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Sample GSM5174589 Query DataSets for GSM5174589
Status Public on Jun 03, 2021
Title prostate_cancer_primary_99
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: 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.99
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 0.322450818571429
2315633 0.161876169615385
2315674 -0.0144823192982456
2315739 0.286675035517241
2315894 -0.12671960125
2315918 0.30672827
2315951 -0.315209083529412
2316218 0.1808822
2316245 0.5011850708
2316379 0.355869988888889
2316558 1.3174243125
2316605 -0.090894648
2316746 0.55158393875
2316905 -0.339609555
2316953 -0.0208651862616822
2317246 -0.00964200674418605
2317317 -0.0798709824561404
2317434 0.429911666875
2317472 0.0636699401785714
2317512 0.0232877135714286

Total number of rows: 22011

Table truncated, full table size 511 Kbytes.




Supplementary file Size Download File type/resource
GSM5174589_99.CEL.gz 21.9 Mb (ftp)(http) CEL
Processed data included within Sample table
Processed data are available on Series record

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