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Sample GSM5175636 Query DataSets for GSM5175636
Status Public on Jun 03, 2021
Title prostate_cancer_primary_1146
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.1146
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 0.433184942
2315633 0.123491084230769
2315674 0.0749709487719298
2315739 0.49660552137931
2315894 0.06169784
2315918 0.577687865
2315951 -0.0856999311764706
2316218 0.3774687325
2316245 0.6048943144
2316379 0.632333174920635
2316558 1.3106431309375
2316605 -0.0182597884705882
2316746 0.548256055
2316905 -0.25115031625
2316953 0.0330917399065421
2317246 0.118682528372093
2317317 -0.0591561119298246
2317434 0.69143846
2317472 0.107059297857143
2317512 0.0812808130952381

Total number of rows: 22011

Table truncated, full table size 511 Kbytes.




Supplementary file Size Download File type/resource
GSM5175636_1146.CEL.gz 21.8 Mb (ftp)(http) CEL
Processed data included within Sample table
Processed data are available on Series record

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