Multisite evaluation of next-generation methods for small RNA quantification

Zachary T. Herbert, Jyothi Thimmapuram, Shaojun Xie, Jamie P. Kershner, Fred W. Kolling, Carol S. Ringelberg, Ashley Leclerc, Yuriy O. Alekseyev, Jun Fan, Jessica W. Podnar, Holly S. Stevenson, Gary Sommerville, Shipra Gupta, Maura Berkeley, Julie Koeman, Anoja Perera, Allison R. Scott, Jennifer K. Grenier, Jeffrey Malik, John M. AshtonKara L. Pivarski, Xinkun Wang, Gina Kuffel, Tania E. Mesa, Andrew T. Smith, Jianjun Shen, Yoko Takata, Thomas L. Volkert, Jennifer A. Love, Yanping Zhang, Jun Wang, Xiaoling Xuei, Marie Adams, Stuart S. Levine

Research output: Contribution to journalArticle

Abstract

Small RNAs (smRNAs) are important regulators of many biologic processes and are now most frequently characterized using Illumina sequencing. However, although standard RNA sequencing library preparation has become routine in most sequencing facilities, smRNA sequencing library preparation has historically been challenging because of high input requirements, laborious protocols involving gel purifications, inability to automate, and a lack of benchmarking standards. Additionally, studies have suggested that many of these methods are nonlinear and do not accurately reflect the amounts of smRNAs in vivo. Recently, a number of new kits have become available that permit lower input amounts and less laborious, gel-free protocol options. Several of these new kits claim to reduce RNA ligase-dependent sequence bias through novel adapter modifications and to lessen adapter-dimer contamination in the resulting libraries. With the increasing number of smRNA kits available, understanding the relative strengths of each method is crucial for appropriate experimental design. In this study, we systematically compared 9 commercially available smRNA library preparation kits as well as NanoString probe hybridization across multiple study sites. Although several of the new methodologies do reduce the amount of artificially over-and underrepresented microRNAs (miRNAs), we observed that none of the methods was able to remove all of the bias in the library preparation. Identical samples prepared with different methods show highly varied levels of different miRNAs. Even so, many methods excelled in ease of use, lower input requirement, fraction of usable reads, and reproducibility across sites. These differences may help users select the most appropriate methods for their specific question of interest.

Original languageEnglish (US)
Pages (from-to)47-56
Number of pages10
JournalJournal of Biomolecular Techniques
Volume31
Issue number2
DOIs
StatePublished - Jul 2020

Keywords

  • Illumina Library Prep
  • MiRNA sequencing
  • RNA sequencing
  • Small RNA sequencing

ASJC Scopus subject areas

  • Molecular Biology

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  • Cite this

    Herbert, Z. T., Thimmapuram, J., Xie, S., Kershner, J. P., Kolling, F. W., Ringelberg, C. S., Leclerc, A., Alekseyev, Y. O., Fan, J., Podnar, J. W., Stevenson, H. S., Sommerville, G., Gupta, S., Berkeley, M., Koeman, J., Perera, A., Scott, A. R., Grenier, J. K., Malik, J., ... Levine, S. S. (2020). Multisite evaluation of next-generation methods for small RNA quantification. Journal of Biomolecular Techniques, 31(2), 47-56. https://doi.org/10.7171/jbt.20-3102-001