Phase Genomics CytoTerra Hi-C library preparation and Illumina NovaSeqX 2x150 sequencing of the GIAB HG008-T tumor cell line (Pancreatic Ductal Adenocarcinoma)
CytoTerra library preparation was performed using approximately 250,000 viable HG008-T cells from passage 21 of the NIST 2024 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 NovaSeqX (NCS 1.2.2.48004).  The library was sequenced using a 2x150bp paired end (PE) configuration using the Illumina NovaSeq X Series 10B Reagent Kit (PN: 20085594). The library was loaded on a single lane of a flowcell. Image analysis and base calling were conducted by the NovaSeq Control Software (NCS). Raw sequence data (.bcl files) generated from Illumina NovaSeq was converted into fastq files and de-multiplexed using Illumina bcl2fastq 2.20 software. One mis-match was allowed for index sequence identification.