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Sample GSM5174680 Query DataSets for GSM5174680
Status Public on Jun 03, 2021
Title prostate_cancer_primary_190
Sample type RNA
 
Source name FFPE prostate cancer
Organism Homo sapiens
Characteristics tissue: FFPE prostate cancer
primary gleason: 3
secondary gleason: 5
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.190
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 0.259335082285714
2315633 0.12620209
2315674 -0.0192654742105263
2315739 0.415990094827586
2315894 -0.0467786975
2315918 0.3765170575
2315951 -0.0906349611764706
2316218 0.0627205875
2316245 0.6255223198
2316379 0.588467705714286
2316558 1.3096376271875
2316605 -0.0505477412941176
2316746 0.32586978375
2316905 -0.36863773625
2316953 -0.139078579626168
2317246 -0.0371213225581395
2317317 -0.0647830954385965
2317434 0.6782069296875
2317472 -0.0317075278571429
2317512 0.0241228938095238

Total number of rows: 22011

Table truncated, full table size 511 Kbytes.




Supplementary file Size Download File type/resource
GSM5174680_190.CEL.gz 22.6 Mb (ftp)(http) CEL
Processed data included within Sample table
Processed data are available on Series record

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