High-throughput total RNA sequencing in single cells using VASA-seq

Salmén, Fredrik; Jonghe, Joachim De; Kamiński, Tomasz S.; Alemany, Anna; Parada, Guillermo E.; Verity-Legg, Joe; Yanagida, Ayaka; Kohler, Timo N.; Battich, Nicholas; Brekel, Floris van den; Ellermann, Anna L.; Arias, Alfonso Martínez; Nichols, Jennifer; Hemberg, Martin; Hollfelder, Florian; Oudenaarden, Alexander van

doi:10.1038/s41587-022-01361-8

articleNature BiotechnologyJun 27, 2022HYBRID OA

High-throughput total RNA sequencing in single cells using VASA-seq

FSFredrik Salmén JDJoachim De Jonghe TSTomasz S. Kamiński AAAnna Alemany GEGuillermo E. Parada

Royal Netherlands Academy of Arts and Sciences · University Medical Center Utrecht · +11 more institutions

PubMed

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Abstract

Most methods for single-cell transcriptome sequencing amplify the termini of polyadenylated transcripts, capturing only a small fraction of the total cellular transcriptome. This precludes the detection of many long non-coding, short non-coding and non-polyadenylated protein-coding transcripts and hinders alternative splicing analysis. We, therefore, developed VASA-seq to detect the total transcriptome in single cells, which is enabled by fragmenting and tailing all RNA molecules subsequent to cell lysis. The method is compatible with both plate-based formats and droplet microfluidics. We applied VASA-seq to more than 30,000 single cells in the developing mouse embryo during gastrulation and early…

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Topics & keywords

Topics

Keywords

Polyadenylation
Transcriptome
Biology
RNA splicing
RNA
Alternative splicing
Computational biology
RNA-Seq

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