Identification of target genes mediated by two-component regulators of staphylococcus aureus using RNA-seq technology

Ting Lei, Junshu Yang, Aaron Becker, Yinduo Ji

Research output: Chapter in Book/Report/Conference proceedingChapter

3 Scopus citations


Transcriptomics enables us to elucidate comprehensive gene expression profiles in given experimental conditions. Global regulators, which include transcriptional regulators and two-component regulatory systems, have evolved in a variety of bacterial systems. They play important roles in bacterial fitness and pathogenesis by regulating target gene expression. Advanced next-generation RNA sequencing technology (RNA-seq) provides a powerful and effective tool to analyze the transcriptome of bacterial cells. In this chapter, we provide a detailed procedure for the investigation of gene expression profiles and identification of target genes, regulons, and/or pathways that are mediated by a regulator. This procedure is done using RNA-seq analysis, which involves RNA purification, mRNA enrichment, decontamination, RNA-seq data analysis, and quantitative real-time reverse transcription PCR.

Original languageEnglish (US)
Title of host publicationMethods in Molecular Biology
PublisherHumana Press Inc.
Number of pages14
StatePublished - 2020

Publication series

NameMethods in molecular biology (Clifton, N.J.)
PublisherHumana Press
ISSN (Print)1064-3745

Bibliographical note

Funding Information:
We thank Dr. Juan E Abrahante Llorens at the University of Minnesota Informatics Institute (UMII) and Lisa Fazzino for the assistance with data analysis. This work was supported by grant AI057451 from the National Institute of Allergy and Infectious Disease and partially supported by grant MIN-63-082 and MIN-63-113 from CVM research Office UMN Ag Experimental Station General Agricultural Research Funds.

Publisher Copyright:
© Springer Science+Business Media, LLC, part of Springer Nature 2020.


  • Gene expression profile
  • RNA sequencing technologies (RNA-seq)
  • Real-time reverse transcription polymerase chain reaction
  • Staphylococcus aureus
  • Two-component system (TCS)
  • RNA-Seq
  • Regulatory Sequences, Nucleic Acid
  • Transcriptome
  • Staphylococcus aureus/genetics
  • Gene Expression Regulation, Bacterial
  • Reverse Transcriptase Polymerase Chain Reaction
  • Real-Time Polymerase Chain Reaction

PubMed: MeSH publication types

  • Research Support, Non-U.S. Gov't
  • Journal Article
  • Research Support, N.I.H., Extramural


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