PhaseGenomics HiC Library preparation and Illumina 2x150  sequencing of the GIAB HG008-T tumor cell line (Pancreatic Ductal Adenocarcinoma)
CytoTerra library preparation was performed  starting with approximately 500,000 viable  HG008-T cells (passage 38 from 2022 culture).  Proximity ligation preparation was performed with the Phase Genomics Proximo Hi-C v4.5 kit (PN: KT4045) and associated Proximo human protocol (v4.5 0202301, https://4408603.fs1.hubspotusercontent-na1.net/hubfs/4408603/Protocols_latest/Proximo_Human_v4.5_202301.pdf ) to generate a dual-indexed Illumina-compatible library.   In brief, intact cells are crosslinked, lysed, and chromatin digested with a cocktail of restriction endonucleases.  Ends are filled in with biotinylated nucleotides and subjected to proximity ligation.  Following ligation, crosslinks are enzymatically reversed and DNA purified.  Proximity ligated junctions are purified using streptavidin beads.  Bead-bound DNA is used as input for generation of a paired-end Illumina compatible library.The Proximo Hi-C library was run on an Illumina NovaSeq 6000 (ICS v1.7.5, RTA v3.4.4)  with 2x150 paired end reads using the NovaSeq 6000 S4 Reagent Kit v1.5 300 cycles (PN: 20028312).  The library was loaded across one lane of a single flowcell.