Journal article
Accurate expression quantification from nanopore direct RNA sequencing with NanoCount
J Gleeson, A Leger, YDJ Prawer, TA Lane, PJ Harrison, W Haerty, MB Clark
Nucleic Acids Research | Published : 2022
DOI: 10.1093/nar/gkab1129
Abstract
Accurately quantifying gene and isoform expression changes is essential to understanding cell functions, differentiation and disease. Sequencing full-length native RNAs using long-read direct RNA sequencing (DRS) has the potential to overcome many limitations of short and long-read sequencing methods that require RNA fragmentation, cDNA synthesis or PCR. However, there are a lack of tools specifically designed for DRS and its ability to identify differential expression in complex organisms is poorly characterised. We developed NanoCount for fast, accurate transcript isoform quantification in DRS and demonstrate it outperforms similar methods. Using synthetic controls and human SH-SY5Y cell d..
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Awarded by National Health and Medical Research Council
Funding Acknowledgements
Australian National Health and Medical Research Council Early Career Fellowship [APP1072662]; Investigator Fellowship [APP1196841 to M.B.C.]; Wellcome Trust (Seed Award in Science) [201879/Z/16/Z to M.B.C.]; Strategic Award [102616 to P.J.H.]; UK Medical Research Council [MR/P026028/1 to P.J.H.]; National Institute for Health Research (NIHR) Oxford Health Biomedical Research Centre [BRC-1215-20005 to P.J.H.]; BBSRC, Institute Strategic Programme Grant [BB/J004669/1]; BBSRC Core Strategic Programme Grant [BB/P016774/1 toW.H.]; A.L. was supported by the EMBL Interdisciplinary Postdocs Programme (EIPOD) with co-funding from Marie Sklodowska-Curie actions COFUND [847543]. Funding for open access charge: Lab funds. Conflict of interest statement. J.G., W.H. and M.B.C. have received support from Oxford Nanopore Technologies (ONT) to present their findings at scientific conferences. A.L. has received a small consumable grant from ONT in return for methodology development and is now an ONT employee. However, ONT played no role in study design, execution, analysis or publication.