|
| Status |
Public on Nov 18, 2020 |
| Title |
PCA.530: prostate_cancer_primary_530 |
| Sample type |
RNA |
| |
|
| Source name |
FFPE prostate cancer
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: FFPE prostate cancer
age: 54
psa: 9.7
grade group: 2
non-organ confined: Yes
plasma cell content: 1231.21899442749
inflammation signature: -0.523274870855516
ifng signature: 0.856228297036735
igg production: 5.3441777489908
nk activity: 0.85793816177183
|
| Extracted molecule |
total RNA |
| Extraction protocol |
After histopathologic review of formalin-fixed, paraffin-embedded (FFPE) tumor blocks from each case by 2 expert genitourinary 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.530
|
| 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 |
Sep 05, 2020 |
| Last update date |
Nov 18, 2020 |
| Contact name |
Elai Davicioni |
| E-mail(s) |
elai@decipherbio.com
|
| Organization name |
Decipher Biosciences, Inc.
|
| Street address |
1152 Mainland St, Suite 430
|
| City |
Vancouver |
| State/province |
BC |
| ZIP/Postal code |
V6B 4X2 |
| Country |
Canada |
| |
|
| Platform ID |
GPL5175 |
| Series (2) |
| GSE157547 |
Plasma cells are enriched in localized prostate cancer in black men and are associated with improved outcomes [Validation Cohort] |
| GSE157548 |
Plasma cells are enriched in localized prostate cancer in black men and are associated with improved outcomes |
|
