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Sample GSM5174632 Query DataSets for GSM5174632
Status Public on Jun 03, 2021
Title prostate_cancer_primary_142
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: 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.142
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 0.334091407428571
2315633 -0.00126652307692308
2315674 0.0568811754385965
2315739 0.135620616206897
2315894 0.34780865
2315918 0.763460515
2315951 -0.175454790588235
2316218 0.3367910925
2316245 0.286794082
2316379 0.178879057619048
2316558 0.5463132903125
2316605 0.0500562323529412
2316746 0.226762304583333
2316905 -0.243183513125
2316953 -0.0050167085046729
2317246 0.0336131888372093
2317317 -0.0827506614035088
2317434 0.1399317146875
2317472 0.0344148571428571
2317512 -0.00113553523809524

Total number of rows: 22011

Table truncated, full table size 517 Kbytes.




Supplementary file Size Download File type/resource
GSM5174632_142.CEL.gz 19.6 Mb (ftp)(http) CEL
Processed data included within Sample table
Processed data are available on Series record

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