Target enrichment was performed based on the SureSelect protocol (Agilent) but incorporating the following modifications: (1) Biotinylated Hi-C ditags bound to streptavidin-beads were amplified prehybridization directly from beads using 24 parallel 25-µL PCR reactions with six to eight cycles using Phusion High-Fidelity DNA polymerase (New England Biolabs) to yield ∼500 ng total DNA. PCR primers to the paired-end adaptors were as described in Belton et al. (2012) (link). Subsequently, PCR products were pooled, purified using Agencourt AMPure XP beads (Beckman Coulter) and dried using a speedvac concentrator, then resuspended in 34 µL of water. (2) Enriched fragments were amplified post-hybridization again directly from the streptavidin beads, using 13 parallel 25-µL reactions of six cycles of PCR. PCR products were again pooled and purified using Agencourt AMPure XP beads (Beckman Coulter).