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    Targeted enrichment outperforms other enrichment techniques and enables more multi-species RNA-Seq analyses

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    Author
    Chung, M.
    Teigen, L.
    Liu, H.
    Date
    2018
    Journal
    Scientific Reports
    Publisher
    Nature Publishing Group
    Type
    Article
    
    Metadata
    Show full item record
    See at
    https://dx.doi.org/10.1038/s41598-018-31420-7
    Abstract
    Enrichment methodologies enable the analysis of minor members in multi-species transcriptomic data. We compared the standard enrichment of bacterial and eukaryotic mRNA to a targeted enrichment using an Agilent SureSelect (AgSS) capture for Brugia malayi, Aspergillus fumigatus, and the Wolbachia endosymbiont of B. malayi (wBm). Without introducing significant systematic bias, the AgSS quantitatively enriched samples, resulting in more reads mapping to the target organism. The AgSS-enriched libraries consistently had a positive linear correlation with their unenriched counterparts (r 2 = 0.559-0.867). Up to a 2,242-fold enrichment of RNA from the target organism was obtained following a power law (r 2 = 0.90), with the greatest fold enrichment achieved in samples with the largest ratio difference between the major and minor members. While using a single total library for prokaryote and eukaryote enrichment from a single RNA sample could be beneficial for samples where RNA is limiting, we observed a decrease in reads mapping to protein coding genes and an increase in multi-mapping reads to rRNAs in AgSS enrichments from eukaryotic total RNA libraries compared to eukaryotic poly(A)-enriched libraries. Our results support a recommendation of using AgSS targeted enrichment on poly(A)-enriched libraries for eukaryotic captures, and total RNA libraries for prokaryotic captures, to increase the robustness of multi-species transcriptomic studies. Copyright 2018, The Author(s).
    Keyword
    Agilent SureSelect (AgSS)
    Sequence Analysis, RNA--methods
    Identifier to cite or link to this item
    https://www.scopus.com/inward/record.uri?eid=2-s2.0-85052884840&doi=10.1038%2fs41598-018-31420-7&partnerID=40&md5=b85b7c4a6e90e1e341b6dd09cd7db6f0; http://hdl.handle.net/10713/9698
    ae974a485f413a2113503eed53cd6c53
    10.1038/s41598-018-31420-7
    Scopus Count
    Collections
    UMB Open Access Articles 2018

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