Extended Data Fig. 2: M2_IL4 and M2_GC macrophage populations share epigenetic landscape.

a The distribution of ATACseq peaks relative to known genomic features in M0, M2_IL4 and M2_Dex populations across replicates (n=3). b Venn diagram shows differential M2_IL4, M2_Cort and M2_Dex H3K27ac peaks relative to M0. c H3K27ac assessed by ChIP-qPCR at enhancers of indicated genes in 2_IL4, M2_Cort and M2_Dex normalizedto that in M0. Student’s t-test; *p < 0.05, **p < 0.01, ***p < 0.001, ****p < 0.0001, ns, non-significant. n=3, error bars are SEM. d Rank shift analysis of mean H3K27ac signals in M0 (baseline) and M2_IL4. Peaks that are also differentially regulated in M2_Dex are colored in red (hyperacetylated) and blue (hypoacetylated). The LOESS regression line (green) shows the relationships between acetylation strength in M0 and signal change in M2_IL4. Enhancer sites associated with representative IL4-specific (orange) and shared (black) genes are marked, and the expression of representative genes as determined by RNAseq (Fig. 1) is plotted on the right.