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Sample GSM5174653 Query DataSets for GSM5174653
Status Public on Jun 03, 2021
Title prostate_cancer_primary_163
Sample type RNA
 
Source name FFPE prostate cancer
Organism Homo sapiens
Characteristics tissue: FFPE prostate cancer
primary gleason: 3
secondary gleason: 4
decipher risk group: Higher
race: African American
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.163
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 0.22962921
2315633 -0.213790428076923
2315674 -0.187300322807018
2315739 0.0722239134482759
2315894 -0.709569435
2315918 0.623994235
2315951 -0.563357657058824
2316218 0.1743453575
2316245 -0.0214842044
2316379 0.0118530866666667
2316558 0.54213171125
2316605 -0.232454972705882
2316746 0.174635944166667
2316905 -0.499242065625
2316953 -0.0679354254205607
2317246 -0.13848471
2317317 -0.193049951403509
2317434 -0.0758073765625
2317472 -0.0110412364285714
2317512 -0.168130806666667

Total number of rows: 22011

Table truncated, full table size 515 Kbytes.




Supplementary file Size Download File type/resource
GSM5174653_163.CEL.gz 22.5 Mb (ftp)(http) CEL
Processed data included within Sample table
Processed data are available on Series record

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