WGS of S. orangutan: fibroblast
PacBio HiFi sequencing at the University of Washington. High-molecular-weight DNA was isolated at PSU from each cell line (5 mln. cells) using the Monarch HMW DNA Extraction Kit for Blood and Cells (New England Biolabs). PacBio HiFi data were collected from each sample as described in (Mao et al. 2023). DNA quantity was assessed at receipt at the University of Washington PacBio Sequencing Services facility and at each subsequent step using the Qubit High Sensitivity DNA kit (ThermoFisher) read on a DS-11 FX instrument (DeNovix) and DNA fragment length distributions evaluated on a FEMTO Pulse capillary electrophoresis instrument (Agilent). Specifically, DNA was sheared using Megaruptor 3 (Diagenode) using settings to target 20kb mode insert length. SMRTbell libraries were generated with the Express Template Prep Kit v2 (PacBio) (all samples) or SMRTbell Prep Kit v3 (PacBio) (Jim_KB3781_GGO) according to manufacturers protocols. Size selection was performed with PippinHT (Sage Science) using a 15- or 17-kbp high-pass protocol. All HiFi libraries were sequenced at the University of Washington on a Sequel II instrument using 30-hour movie times and 2-hour pre-extension. Data sets were generated with P2/C2 chemistry (AG05252_PPY, AG06213_PAB, Jim_KB3781_GGO, PR00251_PPA), P2.2/C2 chemistry (AG05252_PPY, AG06213_PAB, AG18354_PTR, Jambi_SSY, Jim_KB3781_GGO, PR00251_PPA), or P3.2/C2 chemistry (Jim_KB3781_GGO).