Fig. 3

Transcriptional response of the epithelium to infection with the different PAO1 strains. (a) Schematic representation of the analysis. (b) Volcano plot showing the log₂ fold change and -log₁₀ adjusted p-value of all genes, when comparing the transcriptome of 2D organoids exposed to PAO1 WT or PAO1 ΔQS. (c) Volcano plot showing the Log₂ fold change and -log₁₀ adjusted p-value per gene comparing the transcriptome of 2D organoids exposed to PAO1 WT or unexposed controls. Green indicates differentially expressed genes (DEGs) (log₂ fold change > 1 and adjusted p value < 0.05). (d) Gene ontology enrichment analysis showing top 10 categories enriched in 2D organoids exposed to PAO1 WT. Left panel: Healthy organoid line. Right: CF organoid line. (e) Gene expression heat map of genes from “Response to lipopolysaccharide” GO term category (GO:0032496). Color code indicates culture condition (co-culture or mono-culture) and PAO1 genotype (WT, ΔpqsA or ΔQS). Heatmaps were plotted using the pheatmap function of DESeq2⁷⁹ (version 1.36.0) in Rstudio.