Analysis of super-enhancers and typical enhancers
H3K27ac ChIP-seq data were used for identifying typical and super- enhancers using ROSE software 28,35. The H3K27ac ChIP-seq peaks in untreated and treated mast cells were stitched within 12.5 kb of each other and excluding 2.5 kb upstream and downstream of the known transcription start sites (TSS). The combined H3K27ac reads within stitched regions were plotted in a ranked enhancer order. Super-enhancers were defined as the enhancers above the inflection point and the rest were defined as typical enhancers. Annotation of enhancers was performed using the annotatePeaks.pl function (default settings) in HOMER. Pathway enrichment analysis of super enhancers was performed using Metascape 54. Differential peaks within super-enhancer regions that overlapped with a TSS region were excluded from downstream analyses.