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Sample GSM5174652 Query DataSets for GSM5174652
Status Public on Jun 03, 2021
Title prostate_cancer_primary_162
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.162
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 0.215979173428571
2315633 -0.00669430461538461
2315674 -0.09788561
2315739 0.433864823793103
2315894 -0.05754845625
2315918 0.7059974
2315951 -0.121886044705882
2316218 0.41933213
2316245 0.3692485842
2316379 0.490894452857143
2316558 0.900431593125
2316605 -0.114003864235294
2316746 0.31654907125
2316905 -0.39972531
2316953 0.0279278168224299
2317246 -0.0415648262790698
2317317 -0.137718190175439
2317434 0.550052591875
2317472 0.0392884782142857
2317512 -0.145529477619048

Total number of rows: 22011

Table truncated, full table size 512 Kbytes.




Supplementary file Size Download File type/resource
GSM5174652_162.CEL.gz 22.1 Mb (ftp)(http) CEL
Processed data included within Sample table
Processed data are available on Series record

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