title: Intra-platform comparison of 25-mer and 60-mer oligonucleotide Nimblegen DNA microarrays.
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.
  
  
  CONCLUSIONS
  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.
authors: Université Lille Nord de France, Lille 1, UMR INRA 1281, SADV, F- 59650 Villeneuve d'Ascq cedex, France.
authors: Stephane
authors: S
authors: Fenart
authors: Malika
authors: M
authors: Chabi
authors: Sophie
authors: S
authors: Gallina
authors: Rudy
authors: R
authors: Huis
authors: Godfrey
authors: G
authors: Neutelings
authors: Nathalie
authors: N
authors: Riviere
authors: Brigitte
authors: B
authors: Thomasset
authors: Simon
authors: S
authors: Hawkins
authors: Anca
authors: A
authors: Lucau-Danila
mesh_terms: D004247:DNA / Q000737:chemistry*; D015342:DNA Probes; D009693:Nucleic Acid Hybridization; D020411:Oligonucleotide Array Sequence Analysis; D015203:Reproducibility of Results
chemical_list: D015342:DNA Probes; D004247:DNA
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