GSM5552062: HCT116 cells, siDDX41_rep2; Homo sapiens; OTHER
Fixed cells were lysed with mild buffers for nuclei extraction. After DSB blunting and A-tailing, BLISS adapters containing a T-overhang were ligated DSB ends. DNA was extracted using a SDS-based buffer and proteinase K, followed by phenol/chloroform extraction and ethanol precipitation. After DNA sonication, the ligated DSB ends were linearly amplified using an in vitro transcription. The generated RNA was subject to a 3' ligation using a truncated RNA ligase 2, followed by a reverse transcription and PCR amplification with barcoded primers (Bouwman et al., 2020 - Nature Protocols).