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. 2020 Nov 19;3:693. doi: 10.1038/s42003-020-01418-x

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© This is a U.S. government work and not under copyright protection in the U.S.; foreign copyright protection may apply 2020

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. 9 — INTACT-DNA samples from Aldh1l1-NuTRAP and Cx3cr1-NuTRAP brains were used for epigenome analyses. a–d Total genomic levels of mCG, hmCG, mCH, and hmCH (n = 8/input, n = 4/positive fraction; One-way ANOVA with Tukey’s multiple comparisons test, *p < 0.05, **p < 0.01, ***p < 0.001). e Principal component analysis of average gene body mCG (%) across astrocytic, microglial, neuronal, and oligodendrocytic cell marker lists separates input, Aldh1l1-NuTRAP-positive (Aldh1l1-Pos), and Cx3cr1-NuTRAP-positive (Cx3cr1-Pos) fractions. f mCG averaged over 200 nucleotide bins upstream, in the gene body, and downstream of published astrocyte genes (McKenzie)¹⁸ in the positive fraction of Aldh1l1-NuTRAP, positive fraction of Cx3cr1-NuTRAP, and input samples combined. g Average percentage mCG in the positive fraction of Aldh1l1-NuTRAP, positive fraction of Cx3cr1-NuTRAP, and input samples combined in genomic DNA upstream 4 kb of the TSS, in the gene body, and downstream 4 kb of the TES of astrocytic genes. h Hypomethylation of astrocytic gene promoters in the Aldh1l1-NuTRAP-positive fraction correlates with higher astrocytic gene expression in the Aldh1l1-positive fraction than input and Cx3cr1-NuTRAP-positive fraction. i mCG averaged over 200 nucleotide bins upstream, in the gene body, and downstream of published microglia genes¹⁸ in the positive fraction of Aldh1l1-NuTRAP, positive fraction of Cx3cr1-NuTRAP, and input. j Average percentage mCG in the positive fraction of Aldh1l1-NuTRAP, positive fraction of Cx3cr1-NuTRAP, and input DNA upstream 4 kb of the TSS, in the gene body, and downstream 4 kb of the TES of microglia genes. k Hypomethylation of microglia gene promoters in the Cx3cr1 positive fraction correlates with higher microglia gene expression. e–i n = 8/input, n = 4/positive fraction; 2-way ANOVA with Sidak’s multiple comparison test, *p < 0.05, **p < 0.01, ***p < 0.001.