What types of controls do you recommend for Stellaris® RNA FISH assays?
The type of Stellaris® RNA FISH controls needed is dictated by the experiment set up and the preferences of the researcher. Whereas sense or scrambled sequences are useful in antisense or RNAi silencing, they do not serve as an appropriate negative control in Stellaris RNA FISH. An ideal negative control would be a specific probe set against an RNA that normally is not expressed in the cell/tissue sample to be tested. Alternatively, you may consider using a probe set targeting the RNA from a gene from a different organism and which is absent from your sample, e.g. GFP. Please read this article on how controls can demystify your Stellaris RNA FISH experiment for more details.
Formalin-fixed paraffin embedded (FFPE) tissue may suffer from RNA degradation, sometimes very significantly. In such cases, detection of an RNA from a reference gene can be useful for verification of the experimental technique. One commonly used reference gene is glyceraldehyde 3-phosphate dehydrogenase (GAPDH). We make available several Stellaris ShipReady probe sets that can serve as controls, including human and mouse GAPDH, and DesignReady probe sets for many other organisms.