Flexible and high-throughput approach for capturing large number of single cells simultaneously using microwell-based technology

Abstract

Abstract Single-cell RNA-seq is a powerful method for studying complex cell populations. As opportunities grow for single-cell multiomics methods in translational research, there is an increased need for high-throughput approaches capable of efficiently capturing and analyzing large numbers of cells simultaneously. Current assays on scRNA-seq platforms have limited throughput due to the low cell recovery and high multiplet rates with high cell inputs. Here we demonstrate the feasibility of profiling the single-cell gene expression of hundreds of thousands of cells in a single experiment using an eight-lane microwell based cartridge. We also increased the cell label diversity of cell capture beads to enable high cell loading with a lower rate of barcode collisions. To show the range of cell capture capabilities of the eight-lane microwell cartridge, we loaded different numbers of cells per lane ranging from 100 to over 40,000 cells. To evaluate the multiplet rates and sensitivity, we labeled two different cell types with antibody-based sample multiplexing prior to cell capture. Cell multiplet rates were also assessed through Sample Tag analysis. Detection of Sample Tags used showed no contamination of Sample Tag between samples. In addition, less than 0.5% barcode collision rate was detected from 360,000 viable cells captured with a bead. Targeted mRNA profiling had high correlation (R 2> 0.95) of gene expression across cell capture lanes. This study demonstrates that the eight-lane microwell-based cartridge technology provides flexibility and high-throughput cell capture of thousands of cells and could be readily extended to other existing single-cell technologies such as surface protein marker detection and immune profiling.