title: HiC library for sample NA19434 (Luhya)
design: 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.