title: Triple-target microarray experiments: a novel experimental strategy.
abstract: BACKGROUND
  High-throughput, parallel gene expression analysis by means of microarray technology has become a widely used technique in recent years. There are currently two main dye-labelling strategies for microarray studies based on custom-spotted cDNA or oligonucleotides arrays: (I) Dye-labelling of a single target sample with a particular dye, followed by subsequent hybridisation to a single microarray slide, (II) Dye-labelling of two different target samples with two different dyes, followed by subsequent co-hybridisation to a single microarray slide. The two dyes most frequently used for either method are Cy3 and Cy5. We propose and evaluate a novel experiment set-up utilising three differently labelled targets co-hybridised to one microarray slide. In addition to Cy3 and Cy5, this incorporates Alexa 594 as a third dye-label. We evaluate this approach in line with current data processing and analysis techniques for microarrays, and run separate analyses on Alexa 594 used in single-target, dual-target and the intended triple-target experiment set-ups (a total of 18 microarray slides). We follow this by pointing out practical applications and suitable analysis methods, and conclude that triple-target microarray experiments can add value to microarray research by reducing material costs for arrays and related processes, and by increasing the number of options for pragmatic experiment design.
  
  
  RESULTS
  The addition of Alexa 594 as a dye-label for an additional--third--target sample works within the framework of more commonplace Cy5/Cy3 labelled target sample combinations. Standard normalisation methods are still applicable, and the resulting data can be expected to allow identification of expression differences in a biological experiment, given sufficient levels of biological replication (as is necessary for most microarray experiments).
  
  
  CONCLUSIONS
  The use of three dye-labelled target samples can be a valuable addition to the standard repertoire of microarray experiment designs. The method enables direct comparison between two experimental populations as well as measuring these two populations in relation to a third reference sample, allowing comparisons within the slide and across slides. These benefits are only offset by the added level of consideration required in the experimental design and data processing of a triple-target study design. Common methods for data processing and analysis are still applicable, but there is scope for the development of custom models for triple-target data. In summary, we do not consider the triple-target approach to be a new standard, but a valuable addition to the existing microarray study toolkit.
authors.affiliation: Scottish Centre for Genomic Technology and Informatics, University of Edinburgh, The Chancellor's Building, College of Medicine, 49 Little France Crescent, Edinburgh, EH16 4SB, UK. Thorsten.Forster@ed.ac.uk
authors.forename: Thorsten
authors.initials: T
authors.lastname: Forster
authors.forename: Yael
authors.initials: Y
authors.lastname: Costa
authors.forename: Douglas
authors.initials: D
authors.lastname: Roy
authors.forename: Howard J
authors.initials: HJ
authors.lastname: Cooke
authors.forename: Klio
authors.initials: K
authors.lastname: Maratou
mesh_terms: D000818:Animals; D002232:Carbocyanines / Q000737:chemistry; D018076:DNA, Complementary / Q000737:chemistry / Q000235:genetics; D005456:Fluorescent Dyes / Q000737:chemistry*; D020869:Gene Expression Profiling / Q000379:methods*; D008297:Male; D051379:Mice; D008810:Mice, Inbred C57BL; D009693:Nucleic Acid Hybridization / Q000379:methods; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D009930:Organic Chemicals; D015203:Reproducibility of Results; D013737:Testis / Q000378:metabolism
chemical_list: C417664:Alexa594; D002232:Carbocyanines; D018076:DNA, Complementary; D005456:Fluorescent Dyes; D009930:Organic Chemicals; C089187:cyanine dye 3; C085321:cyanine dye 5