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Sample GSM5174902 Query DataSets for GSM5174902
Status Public on Jun 03, 2021
Title prostate_cancer_primary_412
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: Higher
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.412
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 0.143061207142857
2315633 0.0218986534615385
2315674 0.00926867333333333
2315739 0.246440666206897
2315894 0.0910967
2315918 0.85684468
2315951 -0.292610938235294
2316218 0.48502595
2316245 0.1737358722
2316379 0.206502604285714
2316558 0.6837736734375
2316605 0.0905700098823529
2316746 0.21230439125
2316905 -0.094712010625
2316953 0.0407182478504673
2317246 -0.0553289469767442
2317317 0.00106984333333333
2317434 0.1543442221875
2317472 0.0388548021428572
2317512 -0.100239599285714

Total number of rows: 22011

Table truncated, full table size 515 Kbytes.




Supplementary file Size Download File type/resource
GSM5174902_412.CEL.gz 17.1 Mb (ftp)(http) CEL
Processed data included within Sample table
Processed data are available on Series record

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