GSM4059849: MEF_input_2; Mus musculus; OTHER
Cells were harvested and genomic DNA was extracted with TIANamp Genomic DNA Kit (TIANGEN, DP304). 0.1 mM desferal (TargetMol, T1637) was added at each step to prevent further DNA oxidation during genomic DNA extraction. Genomic DNA was digested to 100-1000 bp with NEBNext dsDNA Fragmentase (NEB, M0348). DNA fragments were purified with 2×CMPure beads (CWbiotech, CW2508). 2 pg model sequences were spiked into each 10 μg genomic DNA fragments. Half of the DNA mixture was incubated with Fpg (NEB, M0240) at 37℃ for one hour for damage excision. DNA was purified with 2×CMPure beads. 100 ng DNA was separated from each sample as input. For each enrichment, 4 μg genomic DNA was incubated with 4.5 μM hOGG1 in 100 μL system with 1×NEBuffer1(NEB, B7001). To improve the enrichment fold, 20 μg empty vector plasmid pcDNA3.1 was added as blocking DNA in each enrichment system. The mixture was incubated at 37℃ for 40 min and enriched as procedures described above. After elution, DNA was purified with 2×CMPure beads. NGS library construction was performed with VAHTS Universal DNA Library Prep Kit for Illumina (Vazyme, NP604) following the manufacturer's guidelines. Size selection was conducted after PCR amplification by using 0.55× and 0.2× VAHTS DNA clean beads (Vazyme, N411) to obtain 300-500 bp fragments.
GEO Accession
GSM4059849