MIP-seq of C. elegans wild isolates: day 9 starved L1s and recovery rep3
500 ng of total DNA used used per sample. Libraries were generated as described previously (HIATT et al. 2013) with the following modifications - we strived to add 1000 copies of each MIP for every individual copy of the worm genome in the 500 ng input DNA. All 412 MIPs were first pooled in an equimolar ratio at a concentration of 100 uM. The MIP pool was diluted down to 5 uM in 1 mM Tris buffer, and 50 uL of this pool was used in the 100 uL phosphorylation reaction. Next, the probe hybridization reaction for each sample was set with 500 ng DNA and 3.42 picomoles of the phosphorylated probe mixture. Following hybridization, gap filling, ligation, and exonuclease steps were performed as described previously. PCR amplification of the captured DNA was performed in a 50 uL reaction with 18 cycles. Sequencing was performed on the Illumina HiSeq 4000 to obtain 50-bp single end reads.