title: WGS of wild Anas platyrhynchos; male muscle tissue
design: Using the HMW DNA, three Chicago libraries were prepared (Dovetail Genomics) following the methods described in Putman et al (2016) In short, ~500ng of HMW genomic DNA was reconstituted in vitro into chromatin and fixed with formaldehyde. Fixed chromatin was digested with Dpnll, and with the 5 overhangs filled in with biotinylated nucleotides, and free blunt ends were then ligated. After ligation, crosslinks were reversed to remove protein from DNA. Purified DNA was treated to remove biotin that was not internal to ligated fragments and sheared to ~350 bp mean fragment size. Preparation of sequencing libraries were generated from these sheared DNA using NEBNext Ultra enzymes and Illumina-compatible adapters. Biotin-containing fragments were isolated using streptavidin beads before PCR enrichment of each library. Libraries were sequenced for a total of 71Gigabases (i.e., ~70X genomic coverage assuming a ~1.1 Gbp genome) on a single Illumina HiSeqX lane and using PE 150bp chemistry. Next, Omni-C libraries were prepared by Dovetail Genomics following a modified HiC prep Lieberman-Aiden et al. (2009). Briefly, chromatin was fixed in place with formaldehyde in the nucleus and then extracted. Fixed chromatin was digested with DNAse I, followed by chromatin end repair and ligation to a biotinylated bridge adapter followed by proximity ligation of adapter containing ends. After proximity ligation, crosslinks were reversed, and the DNA purified. 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 each library. The library was sequenced for a total of 68 Gigabases (i.e., ~62X genomic coverage assuming a ~1.1 Gbp genome) on a single Illumina HiSeqX lane and using PE 150bp chemistry.