Evaluating the practical aspects and performance of commercial single-cell RNA sequencing technologies

The rapid development of updated and new commercially available single-cell transcriptomics platforms provides users with a range of experimental options. Cost, sensitivity, throughput, flexibility, and ease of use, all influence the selection of an optimal workflow. We performed a comprehensive comparison of single-cell transcriptomic approaches using multiple standardized PBMCs from different donors. We report on standard single-cell metrics including cell recovery, sequencing efficiency, sensitivity, cell annotation, and differential gene expression for seven recently available kits that interrogate whole transcriptome mRNA, and two that include TCR profiling. We also discuss workflow throughput, sample requirements, timing, cost, and labor as critical factors to consider. In addition to variable experimental constraints imposed by each platform, our findings highlight differences in cell recovery and sensitivity, which we found to significantly influence the ability to resolve cell subtypes. This work provides a basis by which users can balance performance and practical considerations when selecting a single-cell RNA sequencing platform.