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. 2020 Nov 24;5:108. doi: 10.1038/s41541-020-00258-4

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© The Author(s) 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. 3 — DEGs at two time points (12 and 40 hpi) in comparison with 0 hpi were identified with Deseq2. Volcano plots comparing gene expression differences between 0 and 12 hpi (a, c), and at 0 and 40 hpi (b, d) are presented for the intramuscular (IM) and the intramammary (IMM) group, respectively. Red dots correspond to genes with a q value < 0.01 and a Abslog2FoldChange > 2. e Heatmap of the top 500 DEG in control and immunized groups during the course of infection is presented. Functional analysis was performed with ToppFun and a dendrogram shows the relationship among biological functions of commonly deregulated genes according to the mammary and systemic scores, the time, and the treatment group. MS mammary score, SS systemic clinical score. Red arrows indicate IMM cows with 0 and 40 hpi profiles that were undistinguishable (further designed as cured cows).