Fig. 4

RNA-Seq Reveals Gut Transcriptomic Changes in irf8^−/− Mutants but No Apparent Intestinal Structural Defects

(A) Volcano plot showing fold change and the statistical significance of all genes analyzed by RNA-seq; each dot represents a different gene. Significantly altered genes with a false discovery rate (FDR) adjusted p ≤ 0.05 are highlighted in red.

(B) Interferon-responsive genes and immune-related genes were prominent groups significantly altered. Unknown represents uncharacterized genes without an informative gene name. Other represents genes of diverse functions and pathways that do not belong in a common category. Pancreas and/or intestine represents genes that are known to be expressed or have functions in pancreas, intestine, or both.

(C) Heatmaps listing the downregulated and upregulated genes. Two independent biological samples per genotype are represented. Color range from −3 to +3 is based on normalized fragments per kilobase of transcript per million mapped reads (FPKM) values using relative deviation per gene over all samples centered on 0.

(D) Differentially expressed gene list generated from DESeq2 using a broader cutoff of a p < 0.05 was used to determine significantly changed pathways in the PANTHER database. Number of genes identified in each pathway is shown in parentheses.

(E and F) Adult intestinal morphology was assessed by (E) H&E and (F) AB-PAS staining on 5-μm sections of the proximal gut regions (S1 and S2).

See also Figures S4 and S5 and Table S2.