Amplification, next-generation sequencing, and genomic DNA mapping of retroviral integration sites

E Serrao, P Cherepanov, AN Engelman - JoVE (Journal of Visualized …, 2016 - jove.com
Retroviruses exhibit signature integration preferences on both the local and global scales.
Here, we present a detailed protocol for (1) generation of diverse libraries of retroviral
integration sites using ligation-mediated PCR (LM-PCR) amplification and next-generation
sequencing (NGS),(2) mapping the genomic location of each virus-host junction using
BEDTools, and (3) analyzing the data for statistical relevance. Genomic DNA extracted from
infected cells is fragmented by digestion with restriction enzymes or by sonication. After …