Array-based approaches to bacterial transcriptome analysis

Microarray technology has been extensively used to compare or quantify genome-wide mRNA levels, a key factor in the adaptive response of bacteria to the environment. Classical gene expression arrays based on an existing genome annotation with relatively few probes for each gene, are well suited to assess the expression levels of all annotated transcripts under many different conditions. Newer genomic tiling arrays that cover both strands of a genome by overlapping probes and, more recently, RNA-seq approaches have opened the way to unbiased whole-transcriptome studies. The analysis of transcriptomes with both types of arrays has reached a mature stage with respect to experimental procedures and data analysis strategies. In this chapter we discuss the steps leading from the design of a microarray experiment to the biological interpretation of the expression profiles