|
| Status |
Public on Jun 03, 2021 |
| Title |
prostate_cancer_primary_454 |
| Sample type |
RNA |
| |
|
| Source name |
FFPE prostate cancer
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: FFPE prostate cancer
primary gleason: 3
secondary gleason: 4
decipher risk group: Lower
race: African American
|
| 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
|
| Description |
PCA.454
|
| 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 |
Mar 16, 2021 |
| Last update date |
Jun 03, 2021 |
| 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 |
GPL5175 |
| Series (1) |
| GSE169038 |
Comparative Analysis of 1,152 African-American and European-American Men with Prostate Cancer Identifies Distinct Genomic and Immunological Differences |
|
