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Sample GSM5174697 Query DataSets for GSM5174697
Status Public on Jun 03, 2021
Title prostate_cancer_primary_207
Sample type RNA
 
Source name FFPE prostate cancer
Organism Homo sapiens
Characteristics tissue: FFPE prostate cancer
primary gleason: 4
secondary gleason: 5
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.207
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 0.268786969142857
2315633 0.0378964669230769
2315674 0.0253632568421053
2315739 0.242858853793103
2315894 -0.16903523125
2315918 0.559377425
2315951 -0.419463822941176
2316218 0.379128855
2316245 0.4666368848
2316379 0.415964893174603
2316558 1.2436766934375
2316605 0.00113861847058823
2316746 0.42012468875
2316905 -0.255962570625
2316953 -0.044363011588785
2317246 0.0311753360465116
2317317 -0.071629081754386
2317434 0.5992531034375
2317472 0.0482324423214286
2317512 -0.0888386354761905

Total number of rows: 22011

Table truncated, full table size 511 Kbytes.




Supplementary file Size Download File type/resource
GSM5174697_207.CEL.gz 22.7 Mb (ftp)(http) CEL
Processed data included within Sample table
Processed data are available on Series record

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