title: Advances in bacterial transcriptome and transposon insertion-site profiling using second-generation sequencing.
abstract: The arrival of second-generation sequencing has revolutionized the study of bacteria within a short period. The sequence information generated from these platforms has helped in our understanding of bacterial development, adaptation and diversity and how bacteria cause disease. Furthermore, these technologies have quickly been adapted for high-throughput studies that were previously performed using DNA cloning or microarray-based applications. This has facilitated a more comprehensive study of bacterial transcriptomes through RNA sequencing (RNA-Seq) and the systematic determination of gene function by 'transposon monitoring'. In this review, we provide an outline of these powerful tools and the in silico analyses used in their application, and also highlight the biological questions being addressed in these approaches.
authors.affiliation: The Genome Analysis Centre, Norwich Research Park, Colney Lane, Norwich NR4 7UH, UK.
authors.forename: Melanie
authors.initials: M
authors.lastname: Febrer
authors.forename: Kirsten
authors.initials: K
authors.lastname: McLay
authors.forename: Mario
authors.initials: M
authors.lastname: Caccamo
authors.forename: Kate B
authors.initials: KB
authors.lastname: Twomey
authors.forename: Robert P
authors.initials: RP
authors.lastname: Ryan
mesh_terms: D001419:Bacteria / Q000235:genetics*; D003198:Computer Simulation; D004251:DNA Transposable Elements / Q000235:genetics*; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D017423:Sequence Analysis, RNA / Q000379:methods*; D059467:Transcriptome / Q000235:genetics*
chemical_list: D004251:DNA Transposable Elements