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Sample GSM5174531 Query DataSets for GSM5174531
Status Public on Jun 03, 2021
Title prostate_cancer_primary_41
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: White (Non-Hispanic)
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.41
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 0.324966822857143
2315633 -0.0571509696153846
2315674 -0.0597842836842105
2315739 0.260313372413793
2315894 -0.52876717125
2315918 0.8720823225
2315951 -0.468282975882353
2316218 0.490368225
2316245 0.3527842126
2316379 0.228142703809524
2316558 1.0731432665625
2316605 -0.133355433294118
2316746 0.380049454166667
2316905 -0.347819071875
2316953 -0.0462610982242991
2317246 -0.0619979909302326
2317317 -0.169358561052632
2317434 0.248605545
2317472 0.0716925257142857
2317512 -0.0554840342857143

Total number of rows: 22011

Table truncated, full table size 513 Kbytes.




Supplementary file Size Download File type/resource
GSM5174531_41.CEL.gz 22.1 Mb (ftp)(http) CEL
Processed data included within Sample table
Processed data are available on Series record

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