rAAV9 integrations - mouse 37, MiSeq run
We amplified DNA fragments containing the end of the AAV provirus using a modified version of the LM-PCR method described in http://dx.doi.org/10.1093/nar/gkt1399. We began with ten tissue samples; we split the DNA from each well into thirds, each of which was digested overnight with one of MseI, BfaI, or Csp6I. Each is a 4-bp cutter that produces a 5’ TA overhang. We annealed 6-bp barcoded linkers to the TA overhangs of the digested with T4 DNA ligase, with each well receiving two unique barcodes. We performed two rounds of nested LM-PCR. The library itself was constructed annealing paired-end adapters from the Paired-End DNA Sample Prep Kit (Illumina) to the purified amplicons from the LM-PCR. The rAAV9 samples were multiplexed with samples from unrelated mouse and zebrafish studies; the barcodes have been used to remove the reads from these other studies from the file presented here.