Single-cell RNA sequencing in yeast using the 10× genomics chromium device.
journal contributionposted on 2022-06-07, 11:05 authored by Lieselotte Vermeersch, Abbas Jariani, Jana Helsen, Benjamin M Heineike, Kevin J Verstrepen
Single-cell RNA sequencing (scRNA-seq) is emerging as an essential technique for studying the physiology of individual cells in populations. Although well-established and optimized for mammalian cells, research of microorganisms has been faced with major technical challenges for using scRNA-seq, because of their rigid cell wall, smaller cell size and overall lower total RNA content per cell. Here, we describe an easy-to-implement adaptation of the protocol for the yeast Saccharomyces cerevisiae using the 10× Genomics platform, originally optimized for mammalian cells. Introducing Zymolyase, a cell wall-digesting enzyme, to one of the initial steps of single-cell droplet formation allows efficient in-droplet lysis of yeast cells, without affecting the droplet emulsion and further sample processing. In addition, we also describe the downstream data analysis, which combines established scRNA-seq analysis protocols with specific adaptations for yeast, and R-scripts for further secondary analysis of the data.
Crick (Grant ID: 10134, Grant title: Ralser FC001134)
AnimalsChromiumGene Expression ProfilingGenomicsMammalsRNARNA-SeqSaccharomyces cerevisiaeSequence Analysis, RNASingle-Cell Analysis10× GenomicsSingle-cell omicsSingle-cell RNA sequencingTranscriptomicsYeastRalser FC0011340399 Other Chemical Sciences0601 Biochemistry and Cell BiologyDevelopmental Biology