Table 1.
16S rRNA-targeted primers and probes sequences, concentrations, and qPCR conditions used for IBD-associated bacterial markers in this work for TaqMan chemistry.
| Target* | Primers and probes a | qPCR conditions | ||||||
|---|---|---|---|---|---|---|---|---|
| Denaturing | Annealing (40 cycles) | |||||||
| Primers | Concentration (nM) | Sequence (5′-3′) | Reference | Time (min:s) | T a (°C) | Time (min:s) | T a (°C) | |
| FPRA | Fpra_F Fpra_R |
250 | TGTAAACTCCTGTTGTTGAGGAAGATAA GCGCTCCCTTTACACCCA |
(Lopez-siles et al., 2014) | 2:00 10:00 |
50 95 |
0:15 1:00 |
95 60 |
| Fpra_PR | 300 | FAM-CAAGGAAGTGACGGCTAACTACGTGCCAG-TAMRA | ||||||
| ECO | Eco_F | 300 | CATGCCGCGTGTATGAAGAA | (Round and Mazmanian, 2009) | 2:00 10:00 |
50 95 |
0:15 1:00 |
95 60 |
| Eco_R | CGGGTAACGTCAATGAGCAAA | |||||||
| Eco_PR | 100 | FAM-TATTAACTTTACTCCCTTCCTCCCCGCTGAA-TAMRA | ||||||
| PHGI PHGII |
PHG_F PHG_R |
300 | CTCAAAGAGGGGGACAACAGTT GCCATCTCAAAGCGGATTG |
(Lopez-siles et al., 2016) | 2:00 10:00 |
50 95 |
0:15 1:00 |
95 64 |
| PHGI_PR | 900 | FAM-TAAGCCCACGACCCGGCATCG-BHQ1 | ||||||
| PHGII_PR | JOE-TAAGCCCACRGCTCGGCATC-BHQ1 | |||||||
*
EUB, Eubacteria; FPRA, F. prausnitzii; ECO, E. coli; PHGI, F. prausnitzii phylogroup I; PHGII, F. prausnitzii phylogroup II; NA, non-applicable.
a
Probe sequences are in bold font. FAM™, 6-carboxyfluorescin; JOE, 4′,5′-dichloro-2′,7′-dimethoxy-5(6)-carboxyfluorescein; TAMRA™, tetramethylrhodamine; BHQ1, Black Hole Quencher1.