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Triple-target microarray experiments: a novel experimental strategy

BioMed Central
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  • Methodology Article

Abstract ral ss BioMed CentBMC Genomics Open AcceMethodology article Triple-target microarray experiments: a novel experimental strategy Thorsten Forster*1, Yael Costa2, Douglas Roy1, Howard J Cooke2 and Klio Maratou2 Address: 1Scottish Centre for Genomic Technology and Informatics, University of Edinburgh, The Chancellor's Building, College of Medicine, 49 Little France Crescent, Edinburgh, EH16 4SB, UK and 2MRC Human Genetics Unit, The Department of Chromosome Biology, Western General Hospital, Crewe Road, Edinburgh, EH4 2XU, UK Email: Thorsten Forster* -; Yael Costa -; Douglas Roy -; Howard J Cooke -; Klio Maratou - * Corresponding author 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

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