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Single nucleus sequencing fails to detect microglial activation

By N. Thrupp, C. Sala Frigerio, L. Wolfs, N. G. Skene, S. Poovathingal, Y. Fourne, P. M. Matthews, T. Theys, R. Mancuso, B. de Strooper, M. Fiers

Posted 13 Apr 2020
bioRxiv DOI: 10.1101/2020.04.13.035386

Single nucleus RNA-Seq (snRNA-Seq) methods are used as an alternative to single cell RNA-Seq methods, as they allow transcriptomic profiling of frozen tissue. However, it is unclear whether snRNA-Seq is able to detect cellular state. Indeed, snRNA-Seq analyses of human brain samples have failed to detect a consistent microglial activation signature in Alzheimer's Disease. A comparison of microglia from single cells and single nuclei of four human subjects reveals that ~1% of genes is depleted in nuclei compared to whole cells. This small population contains 18% of genes previously implicated in microglial activation, including APOE, CST3, FTL, SPP1, and CD74. We confirm our findings across multiple previous single nucleus and single cell studies. Given the low sensitivity of snRNA-Seq to this population of activation genes, we conclude that snRNA-Seq is not suited to detecting cellular activation in microglia in human disease. ### Competing Interest Statement The authors have declared no competing interest.

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