RNA-Sequencing of Staphylococcus aureus Messenger RNA

Methods Mol Biol. 2016;1373:131-41. doi: 10.1007/7651_2014_192.


RNA-sequencing (RNA-seq) is a technique that employs next-generation DNA-sequencing technology to simultaneously sequence all of the RNA transcripts in a cell. It can provide valuable insights into transcript and operon structure, and is rapidly replacing expression microarrays as the technique of choice for determining global gene expression profiles in bacteria. Herein we outline the procedures involved in performing RNA-seq with samples of RNA from Staphylococcus aureus. We draw particular attention to key aspects of sample preparation, such as RNA integrity and removal of ribosomal RNA, and provide details of critical steps in downstream data analysis.

Keywords: RNA enrichment; RNA-seq; RNA-sequencing; RPKM; S. aureus; rRNA reduction.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • DNA, Complementary / genetics
  • Gene Expression Profiling / methods
  • Gene Expression Regulation, Bacterial
  • High-Throughput Nucleotide Sequencing / methods*
  • Humans
  • RNA, Messenger / genetics*
  • Sequence Analysis, DNA / methods
  • Staphylococcal Infections / genetics
  • Staphylococcal Infections / microbiology
  • Staphylococcus aureus / genetics*
  • Staphylococcus aureus / pathogenicity


  • DNA, Complementary
  • RNA, Messenger