Investigating the role of SMCHD1 in regulating clustered protocadherin (Pcdh) and Hox genes

To investigate the effect of Smchd1 ablation on clustered Pcdh and Hox genes, we generated ChIP-seq profiles of EZH2 in clonal neural progenitor cells (NPCs) from Smchd1+/+ (wild-type, WT) and Smchd1-/- mouse embryonic stem (ES) cells. We also reanalyzed previously published Hi-C data (GSE99991) (Wang et al., 2018, Cell) in these two cell lines. Overall design: ChIP-seq for EZH2 in NPC clones derived from WT and Smchd1-/- female mouse ES cells. Hi-C: The Hi-C summary files of WT and Smchd1-/- cells were downloaded from GEO (GSE99991), with two biological replicates combined: WT: GSM2667262_WT1.HiC.rep1.comp.summary.txt.gz WT: GSM2667264_WT1.HiC.rep2.comp.summary.txt.gz Smchd1-/-: GSM2667263_KO1.HiC.rep1.comp.summary.txt.gz Smchd1-/-: GSM2667265_KO1.HiC.rep2.comp.summary.txt.gz) The combined replicates were converted to .hic files for chromosome 2, 6, 11, 15, and 18. The .hic files can be directly loaded to the Juicebox software (Durand, et al., Cell Syst, 2016).