Snapgene v3.1.4 or higher

PCR products were treated with ExoSAP-IT (Affymetrix) prior to sequencing. DNA sequencing was performed using BigDye Terminator v3.1 Cycle Sequencing Kit (Applied Biosystems), purification by ethanol precipitation, and run on a 3130xl Genetic Analyzer (Applied Biosystems). Sequence alignments were performed using Sequencher v5.1 (Genecodes) or Snapgene v3.1.4 or higher (GSL Biotech LLC.). Sequence trace files with poor base calling confidence were excluded from further analyses.

To verify the DNA repair outcome in the transfected cell populations and picked clones, a genomic region of 700–800 bp surrounding the target site was PCR amplified using the primers listed in Supplementary Table 6. Primers were designed using NCBI Primer-BLAST with optional settings for human repeat filter, SNP handling, and primer pair specificity checking to the H. sapiens reference genome. PCR was performed using Phusion Hot Start II DNA Polymerase (Thermo Scientific) on a Veriti 96-well Thermal Cycler (Applied Biosystems) according to the manufacturer’s instructions. Specific PCR conditions are available upon request.
Prior to sequencing, PCR products were treated with ExoSAP-IT Express Reagent (Affymetrix) according to the manufacturer’s instructions. The BigDye Terminator v3.1 Cycle Sequencing Kit (Applied Biosystems) was applied for DNA sequencing, followed by ethanol precipitation. Subsequently, the sequencing was performed on a 3130 × 1 Genetic Analyzer (Applied Biosystems). Sequence alignments were conducted using Snapgene v.3.1.4 or higher (GSL Biotech LLC.). Sequence trace files with poor base calling confidence were excluded from further analyses.