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. 2022 Oct 5;13:5878. doi: 10.1038/s41467-022-33165-4

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© The Author(s) 2022

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. 2 — a Scheme of the experimental setup. Gastric organoids were generated from gastric healthy tissue and used to obtain 2D monolayers. Monolayers were infected with GFP-expressing H. pylori (MOI 1) for 6 h and subjected to scRNA-seq. b Representative flow cytometry dot plots of naïve and infected monolayers. Cells were gated as indicated based on GFP signal (H. pylori) and propidium iodide (PI) and subjected to scRNA-seq. c Single-cell transcriptomes from the different gates (panel b) were integrated and projected using a t-distributed stochastic neighbour embedding (t-SNE) 2D projection. The sample origin is colour-coded. d Using known gastric marker genes for the specific gastric cell types, cell identities were assigned. e Expression of known markers specific for pit cells (MUC5AC), neck cells (MUC6) and chief cells (PGC) colour-coded and projected on top of the t-SNE displayed in panels (c) and (d). f Percentage of H. pylori-infected cells per cluster as identified in panel (d).