One-third of the total amount of adapter-ligated DNA generated by PCR was combined with 5 micrograms of Cot-I DNA (Invitrogen) and 1 nanomole each of blocking oligonucleotides mws60 and mws61. The mixture was completely lyophilized, then resuspended in 2.5 microliters water, 7.5 microliters Nimblegen 2x hybridization buffer, and 3 microliters Nimblegen hybridization component A. The mixture was heated to 95°C for 10 minutes, the temperature was adjusted to 65°C, and 3 pmol of pooled 120nt biotinylated oligonucleotides were added (Integrated DNA Technologies). After 4 hours, M-270 streptavidin beads (Life Technologies) were added and washes were performed according to the IDT xGen lockdown probe protocol version 2.0. We found that the standard quantity of streptavidin beads (the IDT protocol calls for 100 microliters of beads per 50 microliter PCR reaction) can result in PCR inhibition, so the quantity of beads was decreased to 75 microliters per reaction, and the PCR reaction volume increased to 100 microliters. The product was PCR amplified for 16 cycles with primers mws13 and mws20, and purified with 1.2 volumes of Ampure XP beads. The purified DNA
