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 incorporate TCR profiling. We also discuss workflow throughput, sample requirements, timing, cost, and labor as critical factors to consider. Apart from the platform-specific experimental constraints, our findings highlight how differences in cell recovery and sensitivity influence the ability to resolve niche cell subtypes such as CD4 + and CD8 + T-cells. Platforms with higher intra-sample variation had reduced sequencing efficiency, which cumulatively impacts reproducibility and overall experiment cost. By including TCR chain recovery for multiple donors, we provide the first comparison of T-cell specific performance in the only assays available for single cell TCR recovery. This work provides a basis by which users can balance performance and practical considerations when selecting a single-cell RNA sequencing platform.