Comparative Analysis of Droplet-Based Ultra-High-Throughput Single-Cell RNA-Seq Systems

Since its establishment in 2009, single-cell RNA sequencing (RNA-seq) has been a major driver behind progress in biomedical research. In developmental biology and stem cell studies, the ability to profile single cells confers particular benefits. Although most studies still focus on individual tissues or organs, the recent development of ultra-high-throughput single-cell RNA-seq has demonstrated potential power in characterizing more complex systems or even the entire body. However, although multiple ultra-high-throughput single-cell RNA-seq systems have attracted attention, no systematic comparison of these systems has been performed. Here, with the same cell line and bioinformatics pipeline, we developed directly comparable datasets for each of three widely used droplet-based ultra-high-throughput single-cell RNA-seq systems, inDrop, Drop-seq, and 10X Genomics Chromium. Although each system is capable of profiling single-cell transcriptomes, their detailed comparison revealed the distinguishing features and suitable applications for each system. [Display omitted] •Comprehensive diagrams for comparing the features of the three systems•An open source versatile pipeline for all systems•Systematic comparison on sensitivity, precision, bias, and costs•Demonstration of Smart-seq2 protocols with inDrop platform Zhang et al. compare three prevalent droplet-based high-throughput scRNA-seq systems using unified sample and bioinformatics pipeline. They provide detailed analyses on system designs and performance, which would guide both future experimental design and system improvement.