Comparative Analysis of Whole Transcriptome Single-Cell Sequencing Technologies in Complex Tissues

Abstract

ABSTRACTThe development of single-cell omics tools has enabled scientists to study the tumor microenvironment (TME) in unprecedented detail. However, each of the different techniques may have its unique strengths and limitations. Here we directly compared two commercially available high-throughput single-cell RNA sequencing (scRNA-seq) technologies - droplet-based 10X Chromiumvs.microwell-based BD Rhapsody - using paired samples from patients with localized prostate cancer (PCa) undergoing a radical prostatectomy.Although high technical consistency was observed in unraveling the whole transcriptome, the relative abundance of cell populations differed. Cells with low-mRNA content such as T cells were underrepresented in the droplet-based system, at least partly due to lower RNA capture rates. In contrast, microwell based scRNA-seq recovered less cells of epithelial origin. Moreover, we discovered platform-dependent variabilities in mRNA quantification and cell-type marker annotation. Overall, our study provides important information for selection of the appropriate scRNA-seq platform and for the interpretation of published results.SYNOPSISComparison of scRNA-seq protocols uncovers disparities in RNA-to-library conversionMicrowell-based scRNA-seq technology excels in capturing low-mRNA content cellsBiased transcriptomes due to gene specific RNA detection efficacies by both platformsThe study guides in informed scRNA-seq platform selection and data interpretation