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Sample GSM5174826 Query DataSets for GSM5174826
Status Public on Jun 03, 2021
Title prostate_cancer_primary_336
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.336
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 0.190029834571429
2315633 -0.197360480384615
2315674 -0.17531144754386
2315739 0.0660671334482759
2315894 -0.51901441
2315918 0.525558575
2315951 -0.455466241176471
2316218 0.60084314
2316245 0.2685342294
2316379 0.104569426031746
2316558 0.941108995
2316605 -0.241141648
2316746 0.192294855833333
2316905 -0.501371375625
2316953 -0.13352743271028
2317246 -0.090864868372093
2317317 -0.280111341052632
2317434 0.2024217621875
2317472 -0.00435752517857143
2317512 -0.150405054047619

Total number of rows: 22011

Table truncated, full table size 515 Kbytes.




Supplementary file Size Download File type/resource
GSM5174826_336.CEL.gz 21.5 Mb (ftp)(http) CEL
Processed data included within Sample table
Processed data are available on Series record

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