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An image-based transcriptomics atlas reveals the regional and microbiota-dependent molecular, cellular, and spatial structure of the murine gut.

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Title: An image-based transcriptomics atlas reveals the regional and microbiota-dependent molecular, cellular, and spatial structure of the murine gut.
Authors: Xu RJ; Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA; Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA; Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA., Zhang H; Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA; Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA., Cadinu P; Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA; Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA., Nicol PB; Department of Data Science, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA., Herrmann US; Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA; Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA., Lee T; Core for Computational Biomedicine, Department of Biomedical Informatics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA., Geistlinger L; Core for Computational Biomedicine, Department of Biomedical Informatics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA., Irizarry RA; Department of Data Science, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA., Moffitt JR; Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA; Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA. Electronic address: jeffrey.moffitt@childrens.harvard.edu.
Source: Cell host & microbe [Cell Host Microbe] 2026 Mar 11; Vol. 34 (3), pp. 509-525.e13. Date of Electronic Publication: 2026 Feb 19.
Publication Type: Journal Article
Journal Info: Publisher: Cell Press Country of Publication: United States NLM ID: 101302316 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1934-6069 (Electronic) Linking ISSN: 19313128 NLM ISO Abbreviation: Cell Host Microbe Subsets: MEDLINE
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  Data: An image-based transcriptomics atlas reveals the regional and microbiota-dependent molecular, cellular, and spatial structure of the murine gut.
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  Data: <searchLink fieldCode="AU" term="%22Xu+RJ%22">Xu RJ</searchLink>; Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA; Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA; Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA.<br /><searchLink fieldCode="AU" term="%22Zhang+H%22">Zhang H</searchLink>; Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA; Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA.<br /><searchLink fieldCode="AU" term="%22Cadinu+P%22">Cadinu P</searchLink>; Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA; Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA.<br /><searchLink fieldCode="AU" term="%22Nicol+PB%22">Nicol PB</searchLink>; Department of Data Science, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA.<br /><searchLink fieldCode="AU" term="%22Herrmann+US%22">Herrmann US</searchLink>; Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA; Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA.<br /><searchLink fieldCode="AU" term="%22Lee+T%22">Lee T</searchLink>; Core for Computational Biomedicine, Department of Biomedical Informatics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA.<br /><searchLink fieldCode="AU" term="%22Geistlinger+L%22">Geistlinger L</searchLink>; Core for Computational Biomedicine, Department of Biomedical Informatics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA.<br /><searchLink fieldCode="AU" term="%22Irizarry+RA%22">Irizarry RA</searchLink>; Department of Data Science, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA.<br /><searchLink fieldCode="AU" term="%22Moffitt+JR%22">Moffitt JR</searchLink>; Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA; Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA. Electronic address: jeffrey.moffitt@childrens.harvard.edu.
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  Data: <searchLink fieldCode="JN" term="%22101302316%22">Cell host & microbe</searchLink> [Cell Host Microbe] 2026 Mar 11; Vol. 34 (3), pp. 509-525.e13. <i>Date of Electronic Publication: </i>2026 Feb 19.
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        Value: 10.1016/j.chom.2026.01.018
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              Text: 2026 Mar 11
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