Advances in transcriptomics have transformed our understanding of gene expression, cellular heterogeneity, developmental processes, disease mechanisms, and responses to environmental stimuli. The rapid evolution of transcriptomic technologies has expanded capabilities from bulk RNA profiling to single-cell, spatially resolved, long-read, and multi-omics approaches, enabling unprecedented insights into biological systems. As transcriptomics becomes an essential tool across biomedical, agricultural, environmental, and biotechnology research, there is a growing need for standardized, reproducible, and accessible methodologies that guide researchers through increasingly complex workflows.

Despite remarkable progress, several challenges continue to limit the accuracy, reproducibility, and interpretability of transcriptomic studies. These include variability in sample collection and preservation, RNA isolation from challenging specimens, library preparation biases, sequencing artifacts, integration of data generated from diverse platforms, batch effects, computational scalability, and the analysis of increasingly large and multidimensional datasets. Furthermore, emerging technologies require specialized protocols and analytical frameworks that are often difficult to implement consistently across laboratories.

This Topical Collection aims to provide a comprehensive platform for methodologies spanning the entire transcriptomics workflow, from experimental design and sample preparation to data generation, processing, interpretation, and integration. The collection welcomes both established and emerging approaches.

By bringing together detailed protocols, technical innovations, and best practices, this collection will serve as a valuable reference for researchers seeking to adopt, optimize, and standardize transcriptomic methodologies, thereby accelerating discoveries and enhancing reproducibility across diverse scientific disciplines.