Understanding plant responses to stress is crucial for improving crop resilience in the face of climate change and environmental challenges. One emerging method for studying these responses is RNA sequencing (RNA-Seq), which comprehensively analyzes transcriptomic changes under various stress conditions. This chapter presents a basic step-by-step bioinformatics protocol for analyzing RNA-Seq data from plants under stress conditions. The protocol covers quality control, read trimming, alignment, gene expression quantification, differential expression analysis, functional enrichment, and interpretation of the results to understand how plants remember and respond to past stress events. The protocol emphasizes the utility of various bioinformatics tools and databases, ensuring reproducibility and clarity in the results. By following these methods, researchers can identify and characterize the genes involved in plant stress memory, paving the way for future advances in plant stress resilience.