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 t...
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2021
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oai:doaj.org-article:b1aa5d4188e746cca4e60723f7229ae12021-11-14T12:42:54ZComprehensive characterization of single-cell full-length isoforms in human and mouse with long-read sequencing10.1186/s13059-021-02525-61474-760Xhttps://doaj.org/article/b1aa5d4188e746cca4e60723f7229ae12021-11-01T00:00:00Zhttps://doi.org/10.1186/s13059-021-02525-6https://doaj.org/toc/1474-760XAbstract 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.Luyi TianJafar S. JabbariRachel ThijssenQuentin GouilShanika L. AmarasingheOliver VoogdHasaru KariyawasamMei R. M. DuJakob SchusterChangqing WangShian SuXueyi DongCharity W. LawAlexis LucattiniYair David Joseph PrawerCoralina Collar-FernándezJin D. ChungTimur NaimAudrey ChanChi Hai LyGordon S. LynchJames G. RyallCasey J. A. AnttilaHongke PengMary Ann AndersonChristoffer FlensburgIan MajewskiAndrew W. RobertsDavid C. S. HuangMichael B. ClarkMatthew E. RitchieBMCarticleSingle-cell gene expressionLong-read sequencingSplicingSingle-cell multi-omicsBiology (General)QH301-705.5GeneticsQH426-470ENGenome Biology, Vol 22, Iss 1, Pp 1-24 (2021) |
| institution |
DOAJ |
| collection |
DOAJ |
| language |
EN |
| topic |
Single-cell gene expression Long-read sequencing Splicing Single-cell multi-omics Biology (General) QH301-705.5 Genetics QH426-470 |
| spellingShingle |
Single-cell gene expression Long-read sequencing Splicing Single-cell multi-omics Biology (General) QH301-705.5 Genetics QH426-470 Luyi Tian Jafar S. Jabbari Rachel Thijssen Quentin Gouil Shanika L. Amarasinghe Oliver Voogd Hasaru Kariyawasam Mei R. M. Du Jakob Schuster Changqing Wang Shian Su Xueyi Dong Charity W. Law Alexis Lucattini Yair David Joseph Prawer Coralina Collar-Fernández Jin D. Chung Timur Naim Audrey Chan Chi Hai Ly Gordon S. Lynch James G. Ryall Casey J. A. Anttila Hongke Peng Mary Ann Anderson Christoffer Flensburg Ian Majewski Andrew W. Roberts David C. S. Huang Michael B. Clark Matthew E. Ritchie Comprehensive characterization of single-cell full-length isoforms in human and mouse with long-read sequencing |
| description |
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. |
| format |
article |
| author |
Luyi Tian Jafar S. Jabbari Rachel Thijssen Quentin Gouil Shanika L. Amarasinghe Oliver Voogd Hasaru Kariyawasam Mei R. M. Du Jakob Schuster Changqing Wang Shian Su Xueyi Dong Charity W. Law Alexis Lucattini Yair David Joseph Prawer Coralina Collar-Fernández Jin D. Chung Timur Naim Audrey Chan Chi Hai Ly Gordon S. Lynch James G. Ryall Casey J. A. Anttila Hongke Peng Mary Ann Anderson Christoffer Flensburg Ian Majewski Andrew W. Roberts David C. S. Huang Michael B. Clark Matthew E. Ritchie |
| author_facet |
Luyi Tian Jafar S. Jabbari Rachel Thijssen Quentin Gouil Shanika L. Amarasinghe Oliver Voogd Hasaru Kariyawasam Mei R. M. Du Jakob Schuster Changqing Wang Shian Su Xueyi Dong Charity W. Law Alexis Lucattini Yair David Joseph Prawer Coralina Collar-Fernández Jin D. Chung Timur Naim Audrey Chan Chi Hai Ly Gordon S. Lynch James G. Ryall Casey J. A. Anttila Hongke Peng Mary Ann Anderson Christoffer Flensburg Ian Majewski Andrew W. Roberts David C. S. Huang Michael B. Clark Matthew E. Ritchie |
| author_sort |
Luyi Tian |
| title |
Comprehensive characterization of single-cell full-length isoforms in human and mouse with long-read sequencing |
| title_short |
Comprehensive characterization of single-cell full-length isoforms in human and mouse with long-read sequencing |
| title_full |
Comprehensive characterization of single-cell full-length isoforms in human and mouse with long-read sequencing |
| title_fullStr |
Comprehensive characterization of single-cell full-length isoforms in human and mouse with long-read sequencing |
| title_full_unstemmed |
Comprehensive characterization of single-cell full-length isoforms in human and mouse with long-read sequencing |
| title_sort |
comprehensive characterization of single-cell full-length isoforms in human and mouse with long-read sequencing |
| publisher |
BMC |
| publishDate |
2021 |
| url |
https://doaj.org/article/b1aa5d4188e746cca4e60723f7229ae1 |
| work_keys_str_mv |
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