Mseek of HepaRG mtDNA
The Mseek method of sample processing and deep sequencing of mtDNA, as well as the procedure for data analysis, was conducted as previously reported (Jayaprakash et al. 2015). Briefly, Mseek consists of (i) isolating total DNA from a thawed DPBS-washed cell pellet, (ii) digesting nuclear DNA (nDNA) with Exonuclease V, (iii) purifying the products using Ampure beads to remove short fragments, (iv) testing the results of the digestion with PCR primers specific for mtDNA and nDNA using 1  microliter of the digested sample, (v) fragmenting the remaining sample using Covaris and end-repair, (vi) ligating barcoded adapters compatible with the sequencing platform to the fragments, (vii) amplifying the library utilizing the universal adapters, and (viii) loading samples onto the Illumina NextSeq 500 platform.