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Sample GSM5174506 Query DataSets for GSM5174506
Status Public on Jun 03, 2021
Title prostate_cancer_primary_16
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: Average
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.16
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

Data table header descriptions
ID_REF
VALUE SCAN normalized signal estimates

Data table
ID_REF VALUE
2315554 0.422639074571429
2315633 0.137515141923077
2315674 0.149451492807018
2315739 0.355803725172414
2315894 0.0443469225
2315918 0.62915482
2315951 -0.216783719411765
2316218 0.26767376
2316245 0.4119012704
2316379 0.281796547936508
2316558 0.726908276875
2316605 0.0351446285882353
2316746 0.410874031666667
2316905 -0.06765976625
2316953 0.105325997943925
2317246 0.0829044634883721
2317317 -0.0643835452631579
2317434 0.3130919740625
2317472 0.118737374821429
2317512 -0.0156031771428571

Total number of rows: 22011

Table truncated, full table size 514 Kbytes.




Supplementary file Size Download File type/resource
GSM5174506_16.CEL.gz 18.7 Mb (ftp)(http) CEL
Processed data included within Sample table
Processed data are available on Series record

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