ArticleGenome biology2021
Mapping and modeling the genomic basis of differential RNA isoform expression at single-cell resolution with LR-Split-seq.
Article in Genome biology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 42 papers.
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Who cites it
42 citing papers in PubMed.
- Review
- Single cell analysis of developing Merkel cells reveals the emergence of non-coding RNA biotypes as a hallmark of terminal differentiation.Cell death and differentiation · 2026Article
- RAD: A Read-structure Agnostic Demultiplexer for Single-Cell Long-Read Sequencing and Analysis.bioRxiv : the preprint server for biology · 2026Article
- SCOTCH: isoform-level characterization of gene expression through long-read single-cell RNA sequencing.Nature communications · 2026Article
- Current trends and challenges in deciphering single molecule resolution maps of single cell transcriptomes.Briefings in bioinformatics · 2026Review
- Systematic cell-type resolved transcriptomes of 8 tissues in 8 lab and wild-derived mouse strains capture global and local expression variation.Cell genomics · 2026Article
- Elucidating the coordination of RNA processing using short-read and long-read RNA-sequencing methods.Nature reviews. Molecular cell biology · 2026Review
- Review
- Leveraging Single-Cell Technologies to Advance Understanding of Myocardial Disease.Circulation research · 2026Review
- Decoding the human PBMC isonome: isoform-level resolution with single-cell long-read transcriptomics.Frontiers in genetics · 2026Article
- Bioinformatics frameworks for single-cell long-read sequencing: unlocking isoform-level resolution.Briefings in bioinformatics · 2025Review
- Decoding the human PBMC isonome: Isoform-level resolution with single-cell long-read transcriptomics.bioRxiv : the preprint server for biology · 2025Article
- Nuclear Protein Aggregates Disrupt RNA Processing and Alter Biomechanics in a Muscle Cell Model of OPMD.Aging and disease · 2025Article
- LMNA R482L mutation causes impairments in C2C12 myoblasts subpopulations, alterations in metabolic reprogramming during differentiation, and oxidative stress.Scientific reports · 2025Article
- Accurate quantification of nascent and mature RNAs from single-cell and single-nucleus RNA-seq.Nucleic acids research · 2025Article
- Advances in long-read single-cell transcriptomics.Human genetics · 2024Review
- Review
- Review
- C5aR1 antagonism suppresses inflammatory glial responses and alters cellular signaling in an Alzheimer's disease mouse model.Nature communications · 2024Article
- Single-cell long-read targeted sequencing reveals transcriptional variation in ovarian cancer.Nature communications · 2024Article
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Authors and funding
10 authors.
Funding
Abstract
The rise in throughput and quality of long-read sequencing should allow unambiguous identification of full-length transcript isoforms. However, its application to single-cell RNA-seq has been limited by throughput and expense. Here we develop and characterize long-read Split-seq (LR-Split-seq), which uses combinatorial barcoding to sequence single cells with long reads. Applied to the C2C12 myogenic system, LR-split-seq associates isoforms to cell types with relative economy and design flexibility. We find widespread evidence of changing isoform expression during differentiation including alternative transcription start sites (TSS) and/or alternative internal exon usage. LR-Split-seq provides an affordable method for identifying cluster-specific isoforms in single cells.
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