Multistep genomics on single cells and live cultures in subnanoliter capsules

Single-cell sequencing methods uncover natural and induced variation between cells. Many functional genomic methods, however, require multiple steps that cannot yet be scaled to high throughput, including assays on living cells. In this study, we developed capsules with amphiphilic gel envelopes (CAGEs), which selectively retain cells and large analytes while being freely accessible to media, enzymes, and reagents. Capsules enable high-throughput multistep assays combining live-cell culture with genome-wide readouts. We established methods for barcoding CAGE DNA libraries and applied them to measure persistence of gene expression programs in cells by capturing the transcriptomes of tens of thousands of expanding clones in CAGEs. The compatibility of CAGEs with diverse enzymatic reactions will facilitate the expansion of the current repertoire of single-cell high-throughput measurements and their extension to live-cell assays.