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. 2020 Jul 23;15:41. doi: 10.1186/s13024-020-00394-4

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© The Author(s) 2020

Open AccessThis 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/. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data.

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Fig. 5 — APOE isoform-specific effect on gene expression. RNA-seq data shown in Fig. 4 were analyzed using edgeR to identify differentially expressed genes between APOE isoforms. Scatterplots depict differentially expressed genes between APP/E3 vs APP/E4 (a), APP/E3/Trem2^ko vs APP/E4/Trem2^ko (b) E3 vs E4 (c), and E3/Trem2^ko vs E4/Trem2^ko mice (d). Shown are genes at p < 0.05 cutoff. Heatmaps and line patterning graphs of DAM and homeostatic microglia genes that are upregulated in either APOE4 (e-f) or in APOE3 mice (g-h) mice in a Trem2 and APOE-isoform dependent manner. Genes of interest are marked with colored circles and shown as line patterning