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Sample GSM5174545 Query DataSets for GSM5174545
Status Public on Jun 03, 2021
Title prostate_cancer_primary_55
Sample type RNA
 
Source name FFPE prostate cancer
Organism Homo sapiens
Characteristics tissue: FFPE prostate cancer
primary gleason: --
secondary gleason: --
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.55
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 0.217856243714286
2315633 -0.0325937838461538
2315674 0.106600235789474
2315739 0.22465271137931
2315894 0.05172106375
2315918 -0.0834006
2315951 -0.249083998823529
2316218 0.46267572
2316245 0.1650177418
2316379 0.455050746507937
2316558 0.80711631125
2316605 0.0612426188235294
2316746 0.574938950833333
2316905 -0.23892020375
2316953 0.0407380898130841
2317246 0.0259925286046512
2317317 -0.0476094878947368
2317434 0.4280090759375
2317472 0.0998134346428571
2317512 -0.0164893364285714

Total number of rows: 22011

Table truncated, full table size 514 Kbytes.




Supplementary file Size Download File type/resource
GSM5174545_55.CEL.gz 18.2 Mb (ftp)(http) CEL
Processed data included within Sample table
Processed data are available on Series record

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