Figure 1

Schematic of AAV genome and experimental design. (A) Overview of AAV genome features (elements of this diagram are not to scale). Inverted terminal repeats (green) cap the ends of the single-strand 4.7 Kb viral genome. Expression of two viral genes, Rep (red) and Cap (blue), is driven by three promoters, P5, P19, P40. L1/L2 and R1/R2 (black arrows) are locations for left and right primer pair binding sites, with biotinylation indicated (grey circle). (B) Modified IC-Seq outline for junction analysis. AAV-2 infected HeLa cells were grown for three weeks prior to DNA extraction. Human genomic DNA was sonicated, blunted, A-tailed, and ligated to T-tailed asymmetric linkers. Integration junctions were amplified by semi-nested ligation-mediated PCR, incorporating bead pull-down target enrichment. Libraries were then cloned into bacterial plasmids, transformed, and sequenced.