|
| Status |
Public on Jul 01, 2013 |
| Title |
prostate_cancer_primary_493 |
| Sample type |
RNA |
| |
|
| Source name |
primary prostate cancer FFPE tissue sample
|
| Organism |
Homo sapiens |
| Characteristics |
gleason score: 7
metastatic event: 1
|
| Treatment protocol |
not applicable
|
| Growth protocol |
not applicable
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted from four 10 um FFPE sections. The highest Gleason grade was macrodissected from surrounding non-neoplastic cells, guided by an H&E stained slide for tumor identification. RNA was extracted and purified using the Roche HighPure FFPE kit.
|
| Label |
biotin
|
| Label protocol |
RNA was amplified, fragmented and biotinylated using the Ovation FFPE system v 2.0 (NuGEN)
|
| |
|
| Hybridization protocol |
Samples were hybridized using Affymetrix hybridization kit materials and protocols
|
| Scan protocol |
Affymetrix Gene ChIP Scanner 3000 7G
|
| Description |
GBX.DISC.PCA493
|
| Data processing |
Data were processed using fRMA package (v.1.4.0) and Bioconductor (v.2.8). The data matrix (available on Series records) contains quantile normalized PSR (probe selection regions) level expression values from fRMA.
probe group file: HuEx-1_0-st-v1.r2.pgf
|
| |
|
| Submission date |
May 07, 2013 |
| Last update date |
Jul 01, 2013 |
| Contact name |
Elai Davicioni |
| E-mail(s) |
elai.davicioni@veracyte.com
|
| Organization name |
Veracyte, Inc
|
| Street address |
9725 Lusk Blvd
|
| City |
San Diego |
| State/province |
California |
| ZIP/Postal code |
92121 |
| Country |
USA |
| |
|
| Platform ID |
GPL5188 |
| Series (1) |
| GSE46691 |
Discovery and validation of a prostate cancer genomic classifier that predicts early metastasis following radical prostatectomy |
|
