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Sample GSM5174746 Query DataSets for GSM5174746
Status Public on Jun 03, 2021
Title prostate_cancer_primary_256
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: 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.256
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 0.298957118285714
2315633 0.0930259576923077
2315674 0.0427607910526316
2315739 0.207486483448276
2315894 -0.19118806
2315918 0.51013622
2315951 -0.289226425294118
2316218 0.6866826425
2316245 0.0455741052
2316379 0.0826334682539683
2316558 0.4994416340625
2316605 0.000762111529411763
2316746 0.50903663
2316905 -0.18875677
2316953 0.0211166071028037
2317246 -0.01601622
2317317 -0.0254744231578947
2317434 0.068604405625
2317472 0.0741790142857143
2317512 -0.165391260714286

Total number of rows: 22011

Table truncated, full table size 515 Kbytes.




Supplementary file Size Download File type/resource
GSM5174746_256.CEL.gz 18.5 Mb (ftp)(http) CEL
Processed data included within Sample table
Processed data are available on Series record

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