Whole exome sequencing of murine melanoma genomes.
Experimental procedures. Genomic DNA (gDNA) was randomly fragmented with a peak of 150–200 bp. Adapters were ligated to both ends of the fragments. The adapter-ligated templates were purified by the AgencourtAMPure SPRI beads and fragments with insert size ~200 bp were excised. Extracted DNA was amplified by ligation-mediated polymerase chain reaction (LM-PCR), purified, and hybridized to the SureSelectBiotinylated RNA Library (BAITS) for enrichment. Hybridized fragments are bound to the strepavidin beads whereas non-hybridized fragments are washed away after 24 hours. Captured LM-PCR products were run on an Agilent 2100 Bioanalyzer to estimate the magnitude of enrichment. Each captured library was then loaded on Hiseq2000 flow cells. High-throughput sequencing for each captured library was carried out to 100X coverage. Raw image files were processed by Illumina base calling Software 1.7 for base calling with default parameters.