Best practices for the execution, analysis, and data storage of plant single-cell/nucleus transcriptomics

• DOI: 10.1093/plcell/koae003
• Publication Date: 2024-01-17T18:31:33Z
• Authors: Carolin Grones; Thomas Eekhout; Dongbo Shi; Manuel Neumann; Lea S Berg; Yuji Ke; Rachel Shahan; Kevin L Cox; Fabio Gomez-Cano; Hilde Nelissen; Jan U Lohmann; Stefania Giacomello; Olivier C Martin; Benjamin Cole; Jia-Wei Wang; Kerstin Kaufmann; Michael T Raissig; Gergo Palfalvi; Thomas Greb; Marc Libault; Bert De Rybel
• Keywords: Comparability

Abstract Single-cell and single-nucleus RNA-sequencing technologies capture the expression of plant genes at an unprecedented resolution. Therefore, these are gaining traction in molecular developmental biology for elucidating transcriptional changes across cell types a specific tissue or organ, upon treatments, response to biotic abiotic stresses, between genotypes. Despite rapidly accelerating use technologies, collective standardized experimental analytical procedures support acquisition high-quality data sets still missing. In this commentary, we discuss common challenges associated with single-cell transcriptomics plants propose general guidelines improve reproducibility, quality, comparability, interpretation make readily available community fast-developing field research.