Targeted Enrichment of Barcoded Libraries

For targeted enrichment, 700–1200 ng of each barcoded library was mixed with 2× hybridization buffer (Agilent, Santa Clara, CA, USA), 10× blocking agent (Agilent), blocking oligonucleotides (Maricic et al., 2010 (link)), human Cot1 (Invitrogen, Carlsbad, CA, USA) and salmon sperm DNA (Invitrogen) (Maricic et al., 2010 (link); Koumbaris et al., 2016 (link)). Immunoprecipitated libraries were incubated with the biotinylated capture probes for 48 hours at 66 °C and were eluted by heating, as previously described (Tsangaras et al., 2014 (link)). Enriched samples were amplified using outwardbound adaptor primers (Tsangaras et al., 2014 (link)) and were quantified using the KAPA Library Quantification KitIllumina (KAPA Biosystems, Boston, MA, USA). The enriched barcoded libraries were then pooled equimolarly and were subjected to pairedend sequencing on an Illumina HiSeq 2500 system (Illumina, San Diego, CA, USA).