HiC library for sample NA19434  (Luhya)
Five million human lymphoblastoid  cells derived from an individual of Luhya descent (1000 Genomes code NA19434)  were resuspended in cold PBS before crosslinking with one-percent  paraformaldehyde (EMS Catalog 15714). Crosslinked cells were lysed in a hypertonic  buffer with one-percent SDS before binding crosslinked chromatin to SPRI  beads in 18% PEG-8000. Bead-bound chromatin was thoroughly washed and then  digested with DpnII restriction enzyme (20 U, NEB Catalog R0543S).  Biotin-11-dCTP (ChemCyte Catalog CC-6002-1) was incorporated by DNA  Polymerase I, Klenow Fragment (10 U, NEB Catalog M0210L) and intra-aggregate  ligation was achieved overnight by T4 DNA Ligase (4000 U, NEB Catalog  M0202T). Proximity-ligated DNA was isolated by SPRI bead purification after  crosslink reversal with Proteinase K (Qiagen Catalog 19133) in an eight  percent SDS solution. The purified proximity-ligation products were randomly  reduced to Illumina library insert size via Diagenode Bioruptor NGS  sonication platform. TruSeq library preparation was accomplished using the  NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB Catalog E7645S) and a  custom Y-adaptor. Adaptor ligation products were SPRI bead purified before  capturing biotinylated molecules using Dynabeads MyOne Streptavidin C1 beads  (ThermoFisher Catalog 65002). After enrichment of biotinylated products by  buffer exchange, the streptavidin-bound DNA was used as input to indexing PCR  with KAPA HiFi HotStart ReadyMix (Catalog no. KK2602) and TruSeq indexing  adaptors with unique index sequences. The resulting library molecules were  purified and simultaneously size-selected using SPRI beads before sequencing.