Supplementary Figure 5: Overexpression of APOBEC3 upregulates the indel formation induced by Cas9 nickase-generated SSB in genomic DNA.

(a), (b) Indel frequencies induced by Cas9 variant-generated breaks in 293FT (a) and HeLa (b) cells. 293FT and HeLa cells were either non-transfected (NT) or co-transfected with indicated sgRNAs together with Cas9, D10A, H840A or dCas9, after which the indel frequencies were determined by deep sequencing. (c) Left: Schematic diagram illustrating that indels induced by Cas9 nickases are more distal to SSB sites, while Cas9 mainly induced indels at DSB site (at the ±3-bp region). Right: Statistical analysis of the fractions of reads containing indels at the ±3-bp region of cleavage site. The data represented are from (a, b) and Fig. 3b. The median, interquartile range (IQR), 1.5 × IQR and outliers are shown. ***: P < 0.001, one-tailed Student’s t-test. (d) Indel frequencies induced by Cas9 variant-generated breaks in 293FT, A3B or A3Bm cells. (e) Indel frequencies at indicated non-relevant genomic loci in A3B cells that are co-transfected with indicated sgRNAs and Cas9, D10A, H840A or dCas9. The data were from two independent experiments. (a, b, d) The means (±s.d.) were from three independent experiments.