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Series GSE69341 Query DataSets for GSE69341
Status Public on Jun 30, 2016
Title Towards a new standardized method for circulating miRNAs profiling in clinical studies: Interest of the exogenous normalization to improve miRNA signature accuracy
Platform organism synthetic construct
Sample organism Homo sapiens
Experiment type Non-coding RNA profiling by array
Summary In our study, we proposed first to reduce the profiling variability by selecting the miRNA isolation kit offering the higher input RNA concentration for microarray profiling and second to control the profiling step variability by adapting the widely used exogenous normalization of the validation step to the profiling one. The new strategy proposed could improve the overlap between independent studies using microarray profiling, but also potentially with other high-throughput methods, to finally identify pertinent miRNA signatures in biofluids.
Because this project is only a methodological study, the cohort of serum and plasma samples used in this study were all obtained from patients with FIGO stages III/IV serous ovarian cancer. This study was approved by the ethics committee Nord-Ouest III [CPP N° 2011-02] and national authorities (AFSSAPS N°B110260-20). Plasma samples were obtained from the Comprehensive Cancer Center F. Baclesse biological collections that have been declared (# DC-2010-1243) to the French Ministry of Research and Superior Education. Prior to scientific use of samples and data, patients were appropriately informed and asked to consent in writing, in compliance with French and European regulations.
Overall design 13 samples of serum from patients with homogeneous clinical status were used to purify circulating miRNAs. Purified miR levels were assessed by qPCR and by hybridization on Affymetrix miRNA V4 arrays. Arrays data were normalized by different methods. Comparison between the data from qPCR and arrays were performed to identify the best normalization approach.
Contributor(s) Vigneron N, Meryet-Figuiere M, Guttin A, Issartel JP, Lambert B, Briand M, Leconte A, Lheureux S, Clarisse B, Krieger S, Joly F, Gauduchon P, Poulain L, Denoyelle C
Citation(s) 27083764
Submission date May 28, 2015
Last update date May 02, 2017
Contact name Christophe DENOYELLE
Phone 332 31 45 51 71
Organization name Université de Caen Normandie
Department Centre de Lutte Contre le Cancer François Baclesse
Lab UMR Inserm 1199 - Unité BioTICLA (Biologie et Thérapies Innovantes des Cancers Localement Agressifs)
Street address 3 Avenue général Harris BP 5026
City Caen cedex 05
ZIP/Postal code 14076
Country France
Platforms (1)
GPL19117 [miRNA-4] Affymetrix Multispecies miRNA-4 Array
Samples (13)
GSM1698244 Patient 1
GSM1698245 Patient 2
GSM1698246 Patient 3
BioProject PRJNA285252

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Supplementary file Size Download File type/resource
GSE69341_RAW.tar 8.8 Mb (http)(custom) TAR (of CEL)
Processed data included within Sample table

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