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. 2022 Oct 24;25(11):1446–1457. doi: 10.1038/s41593-022-01183-6

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© The Author(s) 2022

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. 3 — a, UMAP plot of 44,983 single-cell transcriptomes, colored by major cell types. b, UMAP of T cells and NK cells, colored by T-cell identity, genotype and T-cell marker genes. c, Bar plot showing the relative distribution of each genotype-tissue experimental group within the T/NK cell population. d, UMAP plots of oligodendrocytes in the Rag1^−/− and wild-type integrated dataset, colored by identified clusters, genotype and tissue annotation, as well as selected marker genes. e, Boxplot of the IRO cluster proportion per sample. The central line denotes the median, boxes represent the IQR and whiskers show the distribution except for outliers. Outliers are all points outside 1.5× the IQR. Each dot represents a sample (n = 8 independent experiments) and significant results (scCODA model) are indicated with red bars. f, Immunofluorescence staining and quantification of STAT1⁺CC1⁺ oligodendrocytes in the white matter of 24-month-old wild-type and 24-month-old Rag1^−/− mice (n = 5 mice per group, ^*P = 0.0466; data are mean ± s.e.m.; P values represent a two-sided Student’s t-test). Scale bar, 20 µm. g, Immunofluorescence staining and quantification of CC1⁺ oligodendrocyte density in the gray (GM) and white matter (WM) of 12-, 18- and 24-month-old wild-type and Rag1^−/− mice (GM, n = 3, 3, 5, 4; WM, n = 3, 3, 5, 4; 12 months versus 24 months, ^*P = 0.0185, 24-month versus 24-month Rag1^−/−, ^**P = 0.0083; data are mean ± s.e.m.; P values represent two-sided, one-way ANOVA with post hoc Tukey’s test). Scale bar, 20 µm. h, Immunofluorescence staining and quantification of CC1⁺STAT1⁺ oligodendrocytes in the white matter of 24-month-old wild-type and CD8^−/− mice (n = 4 mice per group, ^**P = 0.0035; data are mean ± s.e.m.; P value represents a two-sided Student’s t-test). Scale bar, 20 µm. i, Immunofluorescence staining and quantification of CC1⁺ oligodendrocyte density (red) in the white matter of 24-month-old wild-type and CD8^−/− mice (n = 4 mice per group, ^*P = 0.0176; data are mean ± s.e.m.; P value represents a two-sided Student’s t-test). Scale bar, 20 µm.

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