Guest Editor
Collection Overview
Single-cell gene expression analysis has allowed the identification of important regulatory elements of the cell fate during several developmental programs in humans and model animals. Microfluidic-based approaches require the isolation of individual cells, so the messenger derived from each one can be labeled in further steps. Cell isolation can be challenging when working with plant material, due to the presence of the cell walls. Generally, protoplast isolation by enzymatic digestion has been the most common procedure for isolating cells in plants. During the last few years, several protoplast isolation protocols have allowed the application of scRNA-seq, mainly focusing on Arabidopsis. However, many plant tissues’ secondary cell wall hinders the enzymatic digestion required for individual protoplast isolation. Thick cell walls require longer digestion that potentially affects the mRNA quality. Moreover, the representation of the cells located in the inner layers of a tissue, or an organ can be compromised. Consequently, several research groups opted for the alternative approach of characterizing the mRNA extracted from individual nuclei instead of cells. In this collection, we aim to present the different methodologies that can be applied in plants for protoplasts and nuclei isolation compatible with scRNA-seq.
The scRNA-seq analysis can be complicated. Usually, the pipelines available are based on a command-line interface that requires a good knowledge of the R programming language, which poses a big barrier for researchers that possess limited expertise in the field of computational biology. In the present Collection, we encourage researchers to present easy-to-install and user-friendly web applications developed to incorporate the necessary tools for a straightforward scRNA-seq data analysis.
