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Fig. 3 | Genome Biology

Fig. 3

From: Effective control of large deletions after double-strand breaks by homology-directed repair and dsODN insertion

Fig. 3

AAV6 donor-mediated HDR considerably reduces large deletions. a Experimental design for RNP-AAV6 editing. Three types of human cells were transfected with Cas9-gRNA RNP, followed by AAV transduction. Small indel (NHEJ) and HDR efficiencies were assessed by amplicon sequencing and CRISPResso2 analysis. Large deletions were determined by long PCR, nanopore sequencing, Minimap2 alignment, and Samtools analysis. b Frequencies of small indels and HDR as determined by amplicon sequencing. The numbers in the bars indicate the mean NHEJ or HDR efficiencies. c Frequencies of deletion indexes. Deletion indexes are deletions in edited cells subtracted by deletions (background noise) in wildtype samples. Error bars represent mean ± SEM of n = 3–12 independent experiments. d Analysis of D100 in c. e Correlation of deletion indexes (DI) and deletion > 100 bp (D100) from data in c. The data in b, c, and d were statistically analyzed by a two-way ANOVA test. Adjusted p values were indicated. "ns" means no significance (p > 0.05)

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