Figure 3.

Effect of Target Site Transcriptional Induction on Number of Unique Sites Targeted

(A) Relative risk ratio of a site having at least one integrated barcode in a doxycycline-treated sample compared to a non-doxycycline-treated sample. Sites from biological duplicates were assembled into a 2 × 2 contingency table for which the exposure is +doxycycline/−doxycycline and the outcome is targeted/not targeted. 95% confidence intervals are shown. We consider the relative risk ratio statistically significant when the 95% confidence interval does not overlap 1, shown by white circles. All sites, all targeted sites (considered out of n = 3,901 provirus sites across all samples); Group-specific, sites targeted in one treatment group and not the other. For group-specific sites, the set of provirus sites was first filtered to sites present in the polyclonal population transduced in both treatment groups but targeted exclusively in one treatment group or the other (n = 277). There were no zero values in the tables. (B) Ideogram of all provirus sites considered for targeting (1,246 sites; black bars, overlay), showing targeted sites below each chromosome in +doxycycline samples (gray bars, first row) and targeted sites in −doxycycline samples (black bars, second row), generated using the NCBI Genome Decoration Page (https://www.ncbi.nlm.nih.gov/genome/tools/gdp/).