Extended Data Figure 6: Altered distributions of Cas9-mediated genotypic products in Prkdc^−/−Lig4^−/− mESCs and mESCs treated with DPKi3, NU7026, and MLN4924 as compared to wild-type mESCs.

a, Comparison of MH deletions among all deletions at Lib-B target sites in wild-type (n = 1,909 target sites), DPKi3 (n = 1,999), MLN4924 (n = 1,995), NU7026 (n = 1,999), and Prkdc^−/−Lig4^−/− (n = 1,446). Statistical tests performed against wild-type population. * P = 5.6×10⁻⁵, ** P = 3.5×10⁻¹³, *** P = 5.0×10⁻⁴¹, two-sided Welch’s t-test. b, Comparison of the frequency of each class of MH-less deletions among all deletion products in wild-type (Lib-A and Lib-B target sites, n = 3,829 target sites), DPKi3 (Lib-B, n = 1,990), MLN4924 (Lib-B, n = 1,980), NU7026 (Lib-B, n = 1,992), and Prkdc^−/−Lig4^−/− (Lib-A and Lib-B target sites, n = 3,344). P values compare to wild-type, two-sided Welch’s t-test. c, Frequency of 1-bp insertions at 1,055 target sites in Lib-A in Prkdc^−/−Lig4^−/− mESCs. d, Frequencies of deletion repair to wild-type genotype in Lib-B in wild-type mESCs (n = 1,480 target sites, combined data from 2 technical replicates) compared to conditions, with combined data from 2 independent biological replicates for each of Prkdc^−/−Lig4^−/− (n = 1,041 target sites), MLN4924 (n = 1,569), NU7026 (n = 1,561), and DPKi3 (n = 1,563). e, Table of Pearson r of the change in disease correction frequency compared to wild-type at n = 791 target sites for each pair of conditions. f, g, Annexin V-568 staining flow cytometry contour plots (f) and mean ± s.d. values (g) in wildtype and Prkdc^−/−Lig4^−/− Lib-A mESCs following transfection with SpCas9-P2A-GFP (representative data for n = 2 experiments). Box plots denote the 25^th, 50^th, and 75^th percentiles, whiskers show 1.5 times the interquartile range, and outliers are depicted as fliers. For detailed statistics on significance tests, see online methods.