Leveraging Two Novel Droplet-Based Single-Cell RNA Sequencing Platforms: a Comparative Study With 10x Genomics

Here we performed a comparison of two droplet-based high-throughput single-cell platforms, namely, SeekOne and MobiDrop with a widely-used commercial platform from 10x Genomics. The use of different types of samples allowed us to evaluate the performance of the platforms on cell suspensions of varying complexity and quality. 10x showed generally superior performance, although all platforms compared in this study showed acceptable gene yield and allowed identification of all expected cell types. Taking into account the cost and availability of devices and reagents required for each platform and the flexibility in the number of samples loaded onto the chip, SeekOne and MobiDrop might serve as a good alternative. The results of the current comparison will support the community's efforts to compare different aspects, including sample amount requirements, throughput, cell quality, gene capture efficiency and cell type representativeness. Overall design: We analyzed the samples of human peripheral blood mononuclear cells, murine adrenal glands and human tumors to compare performance of the three scRNA-seq platforms (10x, SeekOne, MobiDrop). To compare 3-primed assays of 10x, SeekOne and MobiDrop pooled PBMC derived from 4 patients and murine adrenal gland samples obtained from two-week-old or three-day-old mice were used. Human tumor tissue samples were obtained from two operated patients with non-functioning pancreatic neuroendocrine tumors to compare 10x and MobiDrop 5-primed assays.