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Sample GSM5174799 Query DataSets for GSM5174799
Status Public on Jun 03, 2021
Title prostate_cancer_primary_309
Sample type RNA
 
Source name FFPE prostate cancer
Organism Homo sapiens
Characteristics tissue: FFPE prostate cancer
primary gleason: 5
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.309
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 0.173759793428571
2315633 0.0286989884615385
2315674 -0.127133625087719
2315739 0.177773460689655
2315894 -0.17524809625
2315918 0.3803500125
2315951 -0.274547669411765
2316218 0.10518312
2316245 0.192823258
2316379 0.510359763968254
2316558 0.9881491946875
2316605 -0.104534295529412
2316746 0.263270718333333
2316905 -0.549589350625
2316953 -0.0716496456074766
2317246 -0.109224111860465
2317317 -0.187436069122807
2317434 0.52119191375
2317472 -0.0547755580357143
2317512 -0.0562340116666667

Total number of rows: 22011

Table truncated, full table size 512 Kbytes.




Supplementary file Size Download File type/resource
GSM5174799_309.CEL.gz 23.3 Mb (ftp)(http) CEL
Processed data included within Sample table
Processed data are available on Series record

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