Bovine Gene Expression Platforms for Global Transcription Profiling Studies

Microarrays are currently the de facto tool for simultaneously studying expression profiles across thousands of genes. For research purposes, RNAseq will probably supersede them over the next few years as the global expression-profiling tool of choice (Ledford 2008). Currently RNAseq costs are still non-competitive, but they are dropping rapidly. The costs of mainstream array technologies are also steadily coming down, which will allow them to be more widely used as a diagnostic tool. Within this niche they are not likely to be replaced in the near future. For many livestock species, commercial arrays are available and frequently there is more than one platform/supplier. The choice of platform is important in terms of robustness and its ability to address the experimental questions. The three most commonly used bovine gene expression platforms used for global transcription profiling studies are the 'Affymetrix GeneChip Bovine Genome Array', the 'Agilent Bovine Gene Expression Microarray' and the 'Bovine Oligo Microarray Consortium (BOMC) 24K array'. The objective of this work is to summarize and compare these platforms, and propose some suggestions to assist researchers to make a decision about which one to use in their own projects.