GSM4942426: Naked DNA UV Replicate 1 resequencing; Homo sapiens; OTHER
NHF1 genomic DNA was isolated with Puregene Cell and Tissue kits (158388, Qiagen) or GenElute Mammalian Genomic DNA Miniprep kits (G1N70, Sigma), following the manufacturer's manual. CPD-seq procedure is adopted from the recently published emRiboSeq method (Nature Protocols 2015 10, 1433-1444) and our own CPD-seq publication in yeast (Mao et al, PNAS 2016,113, 9057-9062). Briefly, DNA fragments were ligated to a double-stranded adaptor DNA trP1, and free 3'-OHs were blocked by  terminal transferase and dideoxy-ATP.  CPD lesions were cleaved with T4 endonuclease V and apurinic/apyrimidinic (AP) endonuclease, APE1, to generage new 3'-OHs. DNA was then ligated to one of six different barcoded A adaptors (A1: AAGAGGAT; A2: TTCGTGAT; A3: CCTGAGAT; A4:ATCGCGAT; A5: TACTGGA; and A6: GAACTGAT) were used to generate libraries for different time points. DNA was purified with Streptavidin beads and amplified for ~5 cycles in a PCR reaction with primers complimentary to A and trP1, and the resulting DNA libraries were used for DNA sequencing.
GEO
GSM4942426