Formation of DNA triplexes/H-DNA associated with malignant transformation in human cells
Cultured cells were harvested after tripsinization. Benzoquinoquinoxaline (BQQ) 1uM diluted in DMSO -treatment time 24 hours. Doxycycline (DOX) 10mg/mL diluted in water -  treatment time 24 hours BedGraph files were generated by bedtools genomecov, normalized by reads per million (RPM) and then converted to bigWig files using bedGraphToBigWig from UCSC pre-compiled utilities for visualization at UCSC genome browse.  Live cells were harvested and embedded into agarose plugs. Cells were lysed in agarose using proteinase K, follwed by Rnase treatment. DNA was later precipitated after plug melting and shearing. S1-END‑seq libraries are generated by blunting and A‑tailing DNA ends, ligating Illumina-compatible adapters, size‑selecting fragments, and PCR amplifying the repaired DNA using KAPA HiFi HotStart ReadyMix (Roche)