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Sample GSM5174657 Query DataSets for GSM5174657
Status Public on Jun 03, 2021
Title prostate_cancer_primary_167
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: Average
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.167
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 0.286839206857143
2315633 -0.134319681538462
2315674 -0.0820327054385965
2315739 0.106019273103448
2315894 -0.182471115
2315918 0.30289306
2315951 -0.258149038235294
2316218 0.192360935
2316245 0.2704785382
2316379 0.101045376349206
2316558 0.664401038125
2316605 -0.153508934352941
2316746 0.0637844679166667
2316905 -0.343149651875
2316953 -0.0991369457009346
2317246 0.0413476353488372
2317317 -0.116632632807018
2317434 0.3016471021875
2317472 0.00278970285714285
2317512 -0.044399950952381

Total number of rows: 22011

Table truncated, full table size 514 Kbytes.




Supplementary file Size Download File type/resource
GSM5174657_167.CEL.gz 20.5 Mb (ftp)(http) CEL
Processed data included within Sample table
Processed data are available on Series record

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