Pacific herring genome: chromatin conformation capture sequencing
Genomic DNA was prepared for chromatin conformation capture with the Proximo Hi-C (Animal) 4.0 Kit, following the manufacturers protocol. Generally, DNA within intact cells was cross-linked with a formaldehyde solution prior to digestion with restriction enzymes (DPNII, Ddel, Hinfl, and Msel). Proximity ligation with biotinylated nucleotides resulted in chimeric molecules, composed of genomic regions that were physically proximal in vivo. Biotinylated molecules were captured on streptavidin beads and prepared for Illumina sequencing with the Next Ultra DNA kit (New England Biolabs). Sequencing on an Illumina NovaSeq generated 260,583,196 PE150 read pairs.