Dovetail's OmniC sequencing data from Juglans californica: leaf from a mature sample Jcal-S-LA-6.w1
First, specimen tissue is thoroughly ground with a mortar and pestle while cooled with liquid nitrogen. Nuclear isolation was performed using published methods (Workman et al. 2018) and the isolated nuclei were used as the starting input to the DovetailTM Omni-CTM Kit (Dovetail Genomics, CA) Mammalian Cells protocol. Briefly, chromatin was fixed in place in the nucleus. Fixed chromatin was digested under various conditions of DNase I until a suitable fragment length distribution of DNA molecules was obtained. Chromatin ends were repaired and ligated to a biotinylated bridge adapter followed by proximity ligation of adapter containing ends. After proximity ligation, crosslinks were reversed and the DNA purified from proteins. Purified DNA was treated to remove biotin that was not internal to ligated fragments. An NGS library was generated using an NEB Ultra II DNA Library Prep kit (NEB, Ipswich, MA) with an Illumina compatible y-adaptor. Biotin-containing fragments were then captured using streptavidin beads. The post-capture product was split into two replicates prior to PCR enrichment to preserve library complexity with each replicate receiving unique dual indices. The library was sequenced at Vincent J. Coates Genomics Sequencing Lab (Berkeley, CA) on an Illumina NovaSeq platform (Illumina, San Diego, CA) to generate approximately 100 million 2 x 150 bp read pairs per GB of genome size.