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Sample GSM5174938 Query DataSets for GSM5174938
Status Public on Jun 03, 2021
Title prostate_cancer_primary_448
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.448
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 0.463955850857143
2315633 0.117061831923077
2315674 0.0960985980701754
2315739 0.243978237586207
2315894 -0.21984536
2315918 0.5543146
2315951 -0.324309611764706
2316218 0.2223594075
2316245 0.3417304366
2316379 0.325603537301587
2316558 0.7280807228125
2316605 -0.0957845964705882
2316746 0.361922505
2316905 -0.373975714375
2316953 -0.0375260754205608
2317246 0.0547742053488372
2317317 -0.0368766166666667
2317434 0.2788242740625
2317472 0.1413818975
2317512 0.0269809552380952

Total number of rows: 22011

Table truncated, full table size 513 Kbytes.




Supplementary file Size Download File type/resource
GSM5174938_448.CEL.gz 21.7 Mb (ftp)(http) CEL
Processed data included within Sample table
Processed data are available on Series record

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