Figure 2. RNA-seq analysis of THP-1 monocytes exposed to buffered hypercapnia for 4 h in the presence of LPS.

Principal component analysis of THP-1 cells exposed to 5% CO₂ (red) or 10% CO₂ (blue) (4 h) in an LPS stimulated state (2.5 μg mL⁻¹ for 2 h). The x-axis (PC1) is the vector that displays the most variance between samples and the y-axis (PC2) displays the second most. The percentage of total variance per principal component is shown on the axis label (a). Volcano plot of differential expression between 5% and 10% CO₂ (4 h) in an LPS stimulated state (2.5 μg mL⁻¹ for 2 h). The cut off for significance (P-adj < 0.05) is shown with a solid line on the y-axis. Significantly upregulated genes are shown in green and downregulated genes are shown in red (b). List of significant differentially expressed genes in hypercapnia in LPS stimulated state. Includes top 10 most differentially expressed genes up and down ranked by Log₂FC with a P-adj of < 0.05 (c). The top gene ontology terms associated with significantly differentially expressed genes in hypercapnia (4 h) in an LPS stimulated state (2.5 μg mL⁻¹ for 2 h) using a cut off value for significance of P-adj < 0.05. Terms are ranked by fold enrichment (d). Venn diagram representing the number of genes which are commonly and exclusively sensitive to CO₂ in THP-1 cells in the basal (blue) and LPS stimulated (yellow) state. Selected representative examples are included for each group (e). Heat map of the top 50 common differentially expressed genes between THP-1 cells exposed to 5% and 10% CO₂ in the basal and LPS stimulated state. The top 50 genes were selected by significance (P-adj) in the basal state and then ranked by differential expression level (Log₂FC) in the basal state for visualisation. All genes had a P-adj < 0.05 (f). Data are representative of n = 3 independent experiments in all cases (a–f).