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. 2023 Nov 20;42(9):1394–1403. doi: 10.1038/s41587-023-01988-1

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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. 1 — a, Three different mouse conditions used in the study analyzing cross-sections in the mouse gut. b, Tissue sections from mouse colons were placed on a barcoded glass array, with a barcoded surface adapted for simultaneous capture of polyadenylated host transcripts and 16S bacterial rRNA. Tissue sections were imaged, cells were permeabilized and cDNA was synthesized on the array surface before library preparation and sequencing. c, Data analysis identifies regional gene programs, their cell type constituents, association with mouse condition and regional association with specific commensal bacteria. Hyb, hybridization; Ext, extension.