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. 2023 Jun 5;3(7):796–812. doi: 10.1038/s43587-023-00436-8

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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. 7 — a, Volcano plot showing increased expression of inflammatory genes in Mcu^−/− BMDMs, compared to WT BMDMs, treated with zymosan for 3 h. Data normalization, dispersion estimates and model fitting (negative binomial) were carried out with the DESeq function (DESeq2 R package). Wald statistics were used for the significance tests. b, Volcano plot showing reduced expression of inflammatory genes in BAPTA-AM loaded BMDMs, when compared to unloaded BMDMs, treated with zymosan for 3 h. Data normalization, dispersion estimates and model fitting (negative binomial) were carried out with DESeq. Wald statistics were used for the significance tests. c, GSEA pathway analysis of Mcu^−/−, BAPTA-AM loaded (WT) and unloaded WT BMDMs stimulated with zymosan for 3 h. MΦ, macrophage. d, Normalized counts for representative genes in the GSEA hallmark inflammatory response pathway. N = 3–5 biological replicates. Error bars represent the s.e.m.; P values were determined by one-way ANOVA. e, Schematic showing gene transcripts used for BART analysis. f, BART analysis of 668 mCa²⁺-sensitive genes identified in a. Transcription factor (TF) rank was plotted against the −log(P value) for each identified transcription factor. g, Volcano plot showing gene expression of the GSEA inflammatory response pathway in unstimulated Mcu^−/− macrophages, compared to their WT counterparts. Data normalization, dispersion estimates and model fitting (negative binomial) were carried out with DESeq. Wald statistics were used for the significance tests. h, Volcano plot showing expression of genes of the GSEA TNF–NF-κB pathway in unstimulated Mcu^−/− macrophages, compared to their WT counterparts. Data normalization, dispersion estimates and model fitting (negative binomial) were carried out with DESeq. Wald statistics were used for the significance tests. i, Normalized counts for representative genes in the GSEA hallmark inflammatory response pathway. N = 4 biological replicates. Error bars represent the s.e.m.; P value was determined by Welch’s t-test, two-tailed.

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