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    Dual RNA-seq analysis of in vitro infection multiplicity and RNA depletion methods in Chlamydia-infected epithelial cells

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    Author
    Hayward, Regan J
    Humphrys, Michael S
    Huston, Wilhelmina M
    Myers, Garry S A
    Date
    2021-05-17
    Journal
    Scientific Reports
    Publisher
    Springer Nature
    Type
    Article
    
    Metadata
    Show full item record
    See at
    https://doi.org/10.1038/s41598-021-89921-x
    Abstract
    Dual RNA-seq experiments examining viral and bacterial pathogens are increasing, but vary considerably in their experimental designs, such as infection rates and RNA depletion methods. Here, we have applied dual RNA-seq to Chlamydia trachomatis infected epithelial cells to examine transcriptomic responses from both organisms. We compared two time points post infection (1 and 24 h), three multiplicity of infection (MOI) ratios (0.1, 1 and 10) and two RNA depletion methods (rRNA and polyA). Capture of bacterial-specific RNA were greatest when combining rRNA and polyA depletion, and when using a higher MOI. However, under these conditions, host RNA capture was negatively impacted. Although it is tempting to use high infection rates, the implications on host cell survival, the potential reduced length of infection cycles and real world applicability should be considered. This data highlights the delicate nature of balancing host–pathogen RNA capture and will assist future transcriptomic-based studies to achieve more specific and relevant infection-related biological insights. © 2021, The Author(s).
    Keyword
    dual RNA-seq
    Chlamydia trachomatis--genetics
    Host-Pathogen Interactions--genetics
    Sequence Analysis, RNA
    Identifier to cite or link to this item
    http://hdl.handle.net/10713/15881
    ae974a485f413a2113503eed53cd6c53
    10.1038/s41598-021-89921-x
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