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Sample GSM5174967 Query DataSets for GSM5174967
Status Public on Jun 03, 2021
Title prostate_cancer_primary_477
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.477
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 0.221002677714286
2315633 0.028800025
2315674 -0.136664873333333
2315739 0.11933284
2315894 -0.44366054125
2315918 1.040373305
2315951 -0.292544018823529
2316218 0.2124341875
2316245 0.240404152
2316379 0.258942546825397
2316558 1.028919744375
2316605 -0.164380104
2316746 0.319727835
2316905 -0.508114473125
2316953 -0.124049201682243
2317246 -0.0331187025581395
2317317 -0.219344861403509
2317434 0.3844397465625
2317472 0.00966124589285715
2317512 -0.079859725

Total number of rows: 22011

Table truncated, full table size 512 Kbytes.




Supplementary file Size Download File type/resource
GSM5174967_477.CEL.gz 23.5 Mb (ftp)(http) CEL
Processed data included within Sample table
Processed data are available on Series record

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