Arima HiC Library preparation and Illumina 2x150 Sequencing of the GIAB HG008-T tumor cell line (Pancreatic Ductal Adenocarcinoma)
Sequencing was performed on the HG008-T pancreatic ductal adenocarcinoma tumor cell line with matched normal duodenal tissue (HG008-N-D), using similar methods and library preparation protocols tailored for both tumor and normal samples, as described below. The data presented here corresponds to the tumor cell line (HG008-T). Arima HiC library preparation used the Arima HiC High Coverage Kit (PN: A410110) following the associated User Guide for Mammalian Cell Lines (PN: Doc A160161 v01, https://arimagenomics.com/wp-content/files/User-Guide-Arima-High-Coverage-for-Mammalian-Cell-Lines.pdf).  Approximately one million HG008-T and HG008-N-D cells were input into the HiC protocol for crosslinking chromatin.  The crosslinked chromatin is then digested using a restriction enzyme (RE) cocktail optimized for coverage uniformity across a wide range of genomic sequence compositions. The 5-overhangs are then filled in, causing the digested ends to be labeled with a biotinylated nucleotide. Next, spatially proximal digested ends of DNA are ligated, capturing the sequence and structure of the genome. The ligated DNA is then purified, producing pure proximally-ligated DNA. The proximally-ligated DNA is then fragmented, and the biotinylated fragments are enriched.  HiC ligation resulted in 871ng HiC ligation product for HG008-T and 1760 ng of HiC ligation product for HG008-N-D. The HG008-T and HG008-N-D HiC ligation products were prepared for Illumina Sequencing using the Roche KAPA Hyper Prep kit following the KAPA Hyper Prep kit User Guide (PN: A160139 v00, https://arimagenomics.com/wp-content/files/User-Guide-Library-Preparation-using-KAPA-Hyper-Prep-Kit.pdf ). Library preparation begins with DNA fragmentation, DNA size selection , and biotin enrichment. For each sample, 250 ng of sheared and size-selected ligation products were input into a custom Arima-HiC end-repair, dA-tailing and adapter ligation is performed as described in the User Guide. Libraries were shipped to the Baylor College of Medicine Human Genome Sequencing Center (HGSC) for sequencing. The tumor and normal samples were sequenced in a pool of samples in one lane.  Paired end, 2x150bp sequencing, was performed using the Illumina S4 Reagent Kit v1.5 (300 cycles) (PN: 20028312) on an Illumina NovaSeq 6000 (ICS v1.7.5, RTA v3.4.4). The resulting data is referred to as Arima High Coverage HiC data.