Illumina Whole Genome 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 pancreatic tissue (HG008-N-P), 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).Genomic DNA (gDNA) was isolated from approximately 10 million non-viable HG008-T cells (passage 36 from 2022 culture) and 80 mg of non-viable HG008-N-P tissue with the Qiagen Gentra Puregene kit using the manufacturers instruction. Genomic DNA mass yields for tumor and normal samples were approximately 26 and 9 ug, respectively. Resulting DNA size was quantified using the PicoGreen Assay (Quant-iT PicoGreen , catalog# P11496) and the quality was assessed using 1% agarose gel (Invitrogen E-Gel Agarose Gels, catalog# G720801).Library preparation was performed for each sample using an in-house PCR-Free protocol, with the Roche Kapa HyperPrep PCR-free Kit (PN: KK8505). Two libraries were prepared for the tumor from 1ug of gDNA for each library and one library was prepared for the normal duodenal sample from 1ug of gDNA.  For both tumor and normal samples, DNA was sheared into fragments of approximately 450-600 bp using a Covaris E220 system. Fragmentation was followed by purification of the fragmented DNA using double-sided bead clean up with different ratios of AMPure XP beads to remove very small and large fragments. DNA end-repair and 3-adenylation were performed in the same reaction followed by ligation of the barcoded adapters using a set of 96 8-bp barcoded adapters from IDT, Illumina TruSeq RNA unique dual (UD) Indexes (PN: 20040870). Post ligation products were cleaned twice with AMPure XP beads to get rid of leftover adapters/adapter dimers.The resulting tumor and normal PCR-free libraries were sequenced together in one lane using the Illumina NovaSeq 6000 instrument (ICS v1.8.1 and bcl2fastq2 version 2.20.0.422). Paired end, 2x150bp sequencing, was performed using the Illumina NovaSeq 6000 S4 Reagent Kit v1.5 - 300 cycles (PN: 20028312) with the  NovaSeq XP 4-Lane Kit v1.5 (PN: 20043131).