CTCF ChIP-seq in NSCs

Both Smchd1 deletion and its MommeD43 mutant version cause loss of long-range chromatin interactions in NSCs and a strengthening of more local interactions. We assayed CTCF binding in the relevant genotypes to see if this is related to altered CTCF binding. ChIP-seq using an anti-CTCF antibody to check if chromatin binding of CTCF is altered in Smchd1MD43-GFP/MD43-GFP and Smchd1del/del neural stem cells (NSCs) compared to Smchd1GFP/GFP NSCs. 3 independent cell lines for each genotype (2 for Smchd1del/del) were derived from E14.5 embryos' cortices and cultured for less than 10 passages to be used as biological replicates. One cell line of Smchd1GFP/GFP was used for the whole cell extract library (input library).