Development of cell labeling technique for multiplex scRNA-seq. Mus musculus

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.

本研究全新开发了一款适用于单细胞RNA测序（scRNA-seq）样本多重化的细胞标记技术。为验证该新技术（USB标记法，USB methods）的应用价值，本研究将USB标记法标记的细胞，与基于抗体的传统样本多重化技术——即采用抗CDH1抗体的标记方法（Ab标记法，Ab method）——所标记的细胞，在标记效率与基因表达谱两方面进行了对比。本研究以未分化/已分化的小鼠胚胎干细胞（ESCs，包含R1与EB3两个株系）作为实验模型。实验结果表明，经USB标记法处理后，未分化与已分化的ESCs均可实现高效标记；但Ab标记法采用抗CDH1抗体进行标记时，由于多数已分化ESCs中的CDH1基因表达受到抑制，已分化ESCs的标记细胞数量出现了明显下降。本研究同时证实，USB标记法既不会对细胞活性造成影响，也不会干扰基因表达情况。本研究全新开发的USB标记法是一种通用型细胞标记技术，理论上可应用于任意类型的细胞，是一种操作简便、高效且兼具高性价比的scRNA-seq样本多重化方案。