library_construction_protocol: Hi-C libraries were prepared as previously described (Rao et al., 2014). The protocol was adapted slightly for G1 analyses. An asynchronous pool of cells was first crosslinked using 2% formaldehyde. Then the 10% smallest cells were sorted based on Forward Scatter and Side Scatter. 5 million cells were collected for Hi-C analysis and then processed according to protocol following crosslinking. Pulled-down DNA was end-repaired and an A-overhang was added. Sequencing adapters were ligated to the DNA samples to create sequencing libraries.