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Real-time biochemical-free targeted sequencing of RNA species with RISER

View ORCID ProfileAlexandra Sneddon, View ORCID ProfileAgin Ravindran, View ORCID ProfileNadine Hein, View ORCID ProfileNikolay Shirokikh, View ORCID ProfileEduardo Eyras
doi: https://doi.org/10.1101/2022.11.29.518281
Alexandra Sneddon
1EMBL Australia Partner Laboratory Network at the Australian National University, Canberra, Australia
2Centre for Computational Biomedical Sciences, The John Curtin School of Medical Research, Australian National University, Canberra, Australia
3The Shine-Dalgarno Centre for RNA Innovation, The John Curtin School of Medical Research, Australian National University, Canberra, Australia
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  • ORCID record for Alexandra Sneddon
Agin Ravindran
1EMBL Australia Partner Laboratory Network at the Australian National University, Canberra, Australia
2Centre for Computational Biomedical Sciences, The John Curtin School of Medical Research, Australian National University, Canberra, Australia
3The Shine-Dalgarno Centre for RNA Innovation, The John Curtin School of Medical Research, Australian National University, Canberra, Australia
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Nadine Hein
4ACRF Department of Cancer Biology and Therapeutics, The John Curtin School of Medical Research, Australian National University, Canberra, Australia
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  • ORCID record for Nadine Hein
Nikolay Shirokikh
3The Shine-Dalgarno Centre for RNA Innovation, The John Curtin School of Medical Research, Australian National University, Canberra, Australia
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Eduardo Eyras
1EMBL Australia Partner Laboratory Network at the Australian National University, Canberra, Australia
2Centre for Computational Biomedical Sciences, The John Curtin School of Medical Research, Australian National University, Canberra, Australia
3The Shine-Dalgarno Centre for RNA Innovation, The John Curtin School of Medical Research, Australian National University, Canberra, Australia
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  • For correspondence: eduardo.eyras@anu.edu.au
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Abstract

We present the first biochemical-free technology for Real-time In Silico Enrichment of RNA species (RISER). RISER classifies RNA species from direct RNA nanopore signals, without the need for basecalling or a reference, and communicates with the sequencing hardware in real-time to enact in silico targeted RNA sequencing. We illustrate RISER for the enrichment and depletion of coding and non-coding RNA, demonstrating a 3.4-3.6x enrichment and 6.2-6.7x depletion of non-coding RNA in live sequencing experiments.

Competing Interest Statement

A.S. has received funds from Oxford Nanopore Technologies for travel and accommodation to speak at the Oxford Nanopore Technologies conference London Calling 2022. The authors declare no other competing interests.

Footnotes

  • https://github.com/comprna/riser

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
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Posted November 29, 2022.
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Real-time biochemical-free targeted sequencing of RNA species with RISER
Alexandra Sneddon, Agin Ravindran, Nadine Hein, Nikolay Shirokikh, Eduardo Eyras
bioRxiv 2022.11.29.518281; doi: https://doi.org/10.1101/2022.11.29.518281
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Real-time biochemical-free targeted sequencing of RNA species with RISER
Alexandra Sneddon, Agin Ravindran, Nadine Hein, Nikolay Shirokikh, Eduardo Eyras
bioRxiv 2022.11.29.518281; doi: https://doi.org/10.1101/2022.11.29.518281

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