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

Genome Biology

Alexis Lucattini¹  Jin D. Chung²  Timur Naim²  Gordon S. Lynch²  Audrey Chan²  Chi Hai Ly³  James G. Ryall⁴  Michael B. Clark⁵  Yair David Joseph Prawer⁵  Coralina Collar-Fernández⁶  Mei R. M. Du⁷  Hasaru Kariyawasam⁷  Jakob Schuster⁷  Oliver Voogd⁷  Casey J. A. Anttila⁷  Changqing Wang⁷  Jafar S. Jabbari⁸  David C. S. Huang⁹  Christoffer Flensburg⁹  Shanika L. Amarasinghe⁹  Luyi Tian⁹  Matthew E. Ritchie⁹  Hongke Peng⁹  Rachel Thijssen⁹  Charity W. Law⁹  Shian Su⁹  Xueyi Dong⁹  Quentin Gouil⁹  Ian Majewski⁹  Mary Ann Anderson^1,10  Andrew W. Roberts^1,11 

[1] Australian Genome Research Facility, Victorian Comprehensive Cancer Centre, Melbourne, VIC, Australia;Centre for Muscle Research, Department of Physiology, The University of Melbourne, Melbourne, VIC, Australia;Centre for Muscle Research, Department of Physiology, The University of Melbourne, Melbourne, VIC, Australia;Present address: Department of Neurology, Stanford University, Stanford, CA, USA;Centre for Muscle Research, Department of Physiology, The University of Melbourne, Melbourne, VIC, Australia;Present address: VOW, North Parramatta, NSW, Australia;Centre for Stem Cell Systems, Department of Anatomy and Neuroscience, The University of Melbourne, Parkville, VIC, Australia;The Florey Institute of Neuroscience and Mental Health, Parkville, VIC, Australia;The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia;The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia;Australian Genome Research Facility, Victorian Comprehensive Cancer Centre, Melbourne, VIC, Australia;The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia;Department of Medical Biology, The University of Melbourne, Parkville, VIC, Australia;The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia;Department of Medical Biology, The University of Melbourne, Parkville, VIC, Australia;Clinical Haematology, Peter MacCallum Cancer Centre and Royal Melbourne Hospital, Melbourne, VIC, Australia;The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia;Department of Medical Biology, The University of Melbourne, Parkville, VIC, Australia;Clinical Haematology, Peter MacCallum Cancer Centre and Royal Melbourne Hospital, Melbourne, VIC, Australia;Centre for Cancer Research, University of Melbourne, Melbourne, VIC, Australia;Victorian Comprehensive Cancer Centre, Melbourne, VIC, Australia;

关键词: Single-cell gene expression;    Long-read sequencing;    Splicing;    Single-cell multi-omics;   

DOI  :  10.1186/s13059-021-02525-6

来源: Springer

【 摘 要 】

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.

【 授权许可】

CC BY