Comprehensive characterization of single-cell full-length isoforms in human and mouse with long-read sequencing.
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 RitchiePublished in: Genome biology (2021)
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.
Keyphrases
- single cell
- rna seq
- high throughput
- induced apoptosis
- single molecule
- cell cycle arrest
- randomized controlled trial
- electronic health record
- endothelial cells
- big data
- oxidative stress
- cell death
- small molecule
- endoplasmic reticulum stress
- genome wide
- signaling pathway
- machine learning
- mesenchymal stem cells
- data analysis
- pi k akt
- network analysis