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Sample GSM5174573 Query DataSets for GSM5174573
Status Public on Jun 03, 2021
Title prostate_cancer_primary_83
Sample type RNA
 
Source name FFPE prostate cancer
Organism Homo sapiens
Characteristics tissue: FFPE prostate cancer
primary gleason: 4
secondary gleason: 5
decipher risk group: Higher
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.83
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 0.373731662
2315633 0.124349234615385
2315674 0.10553229
2315739 0.230906189310345
2315894 0.35267493375
2315918 0.589675695
2315951 0.0999501788235294
2316218 0.59648957
2316245 0.6719351386
2316379 0.440510090634921
2316558 0.994971008125
2316605 0.0394604384705882
2316746 0.438627694166667
2316905 -0.2272922025
2316953 0.0300407365420561
2317246 0.120545775116279
2317317 -0.0239810575438596
2317434 0.6224920765625
2317472 0.227767272857143
2317512 -0.0490001935714286

Total number of rows: 22011

Table truncated, full table size 513 Kbytes.




Supplementary file Size Download File type/resource
GSM5174573_83.CEL.gz 21.2 Mb (ftp)(http) CEL
Processed data included within Sample table
Processed data are available on Series record

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