Concepts and new developments in droplet-based single cell multi-omics

HighlightsSingle cell methods have proliferated in recent years, made feasible by droplet microfluidic technologies, including commercialized technologies.Although the concept of single cell barcoding using these methodologies is straightforward, these assays require several assumptions about the underlying molecular biology for data interpretation.Following the initial droplet-based single cell demonstrations, new experimental and bioinformatics methods have evolved the baseline expectations of these assays, producing more complex and higher quality data, including single cell multi-omics.By generalizing themes from prior bioinformatics and experimental innovation, new users and experienced technology developers can identify opportunities to maximize data generation, improve analytical interpretation, and avoid failure modes in establishing new assays.AbstractSingle cell sequencing technologies have become a fixture in the molecular profiling of cells due to their ease, flexibility, and commercial availability. In particular, partitioning individual cells inside oil droplets via microfluidic reactions enables transcriptomic or multi-omic measurements for thousands of cells in parallel. Complementing the multitude of biological discoveries from genomics analyses, the past decade has brought new capabilities from assay baselines to enable a deeper understanding of the complex data from single cell multi-omics. Here, we highlight four innovations that have improved the reliability and understanding of droplet microfluidic assays. We emphasize new developments that further orient principles of technology development and guidelines for the design, benchmarking, and implementation of new droplet-based methodologies.