Nuclei Isolation from Mature Leaves of Arabidopsis thaliana Infected by Bacterial Pathogens for Single-Nucleus Multi-Omics

Single-nucleus omics technologies are increasingly applied in plant biology to investigate transcriptional and chromatin regulation at cellular resolution. A key requirement for these approaches is the isolation of high-quality nuclei, which can be particularly challenging in plant tissues due to cell wall complexity and residual debris. Here, I present a streamlined protocol for isolating nuclei from fresh Arabidopsis thaliana leaves infected with the bacterial pathogen Pseudomonas syringae. This method eliminates the need for density gradient separation and fluorescence-activated nuclei sorting (FANS), reducing hands-on time while maintaining compatibility with single-nucleus RNA and ATAC sequencing using the 10x Genomics platform.