Capturing Single Cells in Droplets using Density Media

Differences between sub-populations of cells are often biologically important (e.g., T cell clonotypes, tumour subpopulations), but traditionally, methods such as RT-PCR only allow analysis of a population average. Single cells can be co-encapsulated with a reaction mix such as RT-PCR, in picoliter aqueous droplets in oil, and the droplets can then function as micro-reactors, where each droplet contains amplicons from a single cell. For instance, leukocytes may be encapsulated to profile epitope binding sites in natively paired T-cell receptor or antibody coding sequences.

To minimise confounding droplets with two or more cells, cells are typically diluted so that only 1 in 10 droplets contain a cell. However, the number of cells per droplet tends to change over time, because the cells are more dense than the buffers, and sediment out. We show here that adjusting the density so that cells are nearly neutrally buoyant, using density media such as PercollTM or OptiprepTM, minimises the rate of cell sedimentation, and allows encapsulation of cells at a controlled rate of cells per droplet.