title: GSM9605336: WT-HeLa, HSV-1 infection 18h,rep 3; Homo sapiens; Hi-C
library_construction_protocol: Cells were fixed in 1.75% formaldehyde, quenched in a 0.1% BSA solution, washed, and resuspended in 200 μL ice-cold wash buffer (10 mM Tris (pH 8.0), 10 mM NaCl, and 0.1 mg/mL BSA with 20 μL of a protease inhibitor (Sigma P8340). Then, cells were treated in sodium dodecyl sulfate (SDS) and Triton X-100 and digested with the restriction enzyme MboI. After deactivating the enzyme, cells underwent biotinylation and ligation reactions, after which 50 ng of the Hi-C sample was used for library preparation. Library construction protocol Hi-C DNA was purified using the DNA Clean & Concentrator®-5 kit (Zymo Research) and eluted in nuclease-free water. A total of 50 ng DNA was subjected to tagmentation using Vazyme TTE Mix V50 at 55 °C for 10 min, followed by purification. Tagmented DNA was amplified using Nextera i5 and i7 unique dual indices with an initial limited-cycle PCR (2 cycles) to introduce sequencing adapters. Biotin-labeled ligation products were then captured using Dynabeads MyOne Streptavidin C1 beads (Thermo Fisher Scientific) according to the manufacturer's instructions. The bead-bound DNA was further amplified by PCR (10 cycles) to enrich Hi-C fragments. Libraries were purified and size-selected using AMPure XP beads with double-sided selection (0.6×/0.15×). Final libraries were sequenced on an Illumina NovaSeq 6000 platform with 150 bp paired-end reads.