Table 3.
Oligonucleotides
| Primer | Sequence (5’→3’) | Use/locationa | Source or reference |
|---|---|---|---|
| EBS universal | 5’-CGAAATTAGAAACTTGCGTTCAGTAAAC-3’ | Targetron cloning | Sigma-Aldrich |
| oMC44 | 5’-CTAGCTGCTCCTATGTCTCACATC-3’ | rpoC PCR (CD0067) | (McBride and Sonenshein, 2011a) |
| oMC45 | 5'-CCAGTCTCTCCTGGATCAACTA-3’ | rpoC PCR (CD0067) | (McBride and Sonenshein, 2011a) |
| oMC112 | 5'-GGCAAATGTAAGATTTCGTACTCA-3' | tcdB PCR (CD0660) | (Edwards et al., 2014) |
| oMC113 | 5'-TCGACTACAGTATTCTCTGAC-3' | tcdB PCR (CD0660) | (Edwards et al., 2014) |
| oMC339 | 5’-GGGCAAATATACTTCCTCCTCCAT-3’ | sigE PCR (CD2643) | (Edwards et al., 2014) |
| oMC340 | 5’-TGACTTTACACTTTCATCTGTTTCTAGC-3’ | sigE PCR (CD2643) | (Edwards et al., 2014) |
| oMC547 | 5’-TGGATAGGTGGAGAAGTCAGT-3’ | tcdA PCR (CD0663) | (Edwards et al., 2014) |
| oMC548 | 5’-GCTGTAATGCTTCAGTGGTAGA-3’ | tcdA PCR (CD0663) | (Edwards et al., 2014) |
| oMC655 | 5’-GAAATAGTACCAGACCCACCAATA-3’ | eutG PCR (CD1907) | This study |
| oMC656 | 5’-TATTGCAGAACCACCACCTAAT-3’ | eutG PCR (CD1907) | This study |
| oMC657 | 5’-CTAAAGAAGATATACATACAGGAGCAGT-3’ | eutA PCR (CD1912) | This study |
| oMC658 | 5’-TAAATCAGGTCCTGCTGTTGC-3’ | eutA PCR (CD1912) | This study |
| oMC659 | 5’-ATCAGGAGATAAATTAGCAGGTCTT-3’ | eutB PCR (CD1913) | This study |
| oMC660 | 5’-GCCACTGCAGGATTATTTCTTATATC-3’ | eutB PCR (CD1913) | This study |
| oMC661 | 5’-GTTGATGATGAACCACTGTTAAGG-3’ | eutV PCR (CD1910) | This study |
| oMC662 | 5’-TTCAACAGCTTCAAATCCATCAC-3’ | eutV PCR (CD1910) | This study |
| oMC663 | 5’-TGTACTAAGTAAATTTGATGATGAAGCA-3’ | eutW PCR (CD1911) | This study |
| oMC664 | 5’-TGACCAGTTTATATTCCTGTGTTAAAG-3’ | eutW PCR (CD1911) | This study |
| oMC665 | 5’-AAAAGCTTTTGCAACCCACGTCGATCGTGAAGGAAGGCTTGTAGTGCGCCCAGATAGGGT-3’ | eutA intron retargeting (CD1912) | This study |
| oMC666 | 5’-CAGATTGTACAAATGTGGTGATAACAGATAAGTCCTTGTAAATAACTTACCTTTCTTTGT-3’ | eutA intron retargeting (CD1912) | This study |
| oMC667 | 5’-CGCAAGTTTCTAATTTCGGTTCTTCCTCGATAGAGGAAAGTGTCT-3’ | eutA intron retargeting (CD1912) | This study |
| oMC674 | 5’-AAAAGCTTTTGCAACCCACGTCGATCGTGAATCTACCTCGTTAGTGCGCCCAGATAGGGTG-3’ | eutG intron retargeting (CD1907) | This study |
| oMC675 | 5’-CAGATTGTACAAATGTGGTGATAACAGATAAGTCTCGTTAATTAACTTACCTTTCTTTGT-3’ | eutG intron retargeting (CD1907) | This study |
| oMC676 | 5’-CGCAAGTTTCTAATTTCGGTTGTAGATCGATAGAGGAAAGTGTCT-3’ | eutG intron retargeting (CD1907) | This study |
| oMC714 | 5’-GGAGAAGGCTCACTAAAAGC-3’ | eutG verification | This study |
| oMC715 | 5’-GCCTCTTTGCTTGTTTAAGAC-3’ | eutA verification | This study |
| oMC716 | 5’-GTAGCCATTGTACCTACTTGAAG-3’ | eutA verification | This study |
| oMC855 | 5’-TCATAGCTAACCCTAATGAAGACAT-3’ | eutS PCR (CD1908) | This study |
| oMC856 | 5’-GCAACATCTGCTGCTATTATTGA-3’ | eutS PCR (CD1908) | This study |
| oMC857 | 5’-GACACTCCTGGTGAGTATATGG-3’ | eutP PCR (CD1909) | This study |
| oMC858 | 5’-GTGTGGCATCATACACTATTGC-3’ | eutP PCR (CD1909) | This study |
| oMC859 | 5’-TCCTAAGGATGCAGAAGCTTATTT-3’ | eutC PCR (CD1914) | This study |
| oMC860 | 5’-CAGCATGGTCTGCTCTAAATCT-3’ | eutC PCR (CD1914) | This study |
| oMC861 | 5’-ACTGCAGACTGTGATGATGTT-3’ | eutL PCR (CD1915) | This study |
| oMC862 | 5’-CAGCACCTGCATACATTGATTT-3’ | eutL PCR (CD1915) | This study |
| oMC863 | 5’-GGAGATGTCGGTGCTGTAAA-3’ | eutM PCR (CD1916) | This study |
| oMC864 | 5’-TGTTCTTAATGTACCAACTCTGGA-3’ | eutM PCR (CD1916) | This study |
| oMC865 | 5’-TGGTGAAGATAAGGAAGCCAATA-3’ | eutE PCR (CD1917) | This study |
| oMC866 | 5’-GATGTTGGGTTTGTTGAAGGTATAA-3’ | eutE PCR (CD1917) | This study |
| oMC867 | 5’-GCAGCAGATGCAATGGTTAAA-3’ | eutK PCR (CD1918) | This study |
| oMC868 | 5’-CAGCTCCAACATCTCCTCTTAC-3’ | eutK PCR (CD1918) | This study |
| oMC869 | 5’-TTTGGCGCTAAATTGGATGAAA-3’ | eutT PCR (CD1919) | This study |
| oMC870 | 5’-TTCCTTAACAAGCTTTGGCATATC-3’ | eutT PCR (CD1919) | This study |
| oMC871 | 5’-ATAGAAGTTGAAGCATCAGGAAGAC-3’ | eutD PCR (CD1920) | This study |
| oMC872 | 5’-CATGCATATTGACCTGGTTGAGATA-3’ | eutD PCR (CD1920) | This study |
| oMC873 | 5’-CCTAAAGCTGTGATTGTATTTGAACAAG-3’ | eut hyp PCR (CD1921) | This study |
| oMC874 | 5’-ATTTCCAAGTGCTATATTCGATAGTCC-3’ | eut hyp PCR (CD1921) | This study |
| oMC875 | 5’-AACTAAAGACACATACAAGGAAGGC-3’ | eutN PCR (CD1922) | This study |
| oMC876 | 5’-TCTAGCTGAGGAACCTTTGGATATAA-3’ | eutN PCR (CD1922) | This study |
| oMC877 | 5’-AGGCGTTGTTGAAAGTAGTAAAGT-3’ | pduT PCR (CD1923) | This study |
| oMC878 | 5’-ACTGTCTACTGATGGTATTACAGTCT-3’ | pduT PCR (CD1923) | This study |
| oMC879 | 5’-TGGTCTTGGAGAACAATTTGAAGA-3’ | eutH PCR (CD1924) | This study |
| oMC880 | 5’-ATCAGCAAGAACTGGTGCTAAA-3’ | eutH PCR (CD1924) | This study |
| oMC881 | 5’-AAGTGGAACTAAAGACACAGTAGAT-3’ | eutQ PCR (CD1925) | This study |
| oMC882 | 5’-CCTAATCTTGGGCTTTCCTCTAAT-3’ | eutQ PCR (CD1925) | This study |
| oMC972 | 5’-ATAAGAGCCACAGTGGTTGG-3’ | eutA PCR (CD1912) | This study |
| oMC973 | 5’-CTGGCAAGTTCTTAAGTGGAAAC-3’ | eutA PCR (CD1912) | This study |
| oMC1588 | 5’-GGGATTGCATATGGAAATCAATGTTATAG-3’ | CD1906 PCR | This study |
| oMC1589 | 5’-TTTACAAACCAACTAGCTTTATCCATTTC-3’ | CD1906 PCR | This study |
| oMC1593 | 5’-GGCTTTAGGAATGGTTGGTATAGTT-3’ | CD0742 PCR | This study |
| oMC1594 | 5’-CTCCACAGAGATTGAAGATTGGTATT-3’ | CD0742 PCR | This study |
| oMC1595 | 5’-AAACTAGGAGGTCTTGACAGATTAGA-3’ | CD3167 PCR | This study |
| oMC1596 | 5’-GGTCAAGGATAGTATCAAGTGCAAATA-3’ | CD3167 PCR | This study |
| oMC1634 | 5’-CTTGTTTAGCAGGTATGGCATTTAAC-3’ | eutG (CD1907; 3’) PCR | This study |
| oMC1635 | 5’-TTCCACCTAATACATGTGCAATAGAA-3’ | eutG (CD1907; 3’) PCR | This study |
| oMC1687 | 5’-GAAGTACATATGCTAACAGCGATTG-3’ | CDR20291_1847 | This study |
| oMC1688 | 5’-GAGATATTGCACCTTTAGTTCTGTTC-3’ | CDR20291_1847 | This study |
| fliCqF | 5’-TACAAGTTGGAGCAAGTTATGGAAC-3’ | fliC PCR (CD0239) | (McKee et al., 2013) |
| fliCqR | 5’-GTTGTTATACCAGCTGAAGCCATTA-3’ | fliC PCR (CD0239) | (McKee et al., 2013) |
| qRTpilA1F | 5’-TGGCAGTTCCAGCTTTATTTAGTAAT-3’ | pilA1 PCR (CD3513) | (Purcell et al., 2016) |
| qRTpilA1R | 5’-AAGATAATGCTGCACTCTTAACTGAA-3’ | pilA1 PCR (CD3513) | (Purcell et al., 2016) |