Harnessing HetHydrogel: An Approach to Single-Cell Multi-Omics

Developing a single-cell multi-omics technology with mtDNA mutation profiling at its core will enable precise determination of the relationship between mtDNA mutations and cellular phenotypes. To date, the development of permeability-engineered compartmentalization for the isolation and single-cell library preparation of individual cells, which includes Tn5 tagmentation and single-cell barcoding operations in the permeabilized microcapsule format, remains a formidable challenge. Herein, we present a approach for single-cell mitochondrial analysis, harnessing microfluidics to generate heterogeneous hydrogels as artificial membranes. These hydrogels serve to regulate the passage of mitochondrial DNA and nuclear genomes subsequent to the cell lysis step. This approach enables high-throughput mitochondrial DNA genotyping and accessible chromatin profiling at the single-cell level, significantly enhancing the capabilities of permeability-engineered compartmentalization.We conducted a comprehensive evaluation of cell retention and the selective permeability of the capsule reaction system, optimizing conditions for cell lysis, Tn5 tagmentation, and barcode labeling. Validation experiments were performed using Human 293T and Mouse 3T3 cells to assess identification and quantification performance. Our method offers a new strategy for the study of the functions of various mtDNA mutations in biological processes, while also offering a new system for the construction of single-cell multi-omics libraries. Overall design: To assess the impact of different lysis conditions on sequencing data, we performed Tn5 tagmentation-based library preparation on 293T cells encapsulated in hydrogel using fragmentation buffers 1-4.To investigate single-cell library preparation within hydrogel matrices, we conducted scATAC-seq experiments on intact 293T cells and intact 3T3 cells encapsulated in hydrogels.