SCE mapping in HAP1 cells
HAP1 ERCC6LKO cell lines were engineered by Horizon Discovery. Single guide RNAs (sgRNAs) against luciferase (sgLUC), C1orf112/FIRRM, and FIGNL1 were cloned into lentiCRISPRv2 in a single-step digestion-ligation reaction (2 hours at 37°C, 2 h at 16°C, 4 cycles). sgRNAs were introduced through FuGene-mediated transfections, and HAP1 cells were subsequently selected using 1 µg/mL puromycin for 5 days. When indicated, cells were transfected with siRNA against BLM or control siRNA at 24 h prior to BrdU treatment. Strand-seq libraries were prepared as previously described (Heijink et al., 2022)