ChIP-seq of a K562 cell line model with a patient-based t(3;8) translocation

ChIP-seq was performed to assess changes in the activity of the MYC SE upon deletion of its modules or CTCF binding sites. Immunoprecipitation of crosslinked chromatin was performed with antibodies directed against H3K27Ac (Diagenode C15410196), H3K9Ac (Diagenode C15410004), H3K4me3 (Diagenode C15410003) or CTCF (Cell Signalling, 2899S). Crosslinks were reversed overnight at 65°C in the presence of proteinase K (New England Biolabs). De-crosslinked material was purified using a QIAGEN PCR Purification Kit. The purified DNA was processed according to the Nextflex ChIP Sample Preparation Protocol (Perkin Elmer) or the Microplex library preparation kit V2 (Diagnode C05010013) and sequenced on the Illumina NovaSeq6000 platform.