Table S2A: PCR primer sequences for human mtDNA

Primer pair name / Forward sequence / Reverse sequence / MtDNA coordinates (1)
Mt1.1 / CAAATCTTACCCCGCCTGT / GGTCTTCTCGTCTTGCTGTG / 2479-2727
Mt2.1 / CAGCCATTCAAGCAATCCT / AGTCAGGGGTGGAGACCTAA / 12836-13034
Mt3.1 / ACACTCATCGCCCTTACCAC / GTGGGGTTTTGCAGTCCTTA / 5451-5606
Mt4.1 / AAACTGCTCGCCAGAACACT / CATGGGCTACACCTTGACCT / 1125-1345
Mt5.1 / TGAAACTTCGGCTCACTCCT / AGAATATTGAGGCGCCATTG / 14837-15017
Mt7.1 / ATGGCCAACCTCCTACTCCT / GCGGTGATGTAGAGGGTGAT / 3313-3527
Mt8.1 (2) / CCGCCCGCGTCCCTTTCTCC ATAAAATTCTT / GGCTGTGGGTGGTTGTGTTGATTCAAATTATGTGT / 10195-10853
GAPDH (control) / ATCACTGCCACCCAGAAGAC / GGATGACCTTGCCCACAG / 643-766 of NM_002046

(1) According to gene bank accession number NC_012920.

(2) [1]

Table S2B: PCR primer sequences for rat mtDNA

Primer pair name / Forward sequence / Reverse sequence / MtDNA coordinates (1)
mt1.2 / AGGAGCAGTATTCGCCATCA / CGACGAGGTATCCCTGCTAA / 6471-6638
mt2.2 / CGCCCCATCTAACATCTCAT / GTCCCACATGGAGGAATAGG / 14201-14433
mt3.2 / AACCCAAGCTACAGCCTCAA / GGGAATTCCTTGGGTGACTT / 4086-4272
mt4.3 / CCTCACCCCCTTATCAACCT / GGAGCCGCTTATTAGGAGGA / 3013-3216
Tuba1a (2) / ACCAAGCGTACCATCCAGTT / CCACGTACCAGTGCACAAAG / 220 bp
Actb (3) / GTCGTACCACTGGCATTGTG / GCTGTGGTGGTGAAGCTGTA / 175 bp

(1)  according to Genbank Accession number AC_000022

(2)  tubulin, alpha 1A, exon 4 sequence

(3)  actin, beta, exon 4 sequence


Table S2C: PCR primer sequences for human nuclear RNA genes

mtDNA Primers
Gene ID / Name / Entrez Gene # / Forward Primer / Reverse Primer / Product Length
NDUFS3 / NADH dehydrogenase Fe-S protein 3, 30kDa (complex 1) / 4722 / TCCCAGTGCTGACTTTCCTC / GGCGTCAGCTCATCTGTGTA / 175
UQCRC1 / ubiquinol-cytochrome c reductase core protein I (complex 3) / 7384 / ACATCCTCAGAAATGCCCTG / ACGGATCCGGTTGTAGTCTG / 239
UQCRC2 / ubiquinol-cytochrome c reductase core protein II (complex 3) / 7385 / AACTCAGCAGCCATTTGATG / GTTCTTGGCAGCTTGGACAT / 181
UQCRFS1 / ubiquinol-cytochrome c reductase, Rieske iron-sulfur 1 (complex 3) / 7386 / GCTCCTCTCAACCTTGAAGTC / TTCAAGTACAGAAGGCTTCCTC / 151
COX5A / cytochrome c oxidase Va (complex 4) / 9377 / CCCCTATGTCATCCAGGAAC / CCAGGTAACTGTTCACACTCAAG / 150
ATP5A1 / ATP synthase, F1, alpha 1 (complex 5) / 498 / GGGCTATGAAGCAGGTAGCA / TCCTTGCTTCAGCAACTCAG / 152
ATP5B / ATP synthase, F1, beta (complex 5) / 506 / ATGTGCCTGCTGATGACTTG / AATGCTCACTGCCAACAATG / 171
Control Primers
Gene ID / Name / Entrez Gene # / Forward Primer / Reverse Primer / Product Length
CTNNA1 / catenin (cadherin-associated protein), alpha 1, 102kDa / 1495 / TCCGTGTTCTCACAGATGCT / AGCAGCTTAGTGGCTTCCAG / 253
CTNNA1* / catenin (cadherin-associated protein), alpha 1, 102kDa / 1495 / TAAGAAGGCCCATGTTTTGG / AATCAGCAACCGGGTAACAG / 256
EIF1 / eukaryotic translation initiation factor 1 / 10209 / GTGATGACCTGCTTCCTGCT / CTTGCGTTGGTCACCCTGTA / 218
ITM2B / integral membrane protein 2B / 9445 / CATTGTTATGCCACCCAGAA / GCAGTTTGTAAGTTTCCTTGTCA / 213
KRT10 / keratin 10 / 3858 / GGGCGAGTCTTCATCTAAGG / AATGGTCTGTGTGAAGGGAGA / 175
NEFH / neurofilament, heavy polypeptide / 4744 / GAGGAACACCAAGTGGGAGA / TGTGAGTGGACACAGAGGGA / 194
STMN1 / stathmin 1 / 3925 / TCCCATGAAGCTGAGGTCTT / TTGTGCCTCTCGGTTCTCTT / 159

* two primer pairs were used and results averaged

1. Kraytsberg Y, Kudryavtseva E, McKee AC, Geula C, Kowall NW, Khrapko K. (2006) Mitochondrial DNA deletions are abundant and cause functional impairment in aged human substantia nigra neurons. Nat Genet 38:518-520.

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