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Sample GSM6071779 Query DataSets for GSM6071779
Status Public on May 01, 2022
Title FFPE prostate_cancer_primary_1
Sample type RNA
 
Source name FFPE prostate cancer
Organism Homo sapiens
Characteristics primary gleason: 5
secondary gleason: 5
pre-treatment psa (ng/ml): 644
age: 61
race: Caucasian
randomization arm: Placebo
ecog3805 id: 84645
Treatment protocol Not Applicable
Growth protocol Not Applicable
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
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 Apr 28, 2022
Last update date May 01, 2022
Contact name Elai Davicioni
E-mail(s) [email protected]
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)
GSE201805 Transcriptional profiling of primary prostate tumor in metastatic hormonesensitive prostate cancer and association with clinical outcomes: correlative analysis of the E3805 CHAARTED study

Data table header descriptions
ID_REF
VALUE SCAN normalized signal estimates

Data table
ID_REF VALUE
2315554 0.391551695714286
2315633 0.164457255
2315674 -0.115057588947368
2315739 -0.0489509813793104
2315894 0.05109427625
2315918 0.705053585
2315951 -0.258074821176471
2316218 0.2408260825
2316245 0.039075822
2316379 0.146859780952381
2316558 0.550268043125
2316605 -0.144364530235294
2316746 0.233563628333333
2316905 -0.41636904625
2316953 -0.00318814046728972
2317246 -0.08390129
2317317 -0.205029560701754
2317434 0.206111636875
2317472 0.03879040125
2317512 -0.0123347657142857

Total number of rows: 22011

Table truncated, full table size 435 Kbytes.




Supplementary file Size Download File type/resource
GSM6071779_001.CEL.gz 20.4 Mb (ftp)(http) CEL
Processed data included within Sample table

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