Illumina PE reads from a proximity ligated (Omni-C) library
Chromatin was fixed in the nucleus was fixed with formaldehyde and then extracted. Fixed chromatin was digested with DNAse I followed by end repair and ligation to a biotinylated bridge adapter. Adapter containing ends were proximity ligated, the crosslinks were reversed followed by purification of DNA. Purified DNA was treated to remove biotin that was not internal to ligated fragments. Sequencing libraries were generated using NEBNext Ultra enzymes and Illumina-compatible adapters. Biotin-containing fragments were isolated using streptavidin beads before PCR enrichment of the library. The library was sequenced on an Illumina HiSeqX platform  to produce approximately 30x sequence coverage.