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 is providing a range of experimental options. Cost, sensitivity, throughput, flexibility, and ease of use influence that selection. We performed a comprehensive comparison of single-cell transcriptomic approaches using multiple standardized PBMCs. In evaluating seven recently available kits that interrogate whole transcriptome mRNA and two including TCR sequencing, we report on standard single-cell sensitivity metrics including gene saturation, UMI detection, cell recovery, sequencing efficiency, and cell subset resolution. We also discuss workflow throughput, sample requirements, timing, cost, and labor as critical factors to consider based on project goals. 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 cell subset resolution. This work provides a basis by which users can balance performance and practical considerations when selecting an RNA single-cell sequencing platform.