de Wit Lab, Division Of Gene Regulation, Netherlands Cancer Institute
single cell samples were processed using standard 4C protocol using DPNII. digestion and ligation was confirmed by agilent TAPEStation. the usual biotin incorporation and enrichment step were omitted due to low amounts of DNA. Reverse cross-linked DNA was quantified using QUBIT (thermo fisher) and sheared to 700-900bp using the Covaris. paired-end deep-sequencing libraries were generated using the Ovation Ultralow Library Prep kit (Nugen). Libraries were sequenced on the HiSeq or NextSeq.