ChIP-seq Peak Alignment and Functional Annotation

Alignment of ChIP-seq signal was performed using deepTools (version 3.0)⁶¹. “Scale-regions” methods was applied to align the signal coverage from broad regions (RDC and RSC). Heatmaps were directly made using deepTools. Alignment plots were generally made with aligned matrices that were further processed in R.

The RDC and RSC were annotated using a web-version GREAT analysis tool (version 3.0.0)²⁶ against Mouse Genome Informatics (MGI) database (version 6.15)²⁷ using a “basal plus extension” method to link ChIP-seq peaks to their gene targets.