@article{f1bcf97631ea4e9184b1eda56c96145b,
title = "Comprehensive characterization of single-cell full-length isoforms in human and mouse with long-read sequencing",
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.",
keywords = "Long-read sequencing, Single-cell gene expression, Single-cell multi-omics, Splicing",
author = "Luyi Tian and Jabbari, \{Jafar S.\} and Rachel Thijssen and Quentin Gouil and Amarasinghe, \{Shanika L.\} and Oliver Voogd and Hasaru Kariyawasam and Du, \{Mei R.M.\} and Jakob Schuster and Changqing Wang and Shian Su and Xueyi Dong and Law, \{Charity W.\} and Alexis Lucattini and Prawer, \{Yair David Joseph\} and Coralina Collar-Fern{\'a}ndez and Chung, \{Jin D.\} and Timur Naim and Audrey Chan and Ly, \{Chi Hai\} and Lynch, \{Gordon S.\} and Ryall, \{James G.\} and Anttila, \{Casey J.A.\} and Hongke Peng and Anderson, \{Mary Ann\} and Christoffer Flensburg and Ian Majewski and Roberts, \{Andrew W.\} and Huang, \{David C.S.\} and Clark, \{Michael B.\} and Ritchie, \{Matthew E.\}",
note = "Funding Information: We thank Clare Weeden and Marie-Liesse Asselin-Labat for providing the cell lines used in this study, Stephen Wilcox for Illumina sequencing, Kathleen Zeglinski for designing the FLAMES logo and creating Fig. 1 A, and Joan Heath for providing critical feedback on this manuscript. The review history is available as Additional file 6. Barbara Cheifet was the primary editor of this article and managed its editorial process and peer review in collaboration with the rest of the editorial team. Funding Information: 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. Publisher Copyright: {\textcopyright} 2021, The Author(s).",
year = "2021",
month = nov,
day = "11",
doi = "10.1186/s13059-021-02525-6",
language = "English",
volume = "22",
journal = "Genome Biology",
issn = "1474-7596",
publisher = "BioMed Central",
number = "1",
}