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Sample GSM5174525 Query DataSets for GSM5174525
Status Public on Jun 03, 2021
Title prostate_cancer_primary_35
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.35
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 0.333963671428571
2315633 0.0183970553846154
2315674 -0.0418630803508772
2315739 0.212260437931034
2315894 -0.08194562125
2315918 0.7047918875
2315951 -0.383357949411765
2316218 0.5066097575
2316245 0.3362857818
2316379 0.212342634920635
2316558 0.854981796875
2316605 0.0249648071764706
2316746 0.582915862916667
2316905 -0.2278414925
2316953 0.0187888248598131
2317246 0.0299110555813953
2317317 -0.0894341966666667
2317434 0.2552319184375
2317472 0.102655795714286
2317512 0.11623585952381

Total number of rows: 22011

Table truncated, full table size 514 Kbytes.




Supplementary file Size Download File type/resource
GSM5174525_35.CEL.gz 20.3 Mb (ftp)(http) CEL
Processed data included within Sample table
Processed data are available on Series record

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