(A) Clones (n = 72) collected from three independent HDR experiments with a DNA donor template. Lanes 1 to 29, 30 to 48, and 49 to 72 correspond to experiment 1, experiment 2, and experiment 3, respectively. (B) Clones (n = 71) collected from three independent HDR experiments with a chromatin donor template. Lanes 1 to 31, 32 to 50, and 51 to 71 correspond to experiment 1, experiment 2, and experiment 3, respectively. In A and B, the positions of the PCR amplification products from edited and wild-type alleles are indicated. M, DNA size markers (1.65, 2, 3, 4, 5, 6 kb; 1 kb Plus DNA Ladder, Invitrogen). Asterisks denote imperfect clones as defined in Figure 2. (C) Frequency of occurrence of homozygous, heterozygous, and imperfect clones in three independent HDR experiments. n, number of clones analyzed. (D) Long-range PCR analysis of homozygous candidates collected from HDR experiments with a chromatin donor template. The PCR product (10.43 kb) from gDNA of wild-type cells is also shown. The positions of the primers (F2, R2) in the PCR analysis are depicted in Figure 2—figure supplement 1C. (E) Summary of the combined results at the ACTB locus in MCF10A cells. The percentages were calculated based on the data for the ACTB locus in Figure 2C.