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Common analysis of direct RNA sequencinG CUrrently leads to misidentification of m5C at GCU motifs

Kaylee J Watson, Robin E Bromley, Benjamin C Sparklin, Mark T Gasser, Tamanash Bhattacharya, Jarrett F Lebov, Tyonna Tyson, Nan Dai, Laura E Teigen, Karen T Graf, Jeremy M Foster, Michelle Michalski, Vincent M Bruno, Amelia RI Lindsey, Ivan R Corrêa, Richard W Hardy, Irene LG Newton, Julie C Dunning Hotopp  Correspondence email
Published 29 November 2023. DOI: 10.26508/lsa.202302201

Article Information

vol. 7 no. 2 e202302201
DOI 
https://doi.org/10.26508/lsa.202302201
PubMed 
38030223
Published By 
Life Science Alliance
Online ISSN 
2575-1077
History 
  • Received June 6, 2023
  • Revision received November 16, 2023
  • Accepted November 20, 2023
  • Published online November 29, 2023.
Copyright & Usage 
© 2023 Watson et al. This article is available under a Creative Commons License (Attribution 4.0 International, as described at https://creativecommons.org/licenses/by/4.0/).

Author Information

  1. Kaylee J Watson1, Conceptualization, Software, Formal analysis, Validation, Investigation, Visualization, Methodology, Writing—original draft, Writing—review and editing,
  2. Robin E Bromley1, Resources, Data curation, Investigation, Methodology, Writing—original draft, Project administration,
  3. Benjamin C Sparklin1, Resources, Investigation, Methodology,
  4. Mark T Gasser1, Resources, Investigation, Methodology,
  5. Tamanash Bhattacharya2, Resources, Investigation, Methodology, Writing—original draft,
  6. Jarrett F Lebov1, Resources, Investigation, Methodology,
  7. Tyonna Tyson1, Resources, Investigation, Methodology,
  8. Nan Dai3, Resources, Investigation, Methodology,
  9. Laura E Teigen4, Resources, Investigation, Methodology,
  10. Karen T Graf1, Resources, Investigation, Writing—original draft,
  11. Jeremy M Foster3, Resources, Supervision,
  12. Michelle Michalski4, Resources, Supervision,
  13. Vincent M Bruno1,5, Resources, Supervision,
  14. Amelia RI Lindsey2, Resources, Supervision, Investigation, Methodology, Writing—review and editing,
  15. Ivan R Corrêa Jr3, Resources, Investigation, Methodology,
  16. Richard W Hardy2, Conceptualization, Resources, Supervision, Funding acquisition, Investigation, Project administration, Writing—review and editing,
  17. Irene LG Newton2, Conceptualization, Resources, Supervision, Funding acquisition, Investigation, Project administration, Writing—review and editing and
  18. Julie C Dunning Hotopp1,5,6, Conceptualization, Data curation, Supervision, Funding acquisition, Investigation, Methodology, Writing—original draft, Project administration, Writing—review and editing⇑
  1. 1Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
  2. 2Department of Biology, Indiana University, Bloomington, IN, USA
  3. 3New England Biolabs, Ipswich, MA, USA
  4. 4Department of Biology, University of Wisconsin Oshkosh, Oshkosh, WI, USA
  5. 5Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, USA
  6. 6Greenebaum Cancer Center, University of Maryland School of Medicine, Baltimore, MD, USA
  1. Correspondence: jdhotopp{at}som.umaryland.edu

  • Benjamin C Sparklin’s present address is AstraZeneca, Gaithersburg, MD, USA

  • Mark T Gasser’s present address is Johns Hopkins University Applied Physics Laboratory, Laurel, MD, USA

  • Tamanash Bhattacharya’s present address is Division of Basic Sciences, Fred Hutchinson Cancer Center, Seattle, WA, USA

  • Jarrett F Lebov’s present address is Personal Genome Diagnostics, Baltimore, MD, USA

  • Tyonna Tyson’s present address is Hampton University, Hampton, VA, USA

  • Laura E Teigen’s present address is Department of Biological Sciences, Marquette University, Milwaukee, WI, USA

  • Amelia RI Lindsey’s present address is Department of Entomology, University of Minnesota, Saint Paul, MN, USA

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Funding

  • National Science Foundation (NSF)

    EF 2025384
    RW Hardy, ILG Newton, JC Dunning Hotopp

  • HHS | NIH | National Institute of Allergy and Infectious Diseases (NIAID)

    U19AI110820
    JM Foster, M Michalski, VM Bruno, JC Dunning Hotopp

  • HHS | NIH | National Institute of Allergy and Infectious Diseases (NIAID)

    T32AI162579
    KJ Watson, JC Dunning Hotopp
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Misidentification of m5C at GCU in ONT direct RNA sequencing
Kaylee J Watson, Robin E Bromley, Benjamin C Sparklin, Mark T Gasser, Tamanash Bhattacharya, Jarrett F Lebov, Tyonna Tyson, Nan Dai, Laura E Teigen, Karen T Graf, Jeremy M Foster, Michelle Michalski, Vincent M Bruno, Amelia RI Lindsey, Ivan R Corrêa, Richard W Hardy, Irene LG Newton, Julie C Dunning Hotopp
Life Science Alliance Nov 2023, 7 (2) e202302201; DOI: 10.26508/lsa.202302201
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