Co-transcriptomic Analysis by RNA Sequencing to Simultaneously Measure Regulated Gene Expression in Host and Bacterial Pathogen
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Book ChapterAuthors
Ravasi, Timothy
Mavromatis, Charalampos Harris

Bokil, Nilesh J.
Schembri, Mark A.
Sweet, Matthew J.
KAUST Department
Biological and Environmental Sciences and Engineering (BESE) DivisionBioscience Program
Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division
Integrative Systems Biology Lab
Date
2016-01-24Online Publication Date
2016-01-24Print Publication Date
2016Permanent link to this record
http://hdl.handle.net/10754/596609
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Show full item recordAbstract
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.Citation
Ravasi, T., Mavromatis, C.H., Bokil, N.J., Schembri, M.A. and Sweet, M.J., Co-transcriptomic Analysis by RNA Sequencing to Simultaneously Measure Regulated Gene Expression in Host and Bacterial Pathogen.Publisher
Springer NatureJournal
Methods in Molecular BiologyISBN
978-1-4939-3333-4PubMed ID
26803628Additional Links
http://link.springer.com/protocol/10.1007%2F978-1-4939-3335-8_10ae974a485f413a2113503eed53cd6c53
10.1007/978-1-4939-3335-8_10
Scopus Count
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