GSM3658082: No UV control; Homo sapiens; OTHER
Genomic DNA was extracted with QIAgen DNA blood mini kit CPDs were mapped with a modified CPD seq method (Mao et al 2016). Purified DNA 12 ug was sonicated to 400 bp and size selected with SPRI select beads (Life Technologies) and the purified product (approx. 4 ug) subjected to NEBNext end repair and NEBNext dA-tailing modules (NEB). ARC141/142 was then ligated to the sheared and repaired ends O/N with NEBNext Quick Ligation module. DNA was purified with CleanPCR beads and treated with Terminal Transferase (TdT, NEB) and dideoxy ATP (Roche) for 2h at 37 degrees. DNA was purified and incubated with 30 units T4 endonuclease V (NEB) at 37 degrees for 2 h, followed by purification and treatment with APE1 (NEB) at 37 degrees for 1.5 hr. DNA was purified and treated with rSAP (NEB) 37 degrees 1 hr followed by deactivation at 65 degrees for 15 minutes. DNA was purified, denatured at 95 degrees for 5 min, cooled on ice and ligated with the biotin-tagged “ARC double” overnight at 16 degrees with NEBNext quick ligation module. DNA fragments with the biotin tag were captured with Streptavidin Dynabeads (Invitrogen) and the DNA strand without the biotin label was released with 0.15 M NaOH.  This single stranded DNA was used as the template to synthesise double stranded products using ARC153. The now double stranded library was purified and amplified with ARC140 and either ARC78, ARC87 or ARC88 to add Illumina barcodes and indexes.
GEO Accession
GSM3658082