mtDNA deep sequencing in LIG3 knockout and wild-type HEK 293 cells

We addressed alterations in the maintenance of mitochondrial DNA (mtDNA) in HEK 293 cells lacking the mitochondrial DNA ligase, LIG3. DNA samples from mitochondria-enriched fractions were sequenced using long-read (PacBio) sequencing. In order to detect both single-strand breaks (SSBs) and double-strand breaks (DSBs), each sample was devided into native (for DSBs) and S1 nuclease-treated (for DSBs + SSBs) aliquots prior library preparation. Where indicated, cells were treated with 1mM hydrogen peroxide or grown under low oxygen tension.