RNA-seq reveals a differential genotype-driven transcriptome at the intestinal epithelial barrier. RNA-seq was performed on CECs sorted from WT, gp91^phox–/–, and p47^phox–/– mice from IRCM at baseline and after DSS treatment (n = 3). (A) PCA of CEC transcriptomes; each dot represents 1 mouse. The cumulative Q2 and R2 values for PC1 were 0.596 and 0.659, respectively, and 0.591 and 0.752 for PC2. (B) The bar graph represents the top 20 (out of 167) significant pathways generated by Gene Ontology Biological Process (GO:BP) analysis of the 46 DEGs between gp91^phox–/– and p47^phox–/– mice at baseline. The top 20 enriched GO:BP terms were selected to avoid redundancy while keeping the most general terms. (C) Venn diagram showing 865 DEGs common to all baseline and DSS comparisons (red ellipse; WT DSS vs WT baseline, gp91^phox–/– DSS vs gp91^phox–/– baseline, p47^phox–/– DSS vs p47^phox–/– baseline), and number of DEGs identified in the following 3 comparisons: p47^phox–/– vs WT with DSS (green ellipse), gp91^phox–/– vs p47^phox–/– with DSS (blue ellipse), and gp91^phox–/– vs WT with DSS (purple ellipse). (D) Venn diagram extracted from panel C showing the 912 DEGs in the gp91^phox–/– vs p47^phox–/– samples with DSS comparison after exclusion of 865 common DSS-induced genes. All numbers indicate significant DEGs (P < .05) across comparisons. DEGs from each comparison are listed in supplemental Tables 2 and 3. (E) Heat map showing the expression levels of DEGs (from the 912 DEGs derived from the gp91^phox–/– vs p47^phox–/– with DSS comparison) involved in the immune response pathway according to the GO:BP analysis. Each column represents a mouse and each row a gene. The ranges of gene expression are shown; blue indicates high expression and yellow indicates low expression. padj, adjusted P value; PC1, principal component 1; PC2, principal component 2.