Single-Cell Transcriptomics in Arabidopsis in Response to Salicylic Acid and Jasmonic Acid

Salicylic acid (SA) and jasmonic acid (JA) coordinate plant immunity through partially antagonistic signaling pathways that differ across cell types and over time. Single-cell and single-nucleus RNA sequencing now resolve these hormone responses at cellular resolution, allowing clear separation of early primary signaling waves from secondary and downstream transcriptional programs. In the context of plant-pathogen interactions, these approaches are particularly powerful for uncovering how distinct cell populations perceive SA and JA, reprogram defense networks, and balance growth-immunity trade-offs. This chapter provides end-to-end wet-lab protocols for nuclei-based snRNA-seq tailored to SA and JA treatments, including sample preparation, nuclei isolation, and library construction. In parallel, a bioinformatics analysis workflow is described, covering quality control, ambient RNA correction, doublet removal, dataset integration, cell type mapping, differential expression analysis, and pathway and module scoring. Together, these experimental and computational pipelines enable researchers to dissect hormone-driven immune responses at single-cell resolution and to generate cell-type-resolved hypotheses that can guide downstream genetic and physiological studies.