Fig. 1

Macrophage epigenetic landscape for acute and tolerant innate immune response. a Schematic diagram of recurrent epigenetic marks (occurring in at least 30% samples) with varying signals in different macrophage states. b Principal component analysis (PCA) of the chromatin accessibility (n = 6), H3K27ac/ H3K4me3 activity (n = 3) and gene expression (n = 6) upon LPS treatments. Each dot represents an independent sample and colours indicate different macrophage states. c Heatmaps showing ATAC-seq and H3K27ac signals at differential ATAC regions (FDR < 0.05, > 2-fold changes in HD vs. UT and/or LDHD vs. HD). The normalized mean signals across sample replicates in each condition were plotted. d Correlations of log2 fold change of ATACs, H3K27ac, H3K4me3 and gene expression (nGene: nearest gene to ATAC peaks; eGene, genes linked with ATAC peaks based on MDM eQTLs) upon LPS response (HD vs. UT) and LPS tolerance (LDHD vs. HD). See also Fig. S1