Microtechnologies for single-cell and spatial multi-omics

Single-cell omics assays allow the identification of the type, subtype and functional state of a single cell. To put such single-cell data in the context of tissues, spatially resolved omics can be applied to quantify gene expression and regulation in intact tissues at the genome scale. However, to obtain a full picture of gene regulatory networks in a cell, multi-omic assays are required that can assess two or more modalities of omics information. In this Review, we discuss microfabricated systems that can be engineered to isolate, probe, manipulate and process single cells at the micrometre scale for single-cell and spatial multi-omics studies. We outline microchannel-, microarray- and droplet-based microfluidic platforms, examining their application in multimodal cellular profiling at the cellular and subcellular level. Finally, we discuss the key challenges that need to be addressed to advance the translation and commercialization of such microchip-based technologies for fundamental research and medical applications.