Single Cell RNA-Sequencing in Arabidopsis Root Tissues

Yuji Ke; Max Minne; Thomas Eekhout; Bert De Rybel

doi:10.1007/978-1-0716-3354-0_4

Single Cell RNA-Sequencing in Arabidopsis Root Tissues

Methods Mol Biol. 2023:2698:41-56. doi: 10.1007/978-1-0716-3354-0_4.

Authors

Yuji Ke^{1

2}, Max Minne^{1

2}, Thomas Eekhout^{1

2

3}, Bert De Rybel^{4

5}

Affiliations

¹ Ghent University, Department of Plant Biotechnology and Bioinformatics, Ghent, Belgium.
² VIB Center for Plant Systems Biology, Ghent, Belgium.
³ VIB Single Cell Core, VIB, Ghent/Leuven, Belgium.
⁴ Ghent University, Department of Plant Biotechnology and Bioinformatics, Ghent, Belgium. bert.derybel@psb.vib-ugent.be.
⁵ VIB Center for Plant Systems Biology, Ghent, Belgium. bert.derybel@psb.vib-ugent.be.

PMID: 37682468
DOI: 10.1007/978-1-0716-3354-0_4

Abstract

Droplet-based single-cell RNA-sequencing (scRNA-seq) empowers transcriptomic profiling with an unprecedented resolution, facilitating insights into the cellular heterogeneity of tissues, developmental progressions, stress-response dynamics, and more at single-cell level. In this chapter, we describe the experimental workflow of processing Arabidopsis root tissue into protoplasts and generating single-cell transcriptomes. We also describe the general computational workflow of visualizing and utilizing scRNA-seq data. This protocol can be used as a starting point for establishing a scRNA-seq workflow.

Keywords: Arabidopsis; FACS; Protoplast; Root; Single cell; Transcriptomics; scRNA-seq.

MeSH terms

Arabidopsis* / genetics
Disease Progression
Gene Expression Profiling
Humans
Protoplasts
RNA

Substances

RNA