Fig. 2

Co-culture characterization by Dual RNA-seq. (a) Schematic representation of the Dual RNA-seq experiment. (b) Distribution of human and bacterial reads across the different samples (technical replicates in triplicate) included in the run after performing the mapping and count assignment (as in Supplementary Fig. 1, see Supplementary Table 3). (c) Knock-out validation by gene expression. Normalized counts of pqsA, lasI and rhlI across the different samples of the cohort. Color code indicates culture condition (Green: mono-culture; magenta: co-culture) and PAO1 genotype (Dark: WT; middle: ΔpqsA; light: ΔQS). (d) PCA plot of PAO1 samples. (e) PCA plot of 2D organoid samples. Color code indicates PAO1 genotype, culture condition (co-culture or mono-culture) and organoid genotype (Healthy or CF).