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

Genome Biology

Alexis Lucattini¹  James G. Ryall²  Gordon S. Lynch²  Audrey Chan²  Chi Hai Ly²  Jin D. Chung²  Timur Naim²  Michael B. Clark³  Yair David Joseph Prawer³  Coralina Collar-Fernández⁴  Changqing Wang⁵  Oliver Voogd⁵  Luyi Tian⁵  Rachel Thijssen⁵  Hasaru Kariyawasam⁵  Christoffer Flensburg⁵  Xueyi Dong⁵  David C. S. Huang⁵  Mary Ann Anderson⁵  Mei R. M. Du⁵  Jakob Schuster⁵  Shian Su⁵  Casey J. A. Anttila⁵  Quentin Gouil⁵  Jafar S. Jabbari⁵  Shanika L. Amarasinghe⁵  Charity W. Law⁵  Andrew W. Roberts⁵  Matthew E. Ritchie⁵  Hongke Peng⁵  Ian Majewski⁵ 

[1] Australian Genome Research Facility, Victorian Comprehensive Cancer Centre;Centre for Muscle Research, Department of Physiology, The University of Melbourne;Centre for Stem Cell Systems, Department of Anatomy and Neuroscience, The University of Melbourne;The Florey Institute of Neuroscience and Mental Health;The Walter and Eliza Hall Institute of Medical Research;

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

DOI  :  10.1186/s13059-021-02525-6

来源: DOAJ

【 摘 要 】

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.

【 授权许可】

Unknown