We got a great question submitted at www.thermofisher.com/ask so I asked Gina, in Technical Support here at Thermo Fisher Scientific to help us out with an answer.
“Some of your pre-designed Taqman gene expression assays offer species specific options. e.g. human specific with no cross-reactivity with mouse. Could you explain why some Taqman gene expression assay probes are made to span exon boundaries and yet it will detects genomic DNA?”
Our TaqMan Gene Expression Assays are designed to detect within the target species, but for some assays, there may be sequence homology such that the assay will also detect in other species. To check for this, you can use the Transgeneic Cross Reactivity Check Filter on the website. Here’s an example using NFKBIA:
There are 4 human assays to this target. If this assay was going to be used in a transgenic mouse, we would check the box for mouse (Mus musculus). Any assays that would cross react with mouse NFKBIA will be removed. Only assays that will not detect in mouse will remain.
After checking the box for mouse, we find that there are no assays left. So none of the current predesigned assays would be appropriate for use in a transgenic mouse experiment, since they will cross react to some extent.
So is there any way to get an assay that will detect human NFKBIA, but not cross react with mouse? Yes there is. The answer is to use our Custom Assay Design Tool.
In the design preferences, simply select the species that you do not want to be detected by the assay. The new assay that is created will now include this criteria in the design process.
Hope this helps! – Gina