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. 2021 Jun 28;18:145. doi: 10.1186/s12974-021-02193-0

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© The Author(s) 2021

Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data.

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Fig. 3 — Single-cell RNA-seq of the brain cortex and hippocampus reveals hyperactivated microglia in Smek1^-/- mice. a tSNE visualization of individual cell clusters from the cortex and hippocampus of wild-type (n = 2) (left panel) and Smek1^-/- (n = 2) (right panel) mice. b tSNE plots highlighting the marker gene Csf1r for microglia. c Heatmap of total microglial subclusters. d Microglia are divided into 4 clusters according to diverse transcriptional patterns, namely, clusters 0 to 3. e Contribution of wild-type versus Smek1^-/- mouse samples to microglial cell clusters. f Cell number of microglial clusters in different genotypes. g Violin plots representing the distribution of the log-transformed normalized gene expression of IL-1β in microglia (clusters 0–3). The red box represents proinflammatory microglia. h tSNE map representing the distribution of the log-transformed normalized gene expression of IL-1β in microglia (clusters 0–3)