Leveraging two novel droplet-based single-cell RNA Sequencing platforms: a comparative study with 10x genomics

Currently, single cell transcriptome profiling technology is gaining popularity, with an increasing number of novel platforms emerging. The development of new technologies is aimed at improving data quality, scale, cost, or labor intensity. Given the rapid evolution of these technologies, a comprehensive and independent comparison of platforms is crucial to identify the most suitable one for studying various biological objects and achieving specific experimental goals.

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 10× 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. 10× 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.