Ultima UG100 ppmSeq 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 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. One paired plus minus sequencing (ppmSeq) library was prepared starting with 180 ng of HG008-T gDNA. PpmSeq library preparation was performed using the NEBNext Ultra II DNA PCR-free Library Prep Kit (PN: E7410) following the Ultima ppmSeq protocol (UG ppmSeq Genomic DNA Library preparation Protocol for Solaris Free D100093 Rev.02), UG ppmSeq Adapters (96-sample indices plate) (PN: UG0105) for UG 100 Sequencer compatibility were used. Sequencing was performed on the UG 100 Sequencer (software version : APL 5.1.0.19) using iV27 chemistry. 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. Libraries were pooled and single-end, approximately 200 bp reads were generated for both samples using the UG_116cycles_Baseline_1.7.0.0 sequencing recipe and flow order [T,G,C,A] on a single wafer