GSM6122750: HEK293T cells, In vitro G4 DNA-IPdenat; Homo sapiens; ChIP-Seq
For all the G4-quadruplex immunoprecipitations, the cells were processed from two 10 cm dishes for each sample. The inputs were derived either from respective samples or by pooling from CT and KD samples. The immunoprecipitated DNA was purified using ethanol precipitation follwed by dissolution nuclease-free water. Libraries were synthesized as follows: (i) End-repair and pre-processing: As per the manufacturer's instruction for Ion Express Plus Fragment Library kit (Cat. No. 4471269) from ThermoFisher Scientific for samples 1 to 3. (ii) Sequencing library preparation: As per the manufacturer's instruction for PCR sequencing kit (SQK-PSK004) from Oxford Nanopore Technologies for samples 4 to 16. For samples 4 to 16, 4 – 8 ng of DNA were subjected to end-repair, ligation of PCR-adapters followed by fragment size selection using 0.4x AMPure XP beads. The adapter-ligated fragments were subjected to PCR amplification followed by size selection using 0.6x AMPure XP beads. The library was then subjected to sequencing adapter ligation followed by sequencing on MinION device using flow cells (R9.4.1). The mean length of the sequenced reads was in the range of 0.8 – 1 kb. G4-quadruplex immunoprecipitation Ion Torrent S5, ONT MinION Mk1B