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

Luyi Tian(The University of Melbourne), Jafar S. Jabbari(Walter and Eliza Hall Institute of Medical Research), Rachel Thijssen(The University of Melbourne), Quentin Gouil(The University of Melbourne), Shanika L. Amarasinghe(The University of Melbourne), Oliver Voogd(Walter and Eliza Hall Institute of Medical Research), Hasaru Kariyawasam(Walter and Eliza Hall Institute of Medical Research), Mei R. M. Du(Walter and Eliza Hall Institute of Medical Research), Jakob Schuster(Walter and Eliza Hall Institute of Medical Research), Changqing Wang(Walter and Eliza Hall Institute of Medical Research), Shian Su(The University of Melbourne), Xueyi Dong(The University of Melbourne), Charity W. Law(The University of Melbourne), Alexis Lucattini(Victorian Comprehensive Cancer Centre), Yair D. J. Prawer(The University of Melbourne), Coralina Collar-Fernández(Florey Institute of Neuroscience and Mental Health), Jin D. Chung(The University of Melbourne), Timur Naim(The University of Melbourne), Audrey Chan(The University of Melbourne), Chi Ly(The University of Melbourne), Gordon S. Lynch(The University of Melbourne), James G. Ryall(The University of Melbourne), Casey J. A. Anttila(Walter and Eliza Hall Institute of Medical Research), Hongke Peng(The University of Melbourne), Mary Ann Anderson(The Royal Melbourne Hospital), Christoffer Flensburg(The University of Melbourne), Ian J. Majewski(The University of Melbourne), Andrew W. Roberts(The Royal Melbourne Hospital), David C.S. Huang(The University of Melbourne), Michael B. Clark(The University of Melbourne), Matthew E. Ritchie(The University of Melbourne)
Genome biology
November 11, 2021
10.1186/s13059-021-02525-6
Cited by 223Open Access
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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 to transcriptome heterogeneity.

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