Systematic Comparison of 10X Genomics and Parse Single Cell RNA Technologies across PBMC and CD8 ⁺ TEMRA Cells

Single-cell RNA sequencing technologies provide insights into gene expression at the cellular level, enabling detailed analysis of cellular heterogeneity. In this study, we systematically compared two scRNA-seq platforms,10X Genomics and Parse Biosciences, using human peripheral blood mononuclear cells (PBMCs) and terminally differentiated effector memory CD8 ⁺ T cells (TEMRAs). We identified significant differences in gene expression variability and platform-specific biases, such as ribosomal and mitochondrial gene capture. 10X has a bias for shorter genes, while Parse exhibited enhanced detection of longer transcripts. In CD8 ⁺ TEMRAs, the expression of key genes related to antimicrobial immune responses were underrepresented in Parse cells compared to 10X cells (e.g. GNLY , PRF1 and GZMB ). These findings underscore the need for careful selection of scRNA-seq platforms based on specific research objectives, as platform-specific biases can influence cell type identification and as well as mechanistic insights derived from gene expression data. Our results provide insights for selection of scRNA-seq experimental platforms in immunological studies.