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Sample GSM5174618 Query DataSets for GSM5174618
Status Public on Jun 03, 2021
Title prostate_cancer_primary_128
Sample type RNA
 
Source name FFPE prostate cancer
Organism Homo sapiens
Characteristics tissue: FFPE prostate cancer
primary gleason: 3
secondary gleason: 3
decipher risk group: Average
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.128
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 0.331905663428571
2315633 -0.0370478892307692
2315674 -0.0339423163157895
2315739 0.113626606896552
2315894 -0.14224317125
2315918 0.5522077
2315951 -0.335901808235294
2316218 0.12062811
2316245 0.5629754794
2316379 0.305625025238095
2316558 1.156905260625
2316605 -0.0316045927058824
2316746 0.523475864583333
2316905 -0.19005395125
2316953 -0.0460296536448598
2317246 0.0511426723255814
2317317 -0.108339618947368
2317434 0.27620958125
2317472 0.0350914751785714
2317512 0.00555886904761905

Total number of rows: 22011

Table truncated, full table size 513 Kbytes.




Supplementary file Size Download File type/resource
GSM5174618_128.CEL.gz 21.3 Mb (ftp)(http) CEL
Processed data included within Sample table
Processed data are available on Series record

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