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Title: RNAseq Analysis of Formalin-Fixed Paraffin-Embedded Prostate Cancer Tissues      
dateReleased:
04-11-2014
description:
In an effort to identify biomarkers of recurrence, we have performed global RNA-sequencing on 106 formalin-fixed, paraffin-embedded (FFPE) prostatectomy samples from 100 patients at three independent sites, and identified a new set of biomarkers of biochemical recurrence composed of a 24-gene panel. We validated this 24-gene panel on an independent publicly available dataset of 140 patients and this new panel outperformed previously published markers based on cell proliferation gene sets in terms of prediction of biochemical recurrence (BCR). In addition we identified differences in gene expression between Gleason Pattern 4+3 and Gleason Pattern 3+4 tumors. 106 samples from 100 patients were sequenced. Six samples were sequenced from two independent RNA preps and libraries. All samples were taken from FFPE Radical Prostatectomies. Samples were obtained from Atlanta VA Medical Center, U. Toronto Sunnybrook Research Centre, and Moffitt Cancer Center.
privacy:
not applicable
aggregation:
instance of dataset
ID:
E-GEOD-54460
refinement:
raw
alternateIdentifiers:
54460
keywords:
functional genomics
dateModified:
06-01-2014
availability:
available
types:
gene expression
name:
Homo sapiens
accessURL: https://www.ebi.ac.uk/arrayexpress/files/E-GEOD-54460/E-GEOD-54460.raw.1.zip
storedIn:
ArrayExpress
qualifier:
gzip compressed
format:
TXT
accessType:
download
authentication:
none
authorization:
none
accessURL: https://www.ebi.ac.uk/arrayexpress/files/E-GEOD-54460/E-GEOD-54460.processed.1.zip
storedIn:
ArrayExpress
qualifier:
gzip compressed
format:
TXT
accessType:
download
authentication:
none
authorization:
none
accessURL: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE54460
storedIn:
Gene Expression Omnibus
qualifier:
not compressed
format:
HTML
accessType:
landing page
primary:
true
authentication:
none
authorization:
none
abbreviation:
EBI
homePage: http://www.ebi.ac.uk/
ID:
SCR:004727
name:
European Bioinformatics Institute
homePage: https://www.ebi.ac.uk/arrayexpress/
ID:
SCR:002964
name:
ArrayExpress
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