Abstract
The pan-Neisseria microarray was the first bacterial microarray to address multiple strains and species, and is a tool specifically developed for the performance of comparative studies within and between species. To achieve this, its design was based upon a detailed comparison of multiple genomes, prior to probe selection, and serial triage to optimize sensitivity and specificity. While this tool can be used for transcriptional comparisons of the same species, such as isogenic mutants, or strains exposed to different environmental conditions, its features are also particularly suited to population and functional studies of unrelated strains. The optimal use of these tools, including the use of single-channel labeling for genomic studies, the biological replication needed to perform robust transcription studies, and key aspects of data analysis such as the use of cross-channel correction and Bayesian analytical approaches, is discussed.
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Acknowledgments
The original manufacture of the pan-Neisseria microarray v1 was supported in part by a grant from the Royal Society. Subsequent studies developing and using the microarray were supported by the Wellcome Trust, and microarray infrastructure was supported by the EPA Cephalosporin Trust. The input from the Computational Biology Research Group (formerly the Oxford University Bioinformatics Center), including from John Peden, Sarah Butcher, Simon McGowan, and Steve Taylor has been invaluable to work in this area. Bespoke plug-ins for BASE to perform cross-channel correction, a modification of global median ratio normalization (if a significant proportion of transcripts differ), and to perform the Cyber-T analysis are available directly from the Oxford Computational Biology Research Group. Further detailed protocols on the use of these arrays, which are outside the scope of this technical review, can be obtained from the authors on request.
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Saunders, N.J., Davies, J.K. (2012). The Use of the Pan-Neisseria Microarray and Experimental Design for Transcriptomics Studies of Neisseria . In: Christodoulides, M. (eds) Neisseria meningitidis. Methods in Molecular Biology, vol 799. Humana, Totowa, NJ. https://doi.org/10.1007/978-1-61779-346-2_18
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DOI: https://doi.org/10.1007/978-1-61779-346-2_18
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