Figure 2.

Effect of Target Site Transcriptional Induction on AAV-HR Efficiency

Following FACS enrichment of cells with AAV-HR events, the number of unique barcodes mapped to each site (barcode heterogeneity) and average expression were quantified at targeted provirus sites, using the set of barcodes recovered in both iPCR and DNA barcode sequencing samples (see Materials and Methods). Here, measurements are compared only for those provirus sites targeted in both doxycycline- and non-doxycycline-treated samples. (A and B) Barcode heterogeneity (A) and expression (B) at targeted sites, measured at all pairwise targeted sites between treatment groups (concatenated biological replicates). Spearman’s rank correlation coefficient ρ is shown. p values were determined by a one-sided Wilcoxon signed-rank test (H0 = +doxycycline is not greater than −doxycycline) for barcode heterogeneity and a two-sided Wilcoxon signed-rank test for expression (n = 194). (C) Frequency histogram of log₂ fold change in barcode heterogeneity and site expression for each pair of sites plotted in (A) and (B), respectively. For expression, RNA was extracted after administering doxycycline to both groups regardless of doxycycline exposure at the time of rAAV transduction.