GSM6754657: FXS_470_NPC_HiC; Homo sapiens; Hi-C
We prepared Hi-C libraries using the Arima Genomics Hi-C kit (Arima Genomics, A510008) according to the manufacturer's protocol. Briefly, we enzymatically digested genomic DNA within nuclei of crosslinked cell pellets, and created biotinylated ligation junctions between the digested ends at proximity. Then we extracted DNAs and sheared to an average size of ~400 bp using a Covaris S220 sonicator at 140 W peak incident power, 10 % duty factor, and 200 cycles per burst for 55 seconds. We further size selected the sheared DNA to 200-600 bp using AgenCourt Ampure XP beads (Beckman Coulter, A63881) according to manufacturer's protocols. Biotin-tagged ligation junctions via pulldown using streptavidin breads from the Arima Hi-C kit (Arima Genomics, A510008) according to manufacturer's protocol. Streptavidin beads containing Hi-C libraries were stored at -20 °C for no more than 3 days before Illumina sequencing library preparation was performed.  Hi-C libraries were prepped for sequencing by first washing adaptor-ligated Hi-C libraries on streptavidin beads twice in 150 uL of wash buffer at 55 °C and once in 100 ml of elution buffer at room temperature using Hi-C kit (Arima Genomics, A510008). DNA was eluted from streptavidin beads by boiling at 98 °C for 10 min in 15 uL elution buffer. Subsequently the libraries were amplified using NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB, E7645S) with 8 PCR cycles according to the manufacturer's protocol.