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. 2024 Jan 8;25(2):226–239. doi: 10.1038/s41590-023-01722-8

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© The Author(s) 2024

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. 6 — a, Heatmaps of differentially expressed genes (rows) from whole-tissue mRNA profiles ordered by k-means clustering and organ types (top, colors) at 0.5 day after sublethal LPS injection in wild-type (left) or Tnf ^− /− mice (right). Values are log2 fold-changes relative to matching organs from untreated mice for wild-type, or LPS-treated wild-type mice for Tnf ^− /−. Statistical analyses were performed with limma (FDR-adjusted p-value < 0.01, absolute fold change > 2, or FDR-adjusted p-value < 0.05, absolute fold change > 2). Shown are all the genes found to be differentially regulated in at least one of the indicated conditions (row annotations in black). BM, bone marrow; iLN, inguinal lymph node. b, Percentages (x axis) of genes differentially expressed in tissues (rows) upon sublethal LPS injection in Tnf ^− /− mice (left) or mice treated with anti-TNF antibodies (1 h prior to LPS; right) that match the genes regulated by LPS in wild-type mice. c, Heatmaps of differentially expressed genes (rows) from whole-tissue mRNA profiles ordered by k-means clustering and organ types (top, colors) at 0.5 day after cecal ligation and puncture (CLP) with pre-treatment with anti-TNF (right) or isotype control (left) antibodies. Values are log2 fold-changes relative to matching organs from sham operated mice for CLP with isotype control antibodies, or CLP operated mice for CLP with anti-TNF antibodies. Statistical analyses were performed with limma (FDR-adjusted p-value < 0.1, or FDR-adjusted p-value < 0.1). Shown are all the genes found to be differentially regulated in at least one of the indicated conditions (row annotations in black).