Fig. 2: P. aeruginosa transcriptomic profiling.

A Illustration of distance metric applied in (B, C, and D). B, C, D Each panel depicts Euclidean distances of PCA coordinates within (four left boxes) and between (three right boxes) groups. Each dot represents a distance between two coordinates. The tested groups were BHIS solid (red), BHIS liquid (yellow), SCFM (gray) and fresh sputum (blue). Two sets of p-values are given for each analysis: (I) two sided Mann–Whitney U test (MW) testing the null hypothesis that distance distributions within groups are similar to distances between groups, and a Kruskal-Wallis one-way analysis of variance (KW) testing the null hypothesis that distances between all groups are similarly distributed. B PCA conducted for transcriptomic profiles of all P. aeruginosa core genes. C PCA conducted for transcriptomic profiles of all P. aeruginosa genes known to play a role in synthesis of phage binding molecules on the bacterial cell surface. D PCA for transcriptomic profiles of all P. aeruginosa genes involved in the alginate biosynthesis pathway. B–D Each datapoint in the figure represents a distance between two biological repeats. Sample sizes were: human sputum–20, SCFM–6, Solid–8, Liquid–8 (see Supplementary Data 4 for further details). Boxplots represent median (bold horizontal central line), quartiles 0.25 and 0.75 (box edges), minimum and maximum (whiskers). Source data are provided as a Source Data file.