Figure 5. WD Induces Epigenetic Reprogramming of GMPs.
(A) FC-FC plot comparing the LPS response of GMPs with amplitude of difference in LPS responses visualized as color code (red, upregulated genes; blue, downregulated genes).
(B) Total counts of the indicated blood cell populations in female mice fed as shown.
(C and D) Activation status of circulating (C) and splenic (D) myeloid subsets from mice treated as indicated.
(E) Volcano plot displaying open chromatin loci as determined by ATAC-seq in GMPs isolated from mice treated as indicated. Average signal is represented as log2 fold change. Significantly up- (non-adj. p value < 0.05, log2FC > 1) and downregulated (non-adj. p value < 0.05, log2FC < −1) peaks are shown.
(F) Hierarchical clustering, standardized, and visualized as a heatmap show the significant differentially accessible genomic loci (p value < 0.05) in GMPs isolated from mice treated as indicated.
(G) Coverage of ATAC-seq signal for TET2 (top) and TLR4 loci (bottom). n = 3–5 for groups in (B)–(D); ±SEM, p < 0.05 versus CD. Experiments were performed twice independently and data are representative of a single experiment.
See also Figure S4.