Global Expression Analysis of Quorum Sensing-Controlled Genes by RNAseq
RNA sequencing (RNAseq) enables transcriptional profiling of many organisms. This chapter describes the use of RNAseq in prokaryotes to identify quorum sensing (QS)-controlled transcripts by comparing samples from QS-induced and -uninduced conditions. Briefly, each RNA sample is converted to ds-cDNA in a method that limits amplification of ribosomal RNA species. The ds-cDNA contains adapters that enable sequencing and quantification by next-generation sequencing (NGS).
Key wordsRNA sequencing (RNAseq) Next-generation sequencing (NGS) Quorum sensing Not-so-random (NSR) primers Transcriptomics
A number of people contributed to the methods described in this chapter. Christopher Armour developed the NSR primer approach and methods for library construction  and also supported the development of this method for prokaryotic species. Sudha Chugani and Yasuhiro Oda contributed to other aspects of method development, including RNA isolation and library synthesis and analysis. Additionally, this protocol utilizes a number of commercially available kits. Many of the procedures are taken directly from the kit protocols or handbooks.