Fig. 3

Transcriptome sequencing analysis identified Cth as one of the potential mediators of efferocytosis and the resolution phase after I/R. A PCA plot: PCA showing the clustering of the RNA-seq data of mouse intestinal macrophages after intestinal ischaemia‒reperfusion surgery. Macrophages at 36 and 48 h postsurgery were differentiated from those in the first 24 h. PCA was performed on a normalized gene count matrix (FPKM) using DESeq2. B Heatmap: Heatmap showing the 54 most significantly differentiated genes (− log10(P value) > 70) at 12 h and 48 h postsurgery. Colours indicate the gene expression z score. Z normalization was performed on the FPKM for each gene. C Volcano plot, top: Volcano plot showing 5467 genes expressed in postsurgery intestinal macrophages. Dashed lines represent the thresholds (P value < 0.05, log2-fold change > 0.5) for significantly DEGs at 12 h and 36 h after surgery. Cth and a list of known efferocytosis marker genes are labelled. Bottom: Volcano plot showing 5410 genes expressed in postsurgery intestinal macrophages at 12 h and 36 h after surgery. Cth and a list of known efferocytosis marker genes are labelled. D Bar graphs and western blots showing the mRNA and protein expression levels of Cth in the sham-operated group (Sham), the 24-h post-I/R group (24 h) and the 48-h post-I/R group (48 h). n = 6/group. *P ≤ 0.05, **P ≤ 0.01, ***P ≤ 0.001, ****P ≤ 0.0001, one-way ANOVA with Tukey’s multiple comparisons test