Systematic comparison of high-throughput single-cell RNA-seq methods for immune cell profiling [DS]

We systematically benchmarked seven high-throughput single-cell RNA-seq methods. We prepared 21 libraries under identical conditions of a defined mixture of two human and two murine lymphocyte cell lines, simulating heterogeneity across immune-cell types and cell sizes. We evaluate methods by their cell recovery rate, library efficiency, sensitivity, and ability to recover expression signatures for each cell type. We observed higher mRNA detection sensitivity with the 10x Genomics 5’ v1 and 3’ v3 methods. We demonstrate that these methods have fewer drop-out events which facilitates the identification of differentially-expressed genes and improves the concordance of single-cell profiles to immune bulk RNA-seq signatures. Various single-cell RNA-seq methods used to generate libraries using a 1:1:1:1 mixture of four lymphocyte cell lines (Jurkat, TALL-104, EL4, IVA12).