Stereo-Seq Transcriptomics in Arabidopsis Leaves in Response to Salicylic Acid

Spatially resolved transcriptomics captures gene expression in tissue context, enabling direct mapping of defense pathways across organs and cell layers. This chapter describes a complete Stereo-seq workflow for Arabidopsis leaves treated with salicylic acid (SA), from plant growth and hormone application through cryosectioning, fixation, bright-field imaging and optional histology, on-chip permeabilization, in situ reverse transcription and library construction on STOmics V1.3 1 × 1 cm chips, sequencing on DNBSEQ platforms, and analysis using STOmics Analysis Workflow (SAW) with downstream spatial statistics and pathway enrichment. Practical parameters are given for section thickness, fixation, imaging, permeabilization optimization, sequencing configuration, and quality control. The bioinformatics analyses include binning strategies, alignment to TAIR10, normalization, clustering, spatial differential expression, pathway testing, and integration with single-cell RNA-seq references for cell-type deconvolution.