Evaluation of automated and conventional microarray hybridization: a question of data quality and best practice?

Microarray is a widely used technique to study gene expression. The increasing interest in the technology has resulted in increased availability of commercial accessory reagents and instrumentation. In principle, commercial advances in reagents, kits and equipment should greatly improve assay performance, since they each bring a measure of quality assurance and uniformity to the data above that which may be obtained from the original manual hybridization processes. However, independent validation of this perceived benefit remains an essential part of the adoption process and, in microarrays, this has often been overlooked for want of immediate convenience. We describe here the comparative evaluation of two automated hybridization instruments, namely the MAUI(R) (microarray user interface) hybridization system and the GeneTAC HybStation, against the conventional manual coverslip hybridization methodology. Our results show that there is a significant advantage in using automated hybridization instrumentation over the diffusion-based coverslip methodology. We observed an enhancement of the mean signal, signal-to-noise ratio, and reproducibility between replicates when using both the MAUI(R) hybridization system and the GeneTAC HybStation. Automation further reduced labour time, offered simplicity and greater reproducibility and accuracy in the results. The present study has independently validated the benefits automation brings to the microarray hybridization process and highlights the differences between the instruments examined. We further comment on the higher quality of spot morphology when hybridization is performed at a lower temperature in combination with our buffer of choice.