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. 2023 Nov 2;24(12):2068–2079. doi: 10.1038/s41590-023-01661-4

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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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Extended Data Fig. 4 — CD64⁺ macrophages were isolated from BALF of 5 HC, 5 randomly selected WTM, and 10 OM at least 221 days p.i. After 8 hours of culture, they were profiled using the nanoString nCounter System. (a) Principal Component Analysis (PCA) shows clustering patterns of convalescent monkeys. OM samples are represented by purple triangles and WTM samples by red squares. Volcano plots highlight genes significantly up-regulated and down-regulated between WTM and OM. (b) Similar to (a), volcano plots highlight genes significantly up-regulated and down-regulated between WTM and HC (up) or between OM and HC (down). (c) Heat map displays the top 50 genes resulting from Gene Set Enrichment Analysis (GSEA) conducted on the Hallmark gene sets obtained in (a). (d) Enrichment plots show data sets enriched in GSEA Hallmark analysis of CD64⁺ Mac as in (a), displaying the running Enrichment Score (ES) and positions of gene set members on the rank-ordered list. (e) Gating strategy defines different lymphocyte populations in BALF of HC, WTM, and OM at least 221 days p.i. Populations are defined based on specific marker expression. (f) Comparison of various lymphocyte populations in BALF of HC, WTM, and OM. (g) Comparison of marker expression on BALF CD45⁺ lymphocytes as described in (e). In each graph, individual symbols represent individual monkeys, bars indicate medians, and interquartile ranges are shown. p-Values were determined using a Kruskal-Wallis test with Dunn’s post-test in (f) and (g).

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