A drop-based workflow for fast and robust joint profiling of transcriptome and chromatin accessibility in the same cell

Single-cell multiomics technologies have significantly advanced our understanding of cellular heterogeneity and biological complexity. The joint profiling of single-cell RNA sequencing (scRNA-seq) and single-cell ATAC sequencing (scATAC-seq) within the same cell offers a powerful approach for enabling direct linkage between gene expression and chromatin accessibility at single-cell resolution. This integration significantly enhances sensitivity and specificity in identifying rare cell populations and elucidating epigenetic regulatory mechanisms. In this study, we present a robust, high-throughput droplet-based microfluidic protocol that enables simultaneous profiling of RNA and chromatin accessibility from individual cells. The streamlined workflow incorporates key steps, including cell pretreatment, nuclei isolation, gel bead-in-emulsion (GEM) generation, and the construction of scRNA-seq and scATAC-seq libraries. The protocol supports parallel processing of tens of thousands of cells in a single experiment, offering exceptional scalability and reproducibility. The multimodal nature of this approach allows for integrative analysis of multiple features from the same cell, making it an invaluable tool for dissecting complex biological systems.