Journal article

Comprehensive characterization of single-cell full-length isoforms in human and mouse with long-read sequencing

Luyi Tian, Jafar S Jabbari, Rachel Thijssen, Quentin Gouil, Shanika L Amarasinghe, Oliver Voogd, Hasaru Kariyawasam, Mei RM Du, Jakob Schuster, Changqing Wang, Shian Su, Xueyi Dong, Charity W Law, Alexis Lucattini, Yair David Joseph Prawer, Coralina Collar-Fernandez, Jin D Chung, Timur Naim, Audrey Chan, Chi Hai Ly Show all

GENOME BIOLOGY | BMC | Published : 2021

Abstract

A modified Chromium 10x droplet-based protocol that subsamples cells for both short-read and long-read (nanopore) sequencing together with a new computational pipeline (FLAMES) is developed to enable isoform discovery, splicing analysis, and mutation detection in single cells. We identify thousands of unannotated isoforms and find conserved functional modules that are enriched for alternative transcript usage in different cell types and species, including ribosome biogenesis and mRNA splicing. Analysis at the transcript level allows data integration with scATAC-seq on individual promoters, improved correlation with protein expression data, and linked mutations known to confer drug resistance..

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Grants

Awarded by Silicon Valley Community Foundation


Awarded by Leukemia & Lymphoma Society (LLS) of America Fellowship


Awarded by LLS Specialized Center of Research [SCOR]


Awarded by Cancer Australia


Awarded by Australian National Health and Medical Research Council (NHMRC)


Awarded by Australian Research Council


Funding Acknowledgements

This work was supported by funding from the Chan Zuckerberg Initiative DAF, an advised fund of Silicon Valley Community Foundation (grant numbers 2018-182819 and 2019-002443 to M.E.R.), a Melbourne Research Scholarship to L.T, a Leukemia & Lymphoma Society (LLS) of America Fellowship to R.T. (5467-18) and LLS Specialized Center of Research [SCOR] grant no. 7015-18 to A.W.R. and D.C.S.H., a Cure Cancer and Cancer Australia grant (1186003 to R.T.), fellowships and grants from the Australian National Health and Medical Research Council (NHMRC: Project Grant 1143163 to M.E.R.; Program Grants 1016701 to D.C.S.H. and 1113577 to A.W.R.; Research Fellowships 1079560 to A.W.R., 1156024 to D.C.S.H., 1072662 to M.B.C. and 1104924 to M.E.R.; Investigator Grant 1174902 to A.W.R.), the Australian Research Council (Discovery Project 200102903 to M.E.R.), the Genomics Innovation Hub, Victorian State Government Operational Infrastructure Support, and Australian Government NHMRC IRIISS.