local): 3.383984
recurrence/dod: No
cluster: 2
|
| Treatment protocol |
Frozen bladder tissues were examined by a genitourinary pathologist to identify tumor content, which was microdissected. Ten 50-um sections were cut, with confirmation of tumor content by pathologic review.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated with Trizol (Invitrogen) and RNA was cleaned with Rneasy mini kits (Qiagen) according to manufacturer protocols
|
| Label |
biotin
|
| Label protocol |
Expression profiling was performed in the MSKCC Genomics Core Facility. In brief, 5-10 ug of RNA was transcribed utilizing a T7-oligo dT primer and converted to cDNA (Invitrogen cDNA synthesis kit). Biotinylated aRNA was produced from the cDNA using an in vitro transcription kit (Enzo Diagnostics).
|
| |
|
| Hybridization protocol |
Following quality assessment using an Agilent Bioanalyzer, the aRNA was fragmented and hybridized onto Affymetrix U133 Plus 2.0 arrays
|
| Scan protocol |
Standard Affymetrix protocol.
|
| Data processing |
Expression estimates were obtained with GCRMA from Bioconductor with default parameters.
|
| |
|
| Submission date |
Aug 26, 2011 |
| Last update date |
Apr 30, 2012 |
| Contact name |
Markus Riester |
| E-mail(s) |
[email protected]
|
| Organization name |
Dana-Farber Cancer Institute
|
| Department |
Biostatistics & Computational Biology
|
| Lab |
Michor
|
| Street address |
3 Blackfan Circle
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02115 |
| Country |
USA |
| |
|
| Platform ID |
GPL570 |
| Series (1) |
| GSE31684 |
Combination of a novel gene expression signature with a clinical nomogram improves the prediction of survival in high-risk bladder cancer |
|
