title: Amplicon sequencing of HEK 293T: Cas9-VLP tx
design: For MiSeq next generation sequencing analysis of targeted integration, the B2M targeted region was first amplified with nested primer set #2 (Integration_Nested_2_F: GCTCTTCCGATCTAGGTCCGAGCAGTTAACTGG & Integration_Nested_2_R: GCTCTTCCGATCTACTTAGCGGGCGCCTAGA) and cleaned up (SPRI beads, UC Berkeley Sequencing Core) followed by amplification with primer sets to detect targeted integration (Integration_NGS fwd_F: GCTCTTCCGATCTAAGCTGACAGCATTCGGGC & Integration_NGS fwd_R: GCTCTTCCGATCTGAGAGCTCCTCTGGTTTCCC). Pair-end reads were merged, trimmed, and aligned to the expected sequence of lentiviral insertion into the Cas9 target site in the B2M gene (Geneious).