Extended data Table 2.
Oligonucleotides used in this study.
| Name | Sequence (5'–3')1 | Description |
|---|---|---|
|
| ||
| pMSR cloning | ||
| JP449 | CGTTTTGTAAACGAATTGC | 5’ pMSR0 insert screening |
| JP450 | CTCACGTTAAGGGATTTTG | 3’ pMSR0 insert screening |
| MO-008 | TTTTTTGTTACCCTAAGTTTCTCTGACTCTGG AATTATAGAATC | 5’ left arm ΔtcdE VPI10463 |
| MO-018 | CTTTTCATCCAGGTGAACTACTGTGCATTC | 3’ left arm ΔtcdE VPI10463 |
| MO-019 | TAGTTCACCTGGATGAAAAGTAAGTAATGGTAG | 5’ right arm ΔtcdE VPI10463 |
| MO-020 | AGATTATCAAAAAGGAGTTTCTCATTTTCTCT TGGTCTAATG | 3’ right arm ΔtcdE VPI10463 |
| MO-011 | GAATTATGCAAGTTGGATTTG | 5’ ΔtcdE screening VPI10463 |
| MO-006 | CTTTATATATTTTTCCTATAACTTTTAAACTAT C | 3’ ΔtcdE screening VPI10463 |
| MO-021 | TTTTTTGTTACCCTAAGTTTGGAATGCAAAAT ATAGATGATAATTATTTC | 5’ left arm ΔtcdE UK1 |
| MO-022 | CTTACTTTTCGTGCATTCATCATAGTTCAC | 3’ left arm ΔtcdE UK1 |
| MO-023 | ATGAATGCACGAAAAGTAAGTAATGGTAGAT ATAATAAAAATATTAAC | 5’ left arm ΔtcdE UK1 |
| MO-024 | AGATTATCAAAAAGGAGTTTCGTCTAAATTAG TTAGTATAGTTTTATAC | 3’ left arm ΔtcdE UK1 |
| MO-025 | GGATGGAAGGATTTAGAAGATG | 5’ ΔtcdE screening UK1 |
| MO-006 | CTTTATATATTTTTCCTATAACTTTTAAACTATC | 3’ ΔtcdE screening UK1 |
|
| ||
| pMC358 cloning | ||
| JP725 | CGTCAATGTATGGGTAGATATG | 5’ pMC358 linearization for cloning with Hifi DNA assembly |
| JP726 | CAACGTCGTGACTGGG | 3’ pMC358 linearization for cloning with Hifi DNA assembly |
| JP733 | CTATTACGCCAGCTGGC | 5’ pMC358-screening |
| JP734 | GGTAACCCCTAGCAAAGC | 3’ pMC358-screening |
| JP758 | ttttcccagtcacgacgttgGGTTTCTAGATTTCATAAA AGATAC | 5’ tcdR promoter |
| JP759 | tatctacccatacattgacgCTCTTATATTTATAATGAT GCTTTATTTG | 3’ tcdR promoter |
| JP760 | ttttcccagtcacgacgttgGTCTGTTTTTGAGGAAGAT ATTTG | 5’ tcdB promoter |
| JP761 | tatctacccatacattgacgCTTTACTATAATATTTTTA CATCTAAATGC | 3’ tcdB promoter |
| JP764 | tatctacccatacattgacgCTTTTTATTGGTAAATCTT CATATTAG | 5’ tcdA promoter |
| JP765 | ttttcccagtcacgacgttgCATGGTCAGTTGGTAAAAT C | 3’ tcdA promoter |
|
| ||
| qRT-PCR | ||
| RT_polIII-F_Cdiff | TCCATCTATTGCAGGGTGGT | 5' CD1305 |
| RT_polIII-R_Cdiff | CCCAACTCTTCGCTAAGCAC | 3' CD1305 |
| QRTBD013-tcdA | TAATAAAAATACTGCCCTCGACAAA | 5’ tcdA |
| QRTBD014-tcdA | ATAAATTGCATGTTGCTTCATAACT | 3’ tcdA |
| QRT_DL_TcdB_F (JRP4055) | ACCATATAGCTTTGTAGATAGTGAAGGAAA | 5’ tcdB |
| QRT_DL_TcdB_R (JRP4056) | AAGAACTACATCAGGTAATTCAGATACAAA | 3’ tcdB |
| QRTBD35-tcdR | AAATAACTCAGTAGATGATTT GCAAGAA | 5’ tcdR |
| QRTBD36-tcdR | GTTTCTCCCTCTTCATAATGTAAA CT C | 3’ tcdR |
1
Lowercase bases indicate overlapping sequences