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Sample GSM5174894 Query DataSets for GSM5174894
Status Public on Jun 03, 2021
Title prostate_cancer_primary_404
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: 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.404
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 0.257650471428571
2315633 0.0243573903846154
2315674 -0.0194782036842105
2315739 0.332039342068966
2315894 0.05038960125
2315918 0.1469523
2315951 -0.358808374117647
2316218 0.3022808675
2316245 0.5560265684
2316379 0.513712168888889
2316558 0.8920074340625
2316605 -0.0904007978823529
2316746 0.38886429375
2316905 -0.456663869375
2316953 -0.020132736728972
2317246 0.101946951860465
2317317 -0.107036057368421
2317434 0.47035029625
2317472 0.0288209773214286
2317512 -0.224782169047619

Total number of rows: 22011

Table truncated, full table size 512 Kbytes.




Supplementary file Size Download File type/resource
GSM5174894_404.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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