Single-nucleus RNA sequencing (snRNA-seq) is used as an alternative to single-cell RNA-seq, as it allows transcriptomic profiling of frozen tissue. However, it is unclear whether snRNA-seq is able to detect cellular state in human tissue. Indeed, snRNA-seq analyses of human brain samples have failed to detect a consistent microglial activation signature in Alzheimer’s disease. Our comparison of microglia from single cells and single nuclei of four human subjects reveals that, although most genes show similar relative abundances in cells and nuclei, a small population of genes (∼1%) is depleted in nuclei compared to whole cells. This population is enriched for genes previously implicated in microglial activation, including APOE, CST3, SPP1, and CD74, comprising 18% of previously identified microglial-disease-associated genes. Given the low sensitivity of snRNA-seq to detect many activation genes, we conclude that snRNA-seq is not suited for detecting cellular activation in microglia in human disease.
A small set of genes is depleted in microglial nuclei relative to single cells
This set is enriched for microglial activation genes, including APOE and SPP1
This depletion is confirmed in publicly available datasets
Single-nucleus sequencing is not suited for the detection of human microglial activation
Thrupp et al. demonstrate the depletion of a small population of genes in nuclei relative to cells in human microglia by using single-nucleus and single-cell sequencing. This population is enriched for microglial activation genes, suggesting that single-nucleus sequencing is not suited for the detection of microglial activation in humans.