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    Co-transcriptomic Analysis by RNA Sequencing to Simultaneously Measure Regulated Gene Expression in Host and Bacterial Pathogen

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    Name:
    Ravasi_Cotranscriptomics_Book_Chapter_Final.pdf
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    1.127Mb
    Format:
    PDF
    Description:
    Accepted Manuscript
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    Type
    Book Chapter
    Authors
    Ravasi, Timothy cc
    Mavromatis, Charalampos Harris cc
    Bokil, Nilesh J.
    Schembri, Mark A.
    Sweet, Matthew J.
    KAUST Department
    Biological and Environmental Sciences and Engineering (BESE) Division
    Bioscience Program
    Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division
    Integrative Systems Biology Lab
    Date
    2016-01-24
    Online Publication Date
    2016-01-24
    Print Publication Date
    2016
    Permanent link to this record
    http://hdl.handle.net/10754/596609
    
    Metadata
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    Abstract
    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 Nature
    Journal
    Methods in Molecular Biology
    ISBN
    978-1-4939-3333-4
    DOI
    10.1007/978-1-4939-3335-8_10
    PubMed ID
    26803628
    Additional Links
    http://link.springer.com/protocol/10.1007%2F978-1-4939-3335-8_10
    ae974a485f413a2113503eed53cd6c53
    10.1007/978-1-4939-3335-8_10
    Scopus Count
    Collections
    Biological and Environmental Science and Engineering (BESE) Division; Bioscience Program; Book Chapters; Computer, Electrical and Mathematical Science and Engineering (CEMSE) Division

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