Vermeersch2022_Protocol_Single-CellRNASequencingInYeas (1).pdf (683.11 kB)
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Single-cell RNA sequencing in yeast using the 10× genomics chromium device.

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journal contribution
posted on 07.06.2022, 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.

Funding

Crick (Grant ID: 10134, Grant title: Ralser FC001134)

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