Expanding the Dimensions of Single-Cell Multi-Omics To Include Mitochondrial DNA through Fixation and Permeabilization

Single-cell multi-omics has transformed our understanding of cellular heterogeneity, yet incorporating mitochondrial DNA (mtDNA) remains challenging. Recent studies underscore the critical role of fixation and permeabilization techniques in preserving sample integrity, optimizing Tn5 tagmentation, and retaining mtDNA. In this Perspective, we review the chemical principles underlying fixation and permeabilization methods and highlight new single-cell multiomics technologies leveraging these approaches. We also explore future directions, particularly workflows designed to incorporate mtDNA mutations, enabling simultaneous analysis of mitochondrial genotypes and cellular states. These advances promise to deepen insights derived from single-cell multi-omics, broadening its impact on biological research and clinical applications.