Gene Expression Analysis in the Pneumococcus

  • Rory A. Eutsey
  • Carol A. Woolford
  • Surya D. Aggarwal
  • Rolando A. Cuevas
  • N. Luisa HillerEmail author
Part of the Methods in Molecular Biology book series (MIMB, volume 1968)


Bacterial cells modify their gene expression profiles throughout different stages of growth and in response to environmental cues. Analyses of gene expression across conditions reveal both conserved and condition-specific gene responses of bacteria to adapt to these dynamic conditions. In this chapter, we present a guide to pneumococcal RNA extraction for use in the NanoString nCounter platform. The nCounter is a highly effective method to measure gene expression of bacteria not only in a planktonic mode of growth but also in the presence of host cells where the RNA of interest represents only a small portion of the total material.

Key words

RNA isolation Gene expression Transcriptome NanoString 



We would like to thank Dr. Aaron Mitchell and Dr. Wenjie Xu for introducing, training, and guiding us in the use of the NanoString technology. We would like to thank Anagha Kadam for performing the first sets of NanoString experiments in our laboratory. We would like to thank Elnaz Ebrahimi for her assistance with growing biofilms on epithelial cells.


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Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2019

Authors and Affiliations

  • Rory A. Eutsey
    • 1
  • Carol A. Woolford
    • 1
  • Surya D. Aggarwal
    • 1
  • Rolando A. Cuevas
    • 1
  • N. Luisa Hiller
    • 1
    Email author
  1. 1.Department of Biological SciencesCarnegie Mellon UniversityPittsburghUSA

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