Characterization of super‐enhancers in WT and KO macrophages Characterization of super‐enhancers in WT and KO macrophages Summary of total number and median size of BRD4 SEs and TEs.Gene tracks depicting an SE near the Fth1 loci. Red bar represents the length of SE. BRD4 clusters colocalized with those of Pol II and H3K27ac.Box plots and pie charts to compare SEs and TEs for the length, signals (rpm × 1,000), and signal density (rpm/bp).Box plot “length” (LPS): SE (Kb) range 3.6–61.9, median 9.4, positive error bar 4.6, negative error bar 3.3.; TE “length” range 0.05–13.5, median 0.45, positive error bar 0.5, negative error bar 0.25. Box plot “length” (UT): SE (Kb) range 0.5–20.6, median 2.5, positive error bar 1.2, negative error bar 1.3; TE “length” range 0.05–6.6, median 0.35, positive error bar 0.2, negative error bar 0.2.Box plot “signal” (LPS); SE (rpm × 1,000) range 6–86.4, median 10.6, positive error bar 5, negative error bar 1.5. TE “signal” range 0.008–5.9, median 0.19, positive error bar 0.53, negative error bar 0.09. Box plot “signal” (UT): SE (rpm × 1,000) range 1.5–20.8; median 2.5, positive error bar 1.0, negative error bar 0.37. TE “signal” range 0.01–1.5, median 0.12, positive error bar 0.16, negative error bar 0.07.Box plot “signal density” (LPS); SE (rpm/bp) range 0.75–2.5, median 1.15, positive error bar 0.14, negative error bar 0.27. TE range 0.025–3.8, median 0.49, positive error bar 0.24, negative error bar 0.33. Box plot “signal density” (UT): SE (rpm × 1,000) range 0.52–3.28 median 1.02, positive error bar 0.2, negative error bar 0.34. TE range 0.02–2.59, median 0.41, positive error bar 0.13, negative error bar 0.28. Statistical significance was determined by two‐tailed unpaired t‐test SE was called from two independent peak calling parameters.Venn diagrams representing genes neighboring BRD4, H3K27ac, and Pol II SE.de novo motif analysis of common and unique regions of SE from Brd4 WT and KO macrophages. Anup Dey et al. EMBO J. 2019;38:e100293 © as stated in the article, figure or figure legend