Borrelia burgdorferi Transcriptome Analysis by RNA-Sequencing.

Next-Generation Sequencing (NGS) has revolutionized transcriptomics studies in the last decade. Transcriptome analysis experiments using NGS-based RNA-sequencing have several advantages over DNA microarray analysis. Novel unannotated transcripts and transcriptional start sites can be identified. Differential gene expression can be determined on novel and annotated transcripts simultaneously, whereas DNA microarray analysis can only quantify changes of known genes. In the protocol below we describe an Illumina compatible ligation-based method for generating stranded cDNA libraries for total RNA and small RNA transcriptomes in Borrelia burgdorferi.