Fig. 1: A robust workflow for massively parallel in vivo AAV capsid stratification.
a Experimental setup. Shown are the essential experimental and bioinformatic steps, from the (i) cloning of barcoded YFP reporter vectors, (ii) library production, and (iii) animal (mouse here) injection, to (iv) tissue harvest and NGS, followed by (v) data analysis. Also shown is a timeline for the entire workflow or the individual steps. Note that the exact time required in step (ii) depends on the size of the library. Likewise, the time to perform the final bioinformatic analysis in step (v) is determined by available computing (IT) power. The first step (orange arrow) can be skipped if users start with our pre-existing collection of barcoded vector genomes, which will cut down the required overall time to <6 months. Please see the main text for further details. b Ranking of capsids in all three libraries by transcriptional efficiency (Vαβ) in the pancreas. Shown are the top ten AAV variants and the proportion of their transcriptional efficiency after normalization to all capsids or barcodes, respectively, in each library. Depicted values are the average from six C57BL/6 J mice with SD. BC, barcode; i.v., intravenous. This figure contains clipart from Servier Medical Art. Source data are available in the Source data file.
