Comprehensive characterization of single-cell full-length isoforms in human and mouse with long-read sequencing
- Author(s)
- Tian, L; Jabbari, JS; Thijssen, R; Gouil, Q; Amarasinghe, SL; Voogd, O; Kariyawasam, H; Du, MRM; Schuster, J; Wang, C; Su, S; Dong, X; Law, CW; Lucattini, A; Prawer, YDJ; Collar-Fernández, C; Chung, JD; Naim, T; Chan, A; Ly, CH; Lynch, GS; Ryall, JG; Anttila, CJA; Peng, H; Anderson, MA; Flensburg, C; Majewski, I; Roberts, AW; Huang, DCS; Clark, MB; Ritchie, ME;
- Details
- Publication Year 2021-11-11,Volume 22,Issue #1,Page 310
- Journal Title
- Genome Biology
- 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.
- Publisher
- BMC
- Keywords
- Long-read sequencing; Single-cell gene expression; Single-cell multi-omics; Splicing
- Research Division(s)
- Epigenetics And Development; Blood Cells And Blood Cancer; Advanced Technology And Biology
- PubMed ID
- 34763716
- Publisher's Version
- https://doi.org/10.1186/s13059-021-02525-6
- Open Access at Publisher's Site
https://doi.org/10.1186/s13059-021-02525-6- Terms of Use/Rights Notice
- Refer to copyright notice on published article.
Creation Date: 2021-12-07 12:04:16
Last Modified: 2021-12-09 02:06:29