Comparison of cell type distribution between single-cell and single-nucleus RNA sequencing: enrichment of adherent cell types in single-nucleus RNA sequencing

Abstract Single-cell ribonucleic acid (RNA) sequencing (scRNA-seq) is an effective technique for estimating the cellular composition and transcriptional profiles of individual cells from fresh tissue. Single-nucleus RNA sequencing (snRNA-seq) is necessary to perform this type of analysis in frozen or difficult-to-dissociate tissues, which cannot be subjected to scRNA-seq. This difference in the state of tissues leads to variation in cell-type distributions among each platform. To identify the characteristics of these methods and their differences, scRNA-seq and snRNA-seq were performed in parallel for colon and liver tissues. The two platforms revealed similar diversity but different proportions of cell types in matched tissues. The proportions of epithelial cells in the colon and hepatocytes in the liver were relatively high in snRNA-seq and that of immune cells was relatively high in scRNA-seq. This difference could be explained by variations in the expression scores of adhesion genes due to the disruption of the cytoplasmic contents during scRNA-seq. The enrichment of epithelial cells in the colon resulted in a discrepancy in the differentiation of epithelial cells. This enrichment was also well matched with the images of hematoxylin and eosin staining and the estimated distribution of cell types in bulk RNA sequencing. These results showed that snRNA-seq could be used to analyze tissues that cannot be subjected to scRNA-seq and provides more information in specific cell type analysis.