Fig. 4: scRNAseq of Helicobacter pylori infected samples reveal cell-type specific responses. | Nature Communications

Fig. 4: scRNAseq of Helicobacter pylori infected samples reveal cell-type specific responses.

From: Accessible homeostatic gastric organoids reveal secondary cell type-specific host-pathogen interactions in Helicobacter pylori infections

Fig. 4

a Dimensionality reduction (UMAP) plot with annotation of clusters of single cell RNA sequencing results of infected and uninfected samples. b Highly upregulated genes (Fold change > 2 & adjusted p-value < 10-4 in at least one cell type, using a likelihood-ratio test for single cell gene expression with the Seurat FindMarkers (bimod) approach) upon infection per cell type cluster in apically neutral (left) and acidic (right) smples. c Scatter plots of log-fold-changes upon infection in neutral versus acidic conditions with annotation of selected genes. Complete figure is presented as Supplementary Fig. 4d. b–c) Data are provided in Source Data file. d Immunofluorescent staining images for DUOX2 indicating predominant upregulation upon H. pylori (Hp) infection in apically acidic conditions, 6 d p.i. Scale bar, 100 µm. e Live images of infected samples with addition of compound 521 (C521, right) and DMSO control (left) with fluorescent images for bacteria (Hp, red) and dead cells (DRAQ7, magenta). Scale bars, 200 µm. d, e Representative images from three independent experiments.

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