NextSeq 500 paired end sequencing; Single-nucleotide resolution mapping of DNA abasic sites by snAP-seq
Single-nucleotide resolution mapping of DNA abasic sites by snAP-seq
HeLa cells were washed in cold PBS and harvested by scraping into cold PBS followed by centrifugation at 300 x g. DNA from up to 10^6 cells was extracted using a Quick-DNA™ kit (Zymo Research) according to the manufacturer's instructions. Genomic lysis buffer was supplemented with TEMPO (20 mM) to minimise the introduction of oxidative damage and DNA was eluted in Tris-HCl buffer (pH 7.4, 10 mM). Input libraries were prepared for each enriched (snAP-seq) library. DNA was end-prepped using an NEBNext Ultra II kit, followed by adapter ligation using Truseq LT indexed adapters (Illumina). PCR amplification conditions were kept consistent with corresponding enriched (snAP-seq) libraries.
Experimental Factor: RNA interference
scrambled siRNA
Experimental Factor: stimulus
none