Hi-C libraries were prepared from Neotetracus sinensis sample wls18 using a standard in situ Hi-C protocol. Briefly, chromatin was formaldehyde-crosslinked, digested with a 4-bp cutter restriction enzyme, end-filled with biotin-labelled nucleotides and proximity-ligated in nuclei. The ligated DNA was purified, sheared to ~350 bp, size-selected, and biotin-tagged fragments were enriched and PCR-amplified. The final libraries were sequenced on an Illumina platform to generate 150 bp paired-end reads.