I am planning a qPCR experiment in plant model A. lyrata. As an internal control I first selected several actin homologs as house keeping genes, but it seems like the primers designed for actin have very high similarity to several other putative genes and genomic regions which therefore makes them not so useful.
One other gene that I have found so far is pdf1 (protein phosphatase 2A subunit A2) which I read is one potential house keeping genes and the primers for it didn't show significant matches with other genomic regions and available RNAseq annotation data.
Can somebody please suggest something?
Thanks,
You don't even need a reference gene! try this method (easy to use, plots pretty plots, and does not require reference genes):
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0071448
(grab a step-by-step tutorial from my RG page...)
Thanks Dr. Jochen for your insights. For now I have picked two genes that can be of help as reference genes.
Dr. Mikhail,
The suggested paper could be of potential help to me. I will look into it.
Thanks a lot everybody,
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