GSM5597805: CDseq_U2OS_oxidized_Ts_NT; Homo sapiens; OTHER
Genomic DNAs were isolated using Quick-DNA Miniprep Plus Kit (Zymo Research; Irvine, CA) according to the manufacturer's instruction manual. Genomic DNAs were framgmeted to an averge length of 300 bp and circuliarized with T4 DNA ligase at 16°C overnight. Non-circularized linear DNAs were removed with Plasmid-Safe ATP-Dependent DNAse treatment. To generate DNA double-strand breaks at 8-oxo-dG lesions, the circularized DNAs were treated with Fpg and APE1 followed by S1 nuclease to create double-strand breaks with ligatable ends. To generate double-strand breaks at oxidized thymines, the circularized DNA was initially treated with EndoIII, NEIL1 or EndoIII & NEIL1 followed by EndoIV (NEB) treatment, and then S1 nuclease to create double-strand breaks with ligatable ends. A-tailed with Klenow fragment exo- (NEB) and then adaptors were ligated with NEBNext Ultra II Ligation Master Mix and followed by incubation with USER enzyme (NEB). The purified DNA libraries were amplified by PCR with NEBNext Ultra II Q5 Master mix and NEBNext i5 and i7 primers and used for DNA sequencing.
GEO Accession
GSM5597805