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. 2023 Jun 8;24(7):1173–1187. doi: 10.1038/s41590-023-01522-0

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© The Author(s) 2023

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 license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license 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 license, visit http://creativecommons.org/licenses/by/4.0/.

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Fig. 2 — a, UMAP plots of single microglial cells treated with fibrin, iC3b and LPS identified by unsupervised clustering analysis (n = 16,196 cells from two independent experiments). b, Fractions of cells in each Seurat cluster colored based on treatment label. c, UpSet plot showing a matrix layout of DEGs specific to a cluster (single filled circle with no vertical lines) and DEGs shared between clusters (filled circles connected with vertical lines). Vertical bar plot of the unique or overlapping DEGs in clusters (top). Horizontal bar plot of the number of upregulated DEGs for a cluster (left). d, Heat map of top ten DEGs per single-cell cluster. Example GO molecular function terms and genes for a given cluster are shown. Five-hundred cells (maximum) were randomly selected from each cluster, as shown in a, for visualization. Gene expression is depicted as log-normalized scaled expression. e, List of selected top upregulated ligand-induced genes. f, GSEA plots of top GO terms for ligand-induced gene signatures. Adjusted P < 0.05 by Kolmogorov–Smirnov test with BH test correction. Exp., expression; unstim., unstimulated.