Project description: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.
Project description:Single-cell RNA sequencing technologies provide insights into gene expression at the cellular level, enabling detailed analysis of cellular heterogeneity. In this study, we systematically compared two scRNA-seq platforms—10X Genomics and Parse Biosciences—using human peripheral blood mononuclear cells (PBMCs) and terminally differentiated effector memory CD8+ T cells (TEMRAs). We identified significant differences in gene expression variability and platform-specific biases, such as ribosomal and mitochondrial gene capture. 10X has a bias for shorter genes, while Parse exhibited enhanced detection of longer transcripts. In CD8+ TEMRAs, the expression of key genes related to immune responses were underrepresented in Parse cells compared to 10X cells (e.g. GNLY, PRF1 and GZMB). These findings underscore the need for careful selection of scRNA-seq platforms based on specific research objectives, as platform-specific biases can influence cell type identification and as well as mechanistic insights from derived from gene expression data. Our results provide critical insights for selection of scRNA-seq experimental platform in immunological studies.