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Sample GSM5174537 Query DataSets for GSM5174537
Status Public on Jun 03, 2021
Title prostate_cancer_primary_47
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: 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.47
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 0.304647504571429
2315633 0.136912397692308
2315674 0.0485793647368421
2315739 0.190022562413793
2315894 -0.00884037625000001
2315918 0.1275721
2315951 -0.137076679411765
2316218 0.0150799925
2316245 0.5074571034
2316379 0.326485760952381
2316558 0.92073431375
2316605 -0.00121559917647059
2316746 0.475338230416667
2316905 -0.360201385625
2316953 -0.00670150037383178
2317246 0.0130387190697674
2317317 -0.0734047049122807
2317434 0.3374137596875
2317472 0.00276116464285714
2317512 -0.0930787183333333

Total number of rows: 22011

Table truncated, full table size 513 Kbytes.




Supplementary file Size Download File type/resource
GSM5174537_47.CEL.gz 20.4 Mb (ftp)(http) CEL
Processed data included within Sample table
Processed data are available on Series record

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