Single-nucleus RNA sequencing revealed ribosomal genes expression defines the cellular state of oligodendrocytes and precursor cells in post-mortem ischemia mouse brains.

Accurate cell atlas analysis using single-nucleus RNA-seq (snRNA-seq) is highly influenced by RNA quality, with post-mortem interval (PMI) being a major factor. Thus, deciphering the non-cell-autonomous effects induced by PMI is critical for understanding the cellular and molecular disruptions it triggers. Here, we investigated the impact of PMI on cellular composition and gene expression using snRNA-seq of post-mortem mouse brain tissues. Samples were allowed to decay at 25 °C for varying durations prior to sequencing, covering a comprehensive range of RNA integrity number (RIN) values. Our results revealed that mRNA is more stable than rRNA during decay. Notably, we observed a preferential and transient depletion of oligodendrocytes and OPCs with increasing PMI. In parallel, a rapid and widespread upregulation of ribosomal protein (RP) genes occurred across various cell types, reaching a plateau at approximately 36 h PMI. Although overt loss of neuronal cell states was not detected, we observed significant upregulation of PMI-dependent RP genes, accompanied by a reduction in subpopulation cells. RP genes exhibited the most prominent differential expression in subpopulations experiencing greater perturbations, suggesting that their dysregulation may be linked to cell death. Through this work, we systematically characterized PMI-induced transcriptomic alterations in brain tissue at single-cell resolution and identified key factors contributing to these changes. Our findings offer new insights into the molecular consequences of postmortem hypoxia-ischemia and provide a valuable reference for transcriptomic analyses of RNA-degraded samples.