Fig. 2: RNA-seq analysis reveals important changes in inflammatory pathways in CD5L⁻ mice upon CLP, when compared with WT mice.

a Principal component analysis (PCA) of RNA-seq expression data for the 4 groups of peritoneal cells [WT and CD5L⁻ mice, either naive (0 h) or 6 h after CLP; n = 3]. b Volcano plot depicting differentially expressed genes in CD5L⁻ vs. WT mice, 6 h after CLP. Red dots represent genes expressed at higher levels in CD5L⁻ mice, while black dots represent genes with higher expression levels in WT controls. Grey dots represent genes bellow the cutoff of significant (|log₂ fold change| ≥ 0.5 and adjusted P values ≤ 0.05). Differential expression was evaluated using the Wald’s test, followed by adjustment for multiple testing with the Benjamini-Hochberg correction. Log₂-fold change values were shrunk with the apeglm method to increase the signal-over-noise ratio of the effect size. c Dot plot of gene set enrichment analysis (mouse hallmark gene set collection) for CD5L⁻ vs. WT mice, 6 h after CLP. The diameter of the dot indicates the degree of significance of the ontology term. Red dots represent terms enriched in CD5L⁻ mice, while black dots represent terms enriched in WT mice. d Heatmap of the relative expression values (z-score of each gene across samples) of the top 7 upregulated pathways. Only differentially expressed genes were represented, excluding genes belonging to more than one pathway.