Fig.2 |. M2_IL4 and M2_GC macrophage populations share epigenetic landscape.

a, ATACseq was performed on M0, M2_IL4 and M2_Dex. Venn diagram shows the number of differential ATACseq peaks in M2_IL4 and M2_Dex relative to M0 (n=4, FC ≥ 2; FDR <0.05). 4,913 of 8,213 peaks were differential in both populations and regulated in the same direction. b, Heatmaps of the induced (red) and suppressed (blue) signal-specific and shared M2_IL4 and M2_Dex ATACseq peaks (FC ≥ 2; FDR <0.05). c-d, Enriched transcription factor binding motifs with associated p-values were identified by HOMER known motif analysis with JASPAR 2022 motif database in signal-specific and shared up- (c) and downregulated (d) ATACseq peaks in M2_IL4 and M2_Dex. e, Polarization-induced increases in the 5’ Tn5 cut site counts within indicated binding motifs of interest in the M2_IL4 and M2_Dex populations. f, Venn diagram shows the differential M2_IL4 and M2_Dex H3K27ac ChIPseq peaks relative to those in M0 (FDR< 0.05) with 1,304 of 1,667 peaks regulated in the same direction in both populations. g, Heatmaps of induced (red) and suppressed (blue) signal-specific and shared filtered H3K27ac peaks (FC ≥ 2; FDR <0.05) in M2_IL4 and M2_Dex. h, Volcano plots show differential H3K27ac ChIPseq peaks for M2_IL4 (left) and M2_Dex (right) relative to those in M0 (LogFC ≥ 1; FDR< 0.05); the location of selected hyperacetylated sites relative to the TSS of the closest gene are shown in orange (M2_IL4) or green (M2_Dex). Hypoacetylated sites are shown in red for each population. Sites overlapping in M2_IL4 and M2_Dex are underlined. i, Non-promoter 12,211 H3K27ac peaks after excluding 1,650 promoter-proximal peaks (−300/+200 relative to TSS) are shown as a Venn diagram with the number of differential, relative to M0, M2 population-specific and shared peaks (FC ≥ 2; FDR<0.05) indicated. j, Average H3K27ac ChIPseq signals at M2_IL4 (top), M2_Dex (middle)_, and shared (bottom) differential non-promoter peaks from (I) represented as violin plots.