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. 2023 Apr 4;11:60. doi: 10.1186/s40478-023-01547-4

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© The Author(s) 2023

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. 2 — Microglia and MCs adopt unique timepoint-specific transcriptomes connected along a trajectory. a UMAP plot showing 6 microglia and 3 MC clusters. b UMAP plot coloured by pseudotime, determined using trajectory analysis with Monocle3. Increased pseudotime indicates further distance from starting cells (i.e., MG1 and MC1). c Clustered heatmap showing expression of gene modules in each microglia and MC cluster. d Top differentially-expressed genes per cluster. e Top differentially expressed microglia and MC genes at dpi 5 and 7. f UpSet plot showing overlap in the number of gene ontology (GO) biological processes enriched in microglia and MCs clusters. GO processes common to two or more clusters are denoted by a connecting line. g, h Dot plot showing the top 5 GO processes associated with each microglia (g) and MC (h) cluster. Data is presented from one independent experiment with four mice per group