Development of cell labeling technique for multiplex scRNA-seq

We newly developed cell labeling technique for sample multiplexing of scRNA-seq. To verify the usefulness of this new technique (USB methods), we compared the labeling efficiencies and expression profiles of cells labeled by USB method to those by antibody-based conventional sample multiplexing technique using anti-CDH1 antibody (Ab method). As a model, we used undifferentiated/differentiated mouse ESCs (R1 and EB3). By USB method, all cells were labeled efficiently in both undifferentiated and differentiated ESCs, but the number of cells labeled by Ab method with anti-CDH1 antibody in differentiated ESCs was clearly reduced because CDH1 was repressed in most of differentiated ESCs. We also confirmed that USB method did not affect cell viability as well as gene expression. Our newly developed USB method is a universal labeling method that can be theoretically applied to any type of cells and represents a simple, highly efficient and cost-effective method for multiplexing scRNA-seq.