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iGUIDE: an improved pipeline for analyzing CRISPR cleavage specificity
- Nobles, Christopher L., Reddy, Shantan, Salas-McKee, January, Liu, Xiaojun, June, Carl H., Melenhorst, J. Joseph, Davis, Megan M., Zhao, Yangbing, Bushman, Frederic D.
- Genome biology 2019 v.20 no.1 pp. 14
- DNA damage, RNA, chromatin, gene editing, genes, nucleases
- Genome engineering methods have advanced greatly with the development of programmable nucleases, but methods for quantifying on- and off-target cleavage sites and associated deletions remain nascent. Here, we report an improvement of the GUIDE-seq method, iGUIDE, which allows filtering of mispriming events to clarify the true cleavage signal. Using iGUIDE, we specify the locations of Cas9-guided cleavage for four guide RNAs, characterize associated deletions, and show that naturally occurring background DNA double-strand breaks are associated with open chromatin, gene dense regions, and chromosomal fragile sites. iGUIDE is available from https://github.com/cnobles/iGUIDE .