Single nucleus RNA-Seq is not suitable for detection of microglial activation genes in humans
Single nucleus RNA-Seq (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 revealed that, while the majority of genes showed similar relative abundances in cells and nuclei, a small population of genes (~1%) was depleted in nuclei compared to whole cells. This population was 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 to detecting cellular activation in microglia in human disease. Overall design: Single nucleus and single cell sequencing of cortical tissue from 4 neurosurgical patients.