ChIP-seq: Analysis of CTCF occupancy in unaffected and DM1 patient lymphoblastoid cell lines.

We performed CTCF ChIP-seq to determine the extent of CTCF occupancy alterations in two DM1 patient lymphoblastoid cell lines (LCLs) compared to an unaffected control LCL. Our results show that there were no large-scale changes in CTCF occupancy in the DM1 patient cells either genome-wide or in a 2 Mb region centered around the expanded repeats of DMPK. We performed CTCF ChIP-seq using a CTCF antibody (Diagenode) in the unaffected LCL GM04604 (UN-B) and two DM1 patient-derived LCLs GM06077 (DM1-A) and GM04648 (DM1-B). Each CTCF ChIP-seq library was prepared in triplicate.