|
| Status |
Public on May 01, 2022 |
| Title |
FFPE prostate_cancer_primary_22 |
| Sample type |
RNA |
| |
|
| Source name |
FFPE prostate cancer
|
| Organism |
Homo sapiens |
| Characteristics |
primary gleason: 3
secondary gleason: 4
pre-treatment psa (ng/ml): 195
age: 56
race: Caucasian
randomization arm: Placebo
ecog3805 id: 1131090
|
| Treatment protocol |
Not Applicable
|
| Growth protocol |
Not Applicable
|
| Extracted molecule |
total RNA |
| Extraction protocol |
After histopathologic review of formalin-fixed, paraffin-embedded (FFPE) tumor blocks from each case by an expert pathologists, the tumor block with the index lesion was selected for specimen processing. The index lesion was identified as the prostatectomy FFPE block with the highest pathologic Gleason grade, regardless of its volume. Two 0.6-mm diameter tissue biopsy punch tool cores were sampled to enrich for tumor cells from the highest Gleason grade in the index lesion and placed in a microfuge tube for RNA extraction.
|
| Label |
biotin
|
| Label protocol |
RNA was amplified, fragmented and biotinylated using the WT-Ovation FFPE system (NuGen, San Carlos, CA) according to the manufacturer’s recommendations with minor modifications
|
| |
|
| Hybridization protocol |
Samples were hybridized using Affymetrix hybridization kit materials and protocols
|
| Scan protocol |
Affymetrix Gene ChIP Scanner 3000 7G
|
| Data processing |
Data was normalized uisng SCAN (SCAN.UPC package from Bioconductor)
HuEx-1_0-st-v2.r2.pgf
HuEx-1_0-st-v2.r2.dt1.hg38.core.mps
|
| |
|
| Submission date |
Apr 28, 2022 |
| Last update date |
May 01, 2022 |
| Contact name |
Elai Davicioni |
| E-mail(s) |
[email protected]
|
| Organization name |
Veracyte, Inc
|
| Street address |
9725 Lusk Blvd
|
| City |
San Diego |
| State/province |
California |
| ZIP/Postal code |
92121 |
| Country |
USA |
| |
|
| Platform ID |
GPL5175 |
| Series (1) |
| GSE201805 |
Transcriptional profiling of primary prostate tumor in metastatic hormonesensitive prostate cancer and association with clinical outcomes: correlative analysis of the E3805 CHAARTED study |
|
