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Nanopore native RNA sequencing of a human poly(A) transcriptome

Workman, Rachael E.; Tang, Alison D.; Tang, Paul S.; Jain, Miten; Tyson, John R.; Razaghi, Roham; Zuzarte, Philip C.; Gilpatrick, Timothy; Payne, Alexander; Quick, Joshua; Sadowski, Norah; Holmes, Nadine; de Jesus, Jaqueline Goes; Jones, Karen L.; Soulette, Cameron M.; Snutch, Terrance P.; Loman, Nicholas; Paten, Benedict; Loose, Matthew; Simpson, Jared T.; Olsen, Hugh E.; Brooks, Angela N.; Akeson, Mark; Timp, Winston

Authors

Rachael E. Workman

Alison D. Tang

Paul S. Tang

Miten Jain

John R. Tyson

Roham Razaghi

Philip C. Zuzarte

Timothy Gilpatrick

Alexander Payne

Joshua Quick

Norah Sadowski

Nadine Holmes

Jaqueline Goes de Jesus

Karen L. Jones

Cameron M. Soulette

Terrance P. Snutch

Nicholas Loman

Benedict Paten

MATTHEW LOOSE matt.loose@nottingham.ac.uk
Professor of Developmental and Computational Biology

Jared T. Simpson

Hugh E. Olsen

Angela N. Brooks

Mark Akeson

Winston Timp



Abstract

High-throughput complementary DNA sequencing technologies have advanced our understanding of transcriptome complexity and regulation. However, these methods lose information contained in biological RNA because the copied reads are often short and modifications are not retained. We address these limitations using a native poly(A) RNA sequencing strategy developed by Oxford Nanopore Technologies. Our study generated 9.9 million aligned sequence reads for the human cell line GM12878, using thirty MinION flow cells at six institutions. These native RNA reads had a median length of 771 bases, and a maximum aligned length of over 21,000 bases. Mitochondrial poly(A) reads provided an internal measure of read-length quality. We combined these long nanopore reads with higher accuracy short-reads and annotated GM12878 promoter regions to identify 33,984 plausible RNA isoforms. We describe strategies for assessing 3′ poly(A) tail length, base modifications and transcript haplotypes.

Citation

Workman, R. E., Tang, A. D., Tang, P. S., Jain, M., Tyson, J. R., Razaghi, R., …Timp, W. (2019). Nanopore native RNA sequencing of a human poly(A) transcriptome. Nature Methods, https://doi.org/10.1038/s41592-019-0617-2

Journal Article Type Article
Acceptance Date Sep 19, 2019
Online Publication Date Nov 18, 2019
Publication Date Nov 18, 2019
Deposit Date Nov 19, 2019
Publicly Available Date May 19, 2020
Journal Nature Methods
Print ISSN 1548-7091
Electronic ISSN 1548-7105
Publisher Nature Publishing Group
Peer Reviewed Peer Reviewed
DOI https://doi.org/10.1038/s41592-019-0617-2
Keywords Biotechnology; Cell Biology; Biochemistry; Molecular Biology
Public URL https://nottingham-repository.worktribe.com/output/3330879
Publisher URL https://www.nature.com/articles/s41592-019-0617-2

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