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Sample GSM5174910 Query DataSets for GSM5174910
Status Public on Jun 03, 2021
Title prostate_cancer_primary_420
Sample type RNA
 
Source name FFPE prostate cancer
Organism Homo sapiens
Characteristics tissue: FFPE prostate cancer
primary gleason: 4
secondary gleason: 4
decipher risk group: Lower
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.420
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 0.282469436
2315633 -0.0958849373076923
2315674 -0.00253657350877193
2315739 0.267697157586207
2315894 -0.4240287475
2315918 0.518374535
2315951 -0.407781839411765
2316218 0.26092928
2316245 0.3026762384
2316379 0.178663581269841
2316558 0.8333766340625
2316605 -0.0277067055294118
2316746 0.390097449583333
2316905 -0.154053305625
2316953 -0.00815764598130841
2317246 0.00363034255813953
2317317 -0.0928023847368421
2317434 0.0897445290625
2317472 0.0932404475
2317512 -0.0606583980952381

Total number of rows: 22011

Table truncated, full table size 514 Kbytes.




Supplementary file Size Download File type/resource
GSM5174910_420.CEL.gz 20.6 Mb (ftp)(http) CEL
Processed data included within Sample table
Processed data are available on Series record

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