Ultima UG100 Whole Genome  single-end 300bp 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). Genomic DNA (gDNA) was isolated from the non-viable 0823p23 batch of cells of the GIAB HG008-T tumor cell line using the Qiagen Puregene Cell Kit (PN: 158767). Approximately five million cells were input into the Qiagen Puregene protocol. Briefly, cells were lysed, treated with RNase, gDNA precipitated, washed and hydrated in TE buffer (1 mM EDTA, 10 mM TrisCl pH 7.5). The gDNA was viscous and was therefore allowed to homogenize for one week at ambient laboratory temperature. Library preparation for each sample, started with 500 ng of isolated genomic DNA.  PCR-free library preparation was performed using the NEBNext Ultra II FS DNA PCR-free Library Prep Kit (PNs: E7805, E6177) following Ultima Genomics NEB PCR-Free WGS Library Preparation Protocol (Publication #: P00014 Rev. D).  Ultima Genomics PCR-free adapters, xGen PCR-Free Adapters for Ultima P1, 96 rxn (PN: 10016841) for UG 100 sequencer compatibility were used.Sequencing was performed on the UG 100 Sequencer (software version : APL 5.1.0.19) using iV27 Chemstry. Single end, 300 bp reads were generated for both samples using the UG_116cycles_Baseline_1.5.3.2  sequencing recipe and flow order [T,G,C,A] on a single wafer. A human genome control sample HG002 (Coriell Nucleic acid ID: NA24385) was spiked into each run in order to ensure quality of the samples being sequenced.