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Sample GSM5174606 Query DataSets for GSM5174606
Status Public on Jun 03, 2021
Title prostate_cancer_primary_116
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: 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.116
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 0.390443764285714
2315633 0.133858656153846
2315674 0.0404069398245614
2315739 0.17001003862069
2315894 -0.097395735
2315918 0.516683025
2315951 -0.145229188823529
2316218 0.0591543275
2316245 0.588038877
2316379 0.360976201587302
2316558 1.0144977425
2316605 -0.00939201952941176
2316746 0.517996787916667
2316905 -0.360914253125
2316953 0.00144253121495327
2317246 0.0434767855813954
2317317 0.000520598947368417
2317434 0.3713572465625
2317472 0.113837222857143
2317512 0.0299977121428571

Total number of rows: 22011

Table truncated, full table size 512 Kbytes.




Supplementary file Size Download File type/resource
GSM5174606_116.CEL.gz 21.4 Mb (ftp)(http) CEL
Processed data included within Sample table
Processed data are available on Series record

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