Co-transcriptomic analysis by RNA sequencing to simultaneously measure regulated gene expression in host and bacterial pathogen

Ravasi, Timothy, Mavromatis, Charalampos (Harris), Bokil, Nilesh J., Schembri, Mark A. and Sweet, Matthew J. (2016). Co-transcriptomic analysis by RNA sequencing to simultaneously measure regulated gene expression in host and bacterial pathogen. In Claire E. McCoy (Ed.), Toll-like receptors: practice and methods 2nd ed. (pp. 145-158) Heidelberg, Germany: Springer. doi:10.1007/978-1-4939-3335-8_10

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Author Ravasi, Timothy
Mavromatis, Charalampos (Harris)
Bokil, Nilesh J.
Schembri, Mark A.
Sweet, Matthew J.
Title of chapter Co-transcriptomic analysis by RNA sequencing to simultaneously measure regulated gene expression in host and bacterial pathogen
Title of book Toll-like receptors: practice and methods
Place of Publication Heidelberg, Germany
Publisher Springer
Publication Year 2016
Sub-type Research book chapter (original research)
DOI 10.1007/978-1-4939-3335-8_10
Open Access Status Not Open Access
Series Methods in Molecular Biology
Edition 2nd
ISBN 9781493933334
9781493933358
ISSN 1064-3745
1940-6029
Editor Claire E. McCoy
Volume number 1390
Chapter number 10
Start page 145
End page 158
Total pages 14
Total chapters 25
Language eng
Abstract/Summary Intramacrophage pathogens subvert antimicrobial defence pathways using various mechanisms, including the targeting of host TLR-mediated transcriptional responses. Conversely, TLR-inducible host defence mechanisms subject intramacrophage pathogens to stress, thus altering pathogen gene expression programs. Important biological insights can thus be gained through the analysis of gene expression changes in both the host and the pathogen during an infection. Traditionally, research methods have involved the use of qPCR, microarrays and/or RNA sequencing to identify transcriptional changes in either the host or the pathogen. Here we describe the application of RNA sequencing using samples obtained from in vitro infection assays to simultaneously quantify both host and bacterial pathogen gene expression changes, as well as general approaches that can be undertaken to interpret the RNA sequencing data that is generated. These methods can be used to provide insights into host TLR-regulated transcriptional responses to microbial challenge, as well as pathogen subversion mechanisms against such responses.
Keyword Host-pathogen
Innate immunity
Intracellular pathogens
Macrophages
RNA sequencing
Toll-like receptors
Transcriptomics
Urinary tract infections
Uropathogenic E. coli
Q-Index Code B1
Q-Index Status Provisional Code
Institutional Status UQ

 
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Created: Sat, 30 Jan 2016, 01:08:39 EST by Mrs Louise Nimwegen on behalf of School of Chemistry & Molecular Biosciences