Single-Cell versus Single-Nucleus: Transcriptome differences in murine kidney after ischemia-reperfusion injury

The kidney is a complex organ, which consists of multiple components with highly diverse cell types. A detailed understanding of these cell types in health and disease is crucial for future development of preventive and curative treatment strategies. In recent years, single cell RNA sequencing (scRNAseq) and single nucleus RNA sequencing (snRNAseq) technology has opened up completely new possibilities in investigating the variety of renal cell populations in physiological and pathological states. Here, we systematically assess differences between scRNAseq and snRNAseq approaches in transcriptome analysis of murine kidneys after ischemia reperfusion injury. We included tissues from control kidneys and from kidneys harvested one week after mild (17 minutes clamping time) and severe (27 minutes clamping time) transient unilateral ischemia. Our findings reveal important methodological differences in the discovery of inflammatory cells, tubular cells, and other specialized cell types. While the scRNAseq approach is advantageous for investigating immune cells, the snRNAseq approach allows superior insight into healthy and damaged tubular cells. Apart from differences in the quantitative discovery rate, we found important qualitative discrepancies in the captured transcriptomes with crucial consequences for the interpretation of cell states and molecular functions. Together, we provide an overview of method-dependent differences between scRNAseq and snRNAseq results from identical post-ischemic kidney tissues. Our results highlight the importance of choosing the right approach for specific research questions.