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. 2024 Mar 27;27(5):886–900. doi: 10.1038/s41593-024-01600-y

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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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Extended Data Fig. 7 — a, Phenotypic trajectory followed by the human microglia transplanted in App^NL-G-F ApoE^−/− and App^NL-G-F, obtained by an unbiased pseudotime ordering with Monocle 3. Proportion of cells (y-axis) present in each cell state as in Fig. 1b (rows) at different stages of the binned pseudotime trajectory (x-axis), colored by host genotypes (dots represent single mice, n = 11 App^NL-G-F, n = 6 App^NL-G-F ApoE^−/−). b, c, Volcano plots showing a paired comparison between microglia transplanted in App^NL-G-F ApoE^−/− and App^NL-G-F mice, coloured by (b) host genotype and (c) cluster as in Fig. 1a. The number of significant genes per condition is reported in brackets in the legend (Log2 Fold-Change threshold > 0.1). Adjusted p-value threshold < 0.05 (Wilcoxon rank-sum test, P-values adjusted with Bonferroni correction based on the total number of genes in the dataset, ns = not significant). d, Phenotypic trajectory followed by the human microglia after injection of amyloid-b oligomers (Aβο) or scrambled peptide (Scr), obtained by an unbiased pseudotime ordering with Monocle 3. Proportion of cells (y-axis) present in each cell state as in Fig. 1a (rows) at different stages of the binned pseudotime trajectory (x-axis), colored by cells genotypes (dots represent single mice, n = 7 for Scr, n = 13 Aβο). e, f, Volcano plots showing a paired comparison between microglia transplanted in App^WT mice and treated with Aβο or Scr, coloured by (e) treatment and (f) cluster as in Fig. 1a. The number of significant genes per condition is reported in brackets in the legend (Log2 Fold-Change threshold > 0.1). Adjusted p-value threshold < 0.05 (Wilcoxon rank-sum test, P-values adjusted with Bonferroni correction based on the total number of genes in the dataset, ns = not significant). Box plots in a and d, are limited by lower and upper quartiles and midline indicates median; whiskers extend from the box to the smallest or largest value no further than 1.5*inter-quartile range. Unpaired t-test with Welch’s correction, two-tailed, alpha = 0.05, significance was set as P-value < 0.05, *p < 0.05, **p < 0.01, ***p < 0.001,****p < 0.0001.