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. 2024 Apr 1;147(1):65. doi: 10.1007/s00401-024-02704-2

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© The Author(s) 2024

Open Access This 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/ .

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Fig. 2 — Brain myeloid cell similarity across brain regions. a Brain myeloid cell subclustering per brain region. Macrophage cluster numbers are indicated in bold (based on LYVE1, MRC1, CD163, and F13A1 marker genes). b Cross-region integration of subsampled brain myeloid cells across brain regions shows alignment between regions for most cells, except for one EC-enriched population of cells (highlighted in black circles). Shown are combined and per region UMAP plots. c EC enriched population (indicated as green cells in UMAP plot) was compared to all other brain myeloid cells across regions. Biological process GO term enrichment indicates upregulated synapse vesicle cycle changes and ion transport differences. d Up- and downregulated differentially expressed gene (DEG) numbers per region, filtered for microglial genes (average log2FC > 0.25). e Top 5 upregulated microglia genes per region (no significantly upregulated V2 markers identified)