Systematic comparison of single-cell and single-nucleus transcriptomes during cardiomyocyte differentiation

Purpose:To systematically assess the differences between high-throughput single-cell and single-nuclei RNA-seq approaches, we compared Drop-seq and DroNc-seq, two microfluidic-based 3' RNA capture technologies that profile total cellular and nuclear RNA, respectively, during a time course experiment of human induced pluripotent stem cells (iPSCs) differentiating into cardiomyocytes Conclusions: Clustering of time-series transcriptomes from Drop-seq and DroNc-seq revealed six distinct cell types, five of which were found in both techniques. Furthermore, single-cell trajectories reconstructed from both techniques reproduced expected differentiation dynamics. Overall design: Drop-seq and DroNc-seq each on 2 hiPSC cell lines differentiating into cardiomyocytes across 5 time points. DroNc-seq on post-mortem primary heart tissue.