Dean Flow Assisted Single Cell and Bead Encapsulation for High Performance Single Cell Expression Profiling

Droplet microfluidics-based platform (Drop-seq) has been shown to be a powerful tool for single cell expression profiling. Nevertheless, this platform required the simultaneous encapsulation of single cell and single barcoded bead, the incidence of which was very low, limiting its efficiency. Spiral channels were reported to focus the barcoded beads and thus increased the efficiency, but focusing of cells was not demonstrated, which could potentially further enhance the performance. Here, we designed spiral and serpentine channels to focus both bead and cell solutions and implemented this microfluidic design on Drop-seq. We characterized the effect of cell/bead concentration on encapsulation results and tested the performance by coencapsulating barcoded beads and human–mouse cell mixtures followed by sequencing. The results showed ∼300% and ∼40% increase in cell utilization rate compared to the traditional Drop-seq device and the device focusing beads alone, respectively. This chip design showed great potential for high efficiency single cell expression profiling.