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Sample GSM5174795 Query DataSets for GSM5174795
Status Public on Jun 03, 2021
Title prostate_cancer_primary_305
Sample type RNA
 
Source name FFPE prostate cancer
Organism Homo sapiens
Characteristics tissue: FFPE prostate cancer
primary gleason: 4
secondary gleason: 3
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.305
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 0.204881675142857
2315633 0.0250739734615385
2315674 -0.0684102098245614
2315739 0.297045001034483
2315894 0.07882559
2315918 0.2130054875
2315951 -0.148667487647059
2316218 0.05518553
2316245 0.618268378
2316379 0.480240057619048
2316558 1.1654621340625
2316605 -0.0745127223529412
2316746 0.420426995833333
2316905 -0.5473994625
2316953 -0.071097056635514
2317246 0.111392489767442
2317317 -0.124046119298246
2317434 0.5192518865625
2317472 -0.113244101964286
2317512 -0.0525108414285714

Total number of rows: 22011

Table truncated, full table size 511 Kbytes.




Supplementary file Size Download File type/resource
GSM5174795_305.CEL.gz 23.2 Mb (ftp)(http) CEL
Processed data included within Sample table
Processed data are available on Series record

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