I am looking to compare levels of 16S rRNA across a panel of samples, and am having difficulty finding a set of qPCR primers. Does anyone have sequences they are willing to share and the protocol that they follow? I have primers for rt-PCR, but the expected band size is very large and probably will not work. Thanks in advance!
Hi Kerri,
Which primers do you have? The last time i used 341f (optionally with wobble) and 515r for a qPCR targetting the 16S rRNA gene. Am not entirely sure about the sequences right now, but if needed, i can look those up.
Best regards,
Jennifer
Hey
I'm comparing 16S rRNA expression levels on qRT-PCR using F1048 / R1194 primers.
Best regards,
Ferran.
Hi Kerri,
It depends on your sample. There is a bunch of general primers of different sizes evaluated in Silva database in the attached article. We have good results with S-D-Bact-0341-b-S-17/S-D-Bact-0785-a-A-21 or S-D-Bact-0907-a-A-20 from that article.
God speed,
Adam
Article Evaluation of general 16S ribosomal RNA gene PCR primers for...
Hi Kerri, maybe this paper will be useful. It's a commonly used 16S Taqman assay that was suggested to me by someone who knows alot more about qPCR than I do!
Suzuki et al 2000. Quantitative Analysis of Small-Subunit rRNA Genes in Mixed Microbial Populations via 5′-Nuclease Assays. Appl Environ Microbiol. 2000 Nov; 66(11): 4605–4614.
Primers and probe sequences (check paper though):
1369F; CGGTGAATACGTTCYCGG
1492R; GGWTACCTTGTTACGACTT
Probe TM1389F; CTTGTACACACCGCCCGTC
Camilla
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