Open Access Research article

Intra-platform comparison of 25-mer and 60-mer oligonucleotide Nimblegen DNA microarrays

Stephane Fenart12, Malika Chabi1, Sophie Gallina3, Rudy Huis1, Godfrey Neutelings1, Nathalie Riviere4, Brigitte Thomasset5, Simon Hawkins1 and Anca Lucau-Danila1*

Author Affiliations

1 Université Lille Nord de France, Lille 1, UMR INRA 1281, SADV, Villeneuve d’Ascq cedex, F- 59650, France

2 Roche Diagnostics France, 2, Avenue du Vercors, Meylan, 38242, France

3 Université Lille Nord de France, Lille 1, GEPV, Laboratoire de Génétique & Évolution des Populations végétales, CNRS UMR 8198, Villeneuve d’Ascq cedex, F- 59650, France

4 BIOGEMMA, Z.I, du Brezet, 8 rue des Frères Lumières, Clermont-Ferrand cedex 2, 63028, France

5 UMR CNRS 6022, GEC, Université de Technologie de Compiègne, BP 20529, Compiègne cedex, 60205, France

For all author emails, please log on.

BMC Research Notes 2013, 6:43  doi:10.1186/1756-0500-6-43

Published: 4 February 2013

Abstract

Background

We performed a Nimblegen intra-platform microarray comparison by assessing two categories of flax target probes (short 25-mers oligonucleotides and long 60-mers oligonucleotides) in identical conditions of target production, design, labelling, hybridization, image analyses, and data filtering. We compared technical parameters of array hybridizations, precision and accuracy as well as specific gene expression profiles.

Results

Comparison of the hybridization quality, precision and accuracy of expression measurements, as well as an interpretation of differential gene expression in flax tissues were performed. Both array types yielded reproducible, accurate and comparable data that are coherent for expression measurements and identification of differentially expressed genes. 60-mers arrays gave higher hybridization efficiencies and therefore were more sensitive allowing the detection of a higher number of unigenes involved in the same biological process and/or belonging to the same multigene family.

Conclusion

The two flax arrays provide a good resolution of expressed functions; however the 60-mers arrays are more sensitive and provide a more in-depth coverage of candidate genes potentially involved in different biological processes.

Keywords:
Nimblegen; DNA arrays; Gene expression