Neurogenesis 31 1 26 13 1 29 4 23 12 7 6 21 3 8 12 2 9 9 Neuronal differentiation 16 12 8 3 14 12 7 8 15 2 3 5 2 5 6 Endpoint neuronal differentiation 3 2 2  3 2 1 1 3 - - 2 Neuronal ion channel 24 2 16 10 2 16 1 17 4 10 20 1 5 8 1 4 11 Neuronal signal transduction 7 2 3 6 1 7 2 4 2 5 1 5 2 2 4 1 5 Table S6. Fold change in gene expression in undifferentiated and differentiating CC9 cells harbouring Mus musculus, pahari and dunni mtDNA following initial culture with 5-Aza. Arrows indicate up and down regulation, respectively. 5-Aza No. of genes CC9mus Day 0 CC9mus Day 3 CC9mus Day 21 CC9pahari Day 0 CC9pahari Day 3 CC9pahari Day 21 CC9dunni Day 0 CC9dunni Day 3 CC9dunni Day 21 Regulators of DNA methylation 6 6  2 3 Na 6  3 1 6 - 5 2 3 transcription and 5 5  2 Na 4  4  5 - 5 2 2
replication factors Neurogenesis 31 4 12 18 4 Na 1 15 15 5 2  24 3  4  17  4  21 Neuronal Differentiation 16 6 7 3 Na 3 11 5 7 1 13 1 12 1 3 8 Endpoint neuronal differentiation 3 - - Na 2  1 3 - 1 3 Neuronal ion channel 24 3  11 5 5 Na 2 10 5 5  18 2 8 2 19 Neuronal signal transduction 7 1 4  3 3 Na 2 3 2 4 6 1 4 1 1 6
Pyrosequencing (*denotes single strand primers) MousePolG1_Rbiotin MousePolG1_F TTCCCTCTACCAAACAAACCT GGGGGTAATTTGGATTAGTATTTT 285 56 MousePolG1_S1* GTAATTTGGATTAGTATTTT 74 80 MousePolG1_S2* TTATTGGAGGTTTAATTGTTT 80 80 MousePolG1_S4* GGGTTTTGGTGTT 69 80 Table S8. Taqman assays used for the Fluidigm Array. Assay name Type Assay ID NRXN3 Neurogenesis Mm04279482_m1 Neurogenesis Mm01219406_m1 Notch1 Neuronal signal transduction Mm00435249_m1 BMP2 Neuronal differentiation Mm01340178_m1 PAX6 Neuronal differentiation Mm00443081_m1 SOX2 Neuronal differentiation Mm03053810_s1 Bcl2 Neurogenesis Mm00477631_m1 Map2k4 Neurogenesis Mm00436508_m1 Cacna1b Neuronal ion channel Mm01333678_m1 Il1r1 Neurogenesis Mm00434237_m1 Notch2 Neuronal signal transduction Mm00803077_m1 Tgfb1 Neurogenesis Mm00441724_m1 Bax Neurogenesis Mm00432050_m1 STAT1 Neurogenesis Mm00439531_m1 pard3 Neurogenesis Mm00473929_m1 Cacna1c Neuronal ion channel Mm01188822_m1 Cacna1g Neuronal ion channel Mm00486572_m1 RTN4 Neuronal differentiation Mm00445861_m1 Hcn2 Neuronal ion channel Mm00468538_m1 Scn10a Neuronal ion channel Mm00501467_m1 Kcnd3 Neuronal ion channel Mm01302126_m1 Frs2 Neurogenesis Mm00769591_m1
Cacnb2 Neuronal ion channel Mm00659092_m1 Kcnc1 Neuronal ion channel Mm00657708_m1 Trpc3 Neuronal ion channel Mm00444690_m1 Cdk5rap2 Neuronal differentiation Mm00524401_m1 Apc2 Neurogenesis Mm00478649_m1 Neuronal ion channel Mm00434640_m1 Kcnj12 Neuronal ion channel Mm00440058_s1 Kcnb1 Neuronal ion channel Mm00492791_m1 Scn1b Neuronal ion channel Mm00441210_m1 Kcnn1 Neuronal ion channel Mm01349167_m1 Ntn1 Neurogenesis Mm00500896_m1 Kcns1 Neuronal ion channel Mm00492824_m1 Bdnf Neuronal differentiation Mm04230607_s1 Rtn4rl2 Neurogenesis Mm01336368_g1 Neuronal ion channel Mm00439977_s1 Ngfr Neurogenesis Mm00446296_m1 Neurog2 Neuronal differentiation Mm00437603_g1 Pou3f3 Neuronal differentiation Mm00843792_s1 Adcyap1r1 Neurogenesis Mm00431683_m1 Tpbg Neurogenesis Mm00495741_s1 Ntf5 Neurogenesis Mm01701591_m1 Neurogenesis Mm00432670_m1 Slc12a5 Neuronal ion channel Mm00803929_m1 Trpm1 Neuronal ion channel Mm00450619_m1 Il10ra Neurogenesis Mm00434151_m1 Neurog1 Neuronal differentiation Mm00440466_s1 Artn Neurogenesis Mm00507845_m1 Kcnj14 Neuronal ion channel Mm01194051_g1 Galr2 Neurogenesis Mm00726392_s1 Cdh8 Neurogenesis Mm00483238_m1 Ndnl2 Neurogenesis Mm00480974_s1 Neuronal ion channel Mm00496625_s1 Ache Neurogenesis Mm00477274_g1
Nrp1 Neurogenesis Mm00435379_m1 Neuronal ion channel Mm01161732_m1 Hcrtr1 Neurogenesis Mm01185776_m1 Slit2 Neurogenesis Mm00662153_m1 Fos Neurogenesis Mm00487425_m1 Crh Neurogenesis Mm01293920_s1 Hey2 Neuronal signal transduction Mm00469280_m1 Kcnab3 Neuronal ion channel Mm01337143_m1 Nog Neuronal differentiation Mm01297833_s1 Pax5 Neuronal differentiation Mm00435501_m1 Nrp2 Neurogenesis Mm00803099_m1 Clcn3 Neuronal ion channel Mm01348786_m1 Hey1 Neuronal signal transduction Mm00468865_m1 Lif Neurogenesis Mm00434762_g1 Trpv4 Neuronal ion channel Mm00499025_m1 TET1 Methylation regulators Mm01169087_m1 TET2 Methylation regulators Mm00524395_m1 TET3 Methylation regulators Mm00805756_m1 DNMT1 Methylation regulators Mm01151063_m1 DNMT3a Methylation regulators Mm00432881_m1 DNMT3b Methylation regulators Mm01240113_m1 Ncam1 Neuronal differentiation Mm01149710_m1 Nestin Neuronal differentiation Mm00450205_m1 Sox1 Neuronal differentiation Mm00486299_s1 Tubb3 Neuronal differentiation Mm00727586_s1 GFAP End marker Mm01253033_m1 Synaptophysin End marker Mm00436850_m1 Shh Neuronal signal transduction Mm00436528_m1 Wnt3a Neuronal signal transduction Mm00437337_m1 Wnt3 Neuronal signal transduction Mm00437336_m1