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Sample GSM5174779 Query DataSets for GSM5174779
Status Public on Jun 03, 2021
Title prostate_cancer_primary_289
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: Lower
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.289
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 0.342836528857143
2315633 -0.0245379853846154
2315674 0.0538135947368421
2315739 0.29469140862069
2315894 -0.13993431375
2315918 0.7142092925
2315951 -0.304383641176471
2316218 0.2777930775
2316245 0.5164635112
2316379 0.666510997936508
2316558 1.09398470125
2316605 -0.0719580238823529
2316746 0.549805974166667
2316905 -0.319896788125
2316953 -0.00321690429906542
2317246 0.0420680309302326
2317317 -0.0284677942105263
2317434 0.488258595
2317472 0.12262823875
2317512 0.0608535678571429

Total number of rows: 22011

Table truncated, full table size 512 Kbytes.




Supplementary file Size Download File type/resource
GSM5174779_289.CEL.gz 23.0 Mb (ftp)(http) CEL
Processed data included within Sample table
Processed data are available on Series record

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