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. 2023 Aug 31;8(10):1846–1862. doi: 10.1038/s41564-023-01462-3

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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. 7 — a. Zero-centered and normalized expression of select genes in E. coli MG1655 cultures treated with the indicated antibiotics. Data from eBW4 (Supplementary Table 2). Genes were selected from among those related to the following GO terms: ‘Response to DNA damage’, ‘Cell wall stress’, and ‘Ribosome’. b. Same as (A) but for B. subtilis. Genes were selected from among those related to the ‘Response to DNA damage’ and ‘Ribosome’ GO terms and by searching for genes known to be upregulated in response to treatment with cell-wall targeting antibiotics (that is cefuroxime). c. UMAPs of E. coli MG1655 transcriptomes after treatment with indicated antibiotics (top) and corresponding cluster assignments (bottom). Clusters were uniquely defined for each population. d. Same as (C) but for B. subtilis 168.