Single-cell Genomics using Droplet-based Microfluidics

We develop a system to profile the transcriptome of mammalian cells in isolation using reverse emulsion droplet-based microfluidic techniques. This is accomplished by (a) encapsulating and lysing one cell per emulsion droplet, and (b) uniquely barcoding the RNA contents from each cell using unique DNA-barcoded microgel beads. This enables us to study the transcriptional behavior of a large number of cells at single-cell resolution. We then use these techniques to study transcriptional responses of isolated immune cells to precisely controlled chemical and pathological stimuli provided in the emulsion droplet.