Description
Over the past decade, microfluidic technology has greatly impacted the throughput and precision of single-cell genomic analysis such that tens of thousands of cells can be profiled in a single experiment. The dominant method for single-cell genomic analysis has been single-cell RNA sequencing, and recent development of droplet microfluidic platforms has enabled the generation of large-scale human cell atlases based on whole-transcriptome analysis. While the transcriptome provides extensive information about cell type and cell state, there are many aspects of cellular identity that cannot be measured with RNA sequencing, including morphological phenotypes, lipid composition, and even non-coding genetic variation. Furthermore, high-throughput single-cell RNA-seq can be costly, especially if the cell-type of interest is rare. We present a suite of microfluidic tools for multimodal characterization of single cells, that also allow for genotype- and phenotype-based enrichment of single cells prior to RNA-sequencing. First we present a novel strategy for encapsulating cells in hydrogel beads. This approach allows for genotype-based enrichment using fluorescent activated cell sorting. Next, we present a microfluidic platform that enables high-content image-based sorting of single cells before RNA sequencing. Together, these tools allow for deep sequencing of rare cell types that are not identifiable through antibody-based profiling of surface protein markers.