Fig 9. RNA-Seq strand specific reads alignments on Rep/Cap cassette, 48 and 94 hours post transfection.

In dark red the reads correspond to rep sequence alignments on the negative strand and in black, alignments of the cap sequence 48 hours post transfection. Pink color represents the rep mapping 94 hours post transfection and the dark blue the cap alignment 94 hours post transfection. This Rep/Cap cassette used leaky scanning mechanisms to produce all needed proteins. Light blue dots represent the stack of reads aligning to the cassette at specific points. At both time-points we can clearly detect p10 and polh promoters, but also p19 and p40 transcription. Contrary to the WT AAV RNA-Seq the negative strand of both Rep and Cap genes is only less transcribed.