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.