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Sample GSM5174900 Query DataSets for GSM5174900
Status Public on Jun 03, 2021
Title prostate_cancer_primary_410
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.410
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 0.302721441142857
2315633 -0.0379040896153846
2315674 0.0212660461403509
2315739 0.0738375620689655
2315894 0.32613226625
2315918 0.5488627875
2315951 -0.177319407058824
2316218 0.34677505
2316245 0.1330143976
2316379 0.39996270984127
2316558 0.8034441025
2316605 -0.08287539
2316746 0.383630858333333
2316905 -0.147939928125
2316953 0.138238518598131
2317246 -0.0123964527906977
2317317 -0.0271740935087719
2317434 0.4228621475
2317472 0.153536674642857
2317512 0.0290289857142857

Total number of rows: 22011

Table truncated, full table size 513 Kbytes.




Supplementary file Size Download File type/resource
GSM5174900_410.CEL.gz 19.4 Mb (ftp)(http) CEL
Processed data included within Sample table
Processed data are available on Series record

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