Isolation of Plant Root Nuclei for Single Cell RNA Sequencing

Abstract The characterization of the transcriptional similarities and differences existing between plant cells and cell types is important to better understand the biology of each cell composing the plant, to reveal new molecular mechanisms controlling gene activity, and to ultimately implement meaningful strategies to enhance plant cell biology. To gain a deeper understanding of the regulation of plant gene activity, the individual transcriptome of each plant cell needs to be established. Until recently, single cell approaches were mostly limited to bulk transcriptomic studies on selected cell types. Accessing specific cell types required the development of labor‐intensive strategies. Recently, single cell sequencing strategies were successfully applied on isolated Arabidopsis thaliana root protoplasts. However, this strategy relies on the successful isolation of viable protoplasts upon the optimization of the enzymatic cocktails required to digest the cell wall and on the compatibility of fragile plant protoplasts with the use of microfluidic systems to generate single cell transcriptomic libraries. To overcome these difficulties, we present a simple and fast alternative strategy: the isolation and use of plant nuclei to access meaningful transcriptomic information from plant cells. This protocol was specifically developed to enable the use of the plant nuclei with 10× Genomics’ Chromium technology partitions technology. Briefly, the plant nuclei are released from the root by chopping into a nuclei isolation buffer before purification by filtration then nuclei sorting. Upon sorting, the nuclei are resuspended in a low divalent ion buffer compatible with the Chromium technology in order to create single nuclei ribonucleic acid‐sequencing libraries (sNucRNA‐seq). © 2020 Wiley Periodicals LLC. Basic Protocol 1 : Arabidopsis seed sterilization and planting Basic Protocol 2 : Nuclei isolation from Arabidopsis roots Basic Protocol 3 : Fluorescent‐activated nuclei sorting (FANS) purification Support Protocol : Estimation of nuclei density using Countess II automated cell counter Alternate Protocol 1 : Proper growth conditions for Medicago truncatula and Sorghum bicolor Alternate Protocol 2 : Estimation of nuclei density using sNucRNA‐seq technology