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Peer-reviewedCC BY 4.0GigaScience

Genomic in vitro transcription and Nanopore direct RNA sequencing of a human B-Lymphocyte cell line

  • Talia Tzadikario1
  • Stuart Akeson1
  • Sally Dorer1
  • Neda Ghohabi Esfahani1
  • Andrew J Stein1
  • Pooria Daneshvar Kakhaki2
  • Urja Choudhary1
  • Kshitij Amar1
  • Miten Jain1,3,4
4 affiliations
  1. 1Northeastern University Department of Bioengineering, , Boston, MA ,
  2. 2Northeastern University Department of Electrical & Computer Engineering, , Boston, MA ,
  3. 3Northeastern University Department of Physics, , Boston, MA ,
  4. 4Khoury College of Computer Sciences, Northeastern University , Boston, MA ,
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Abstract

Genomic DNA used as a template for in vitro transcription of RNA can serve as a true negative control for benchmarking RNA modification detection by Nanopore direct RNA sequencing (DRS) models. We generated DRS data for in vitro transcribed (IVT) RNA composed of canonical nucleotides using genomic DNA from a human cell line. We applied Dorado modification calling models to these data, and calculated 9-mer specific false-positive rates for eight RNA modifications as a comparison point for future development of RNA modification models.

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Cite

BibTeXRIS
BibTeX
@article{tzadikario2026genomic,
  title = {{Genomic in vitro transcription and Nanopore direct RNA sequencing of a human B-Lymphocyte cell line}},
  author = {Talia Tzadikario and Stuart Akeson and Sally Dorer and Neda Ghohabi Esfahani and Andrew J Stein and Pooria Daneshvar Kakhaki and Urja Choudhary and Kshitij Amar and Miten Jain},
  journal = {GigaScience},
  year = {2026},
  month = oct,
  doi = {10.1093/gigascience/giag098},
  url = {https://academic.oup.com/gigascience/advance-article/doi/10.1093/gigascience/giag098/9002150},
  note = {CC BY 4.0},
}
RIS
TY  - JOUR
TI  - Genomic in vitro transcription and Nanopore direct RNA sequencing of a human B-Lymphocyte cell line
AU  - Talia Tzadikario
AU  - Stuart Akeson
AU  - Sally Dorer
AU  - Neda Ghohabi Esfahani
AU  - Andrew J Stein
AU  - Pooria Daneshvar Kakhaki
AU  - Urja Choudhary
AU  - Kshitij Amar
AU  - Miten Jain
PY  - 2026
DA  - 2026/10/20
JO  - GigaScience
DO  - 10.1093/gigascience/giag098
UR  - https://academic.oup.com/gigascience/advance-article/doi/10.1093/gigascience/giag098/9002150
AB  - Genomic DNA used as a template for in vitro transcription of RNA can serve as a true negative control for benchmarking RNA modification detection by Nanopore direct RNA sequencing (DRS) models. We generated DRS data for in vitro transcribed (IVT) RNA composed of canonical nucleotides using genomic DNA from a human cell line. We applied Dorado modification calling models to these data, and calculated 9-mer specific false-positive rates for eight RNA modifications as a comparison point for future development of RNA modification models.
SN  - 2047-217X
ER  -