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 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 from derived from gene expression data. Our results provide critical insights for selection of scRNA-seq experimental platform in immunological studies. Overall design: Human PBMC samples were collected and sequenced from three healthy donors. Terminally differentiated effector memory CD8+ T cells re-expressing CD45RA were purified using fluorescence-activated cell sorting. For PBMCs we performed both Chromium Next GEM Single Cell 3' Gel Bead Kit v3.1 and the Evercode Whole Transcriptome kit v2 . TEMRA cells were sequences using Chromium Next GEM Single Cell 3' Gel Bead Kit v3.1 and Evercode WT Mini kit v2.