DOI: 10.5061/dryad.7h44j1053
title: Data from: Double-strand break repair pathways differentially affect processing and transduction by dual AAV vectors

description: Recombinant adeno-associated viral vectors (rAAV) are a powerful tool for
 gene delivery but have a limited DNA carrying capacity. Efforts
 to expand this genetic payload have focused on engineering the
 vector components, such as dual trans-splicing vectors which double
 the delivery size by exploiting the natural concatenation of rAAV
 genomes in host nuclei. We hypothesized that inefficient dual
 vector transduction could be improved by modulating host factors
 which affect concatenation. Since factors mediating concatenation are not
 well defined, we performed a genome-wide screen to identify host
 cell regulators. We discovered that Homologous Recombination (HR)
 is inhibitory to dual vector transduction. We demonstrate
 that depletion or inhibition of HR factors BRCA1 and Rad51
 significantly increase reconstitution of a large split transgene
 by increasing both concatenation and expression from rAAVs. Our
 results define new roles for DNA damage repair in rAAV
 transduction and highlight the potential for pharmacological
 intervention to increase genetic payload of rAAV vectors.
description: A Cas9 KO screen was conducted to recover regulators of
 dual-vector AAVS transduction in U2OS cells. This code operates on outputs
 from the hypergeometric analysis in the Broad Institute's GPP Web
 Portal and pathway analysis from Reactome. It primarily tabulates and
 plots these results.
description: # Data in support of "Double-Strand Break Repair Pathways
 Differentially Affect Processing and Transduction by Dual AAV
 Vectors"
 [https://doi.org/10.5061/dryad.7h44j1053](https://doi.org/10.5061/dryad.7h44j1053) ### Files "**hypergeometric.txt**" is the output of the Broad Institute's hypergeometric screen analysis. Headers: * "Gene Symbol": alphanumeric designation for the target of the perturbations * "Average LFC": mean of log-fold change in guide abundance  * "Average -log(p-values)": mean of negative log10 p-values associated with guide log-fold change * "Number of perturbations": number of guide sequences recovered corresponding to this gene * "Perturbations": guide sequences, same number as "Number of perturbations",  separated by semicolons * "Individual LFCs": log-fold changes in guide abundances separated by semicolons. These were averaged to yield "Average LFC". * "Ascending ranks": perturbation-wise log-fold change in guide abundances in increasing order separated by semicolons * "Individual ascending -log(p-values)": perturbation-wise -log10 p-values corresponding to the perturbation's log-fold change in increasing order and separated by semicolons. * "Descending ranks": perturbation-wise log-fold change in guide abundances in decreasing order separated by semicolons * "Individual descending -log(p-values)": perturbation-wise -log10 p-values corresponding to the perturbation's log-fold change in decreasing order and separated by semicolons. "hypergeometric_plotting.ipynb" contains code to make plots given the results of the Broad's hypergeometric screen analysis. The top 5% of positive regulators are used for Reactome pathway analysis, and code to plot these results are in this Jupyter notebook as well.