This might be a naive question, but I just wonder if there are more transcripts in the cells, would it be harder for the knockdown mechanism to degrade all these transcripts? Imaging for a same target gene, which expresses at a very high level in cell type A but at a lower level in cell type B, if you use a same shRNA or siRNA, would you expect differences in knockdown efficiency?
I think that the quantity of molecules that will be targeted by the RNAi will be the same in both scenarios, no matters if the levels of the transcripts are low or high. However, the biological impact can be dramatic depending on the situation. If for instance the low levels of a transcript are highly important for an specific function, you might eliminate most of this transcript with the siRNA and generate a high impact on the downstream function of this gene.
From the quantitaive point of view, by using siRNA at the "classical" concentration range (from 5 to 100 nM) you are completely saturating target cells with siRNA molecules. Thus, you should be able to obtain an appreciable level of down-modulation (unless the siRNA is not working at all...). On the other hand, the use of shRNA could be less powerful by the quantitative point of view but stable over time, therefore it could be more convenient to have a clear phenotype. However, as Adriana said, the amount of targeted transcripts in both conditions could not change, since the "limiting factor" is always the functionality (and availability) of endogenous RNAi machinery.
If you have the same transfection efficiencies for both cell types you should expect the same percentage of down-regulation of your gene as you normally work under saturating conditions.
I feel it will be more efficient to shut down a higly expressed gene since the siRNA signals will be quite amplified,thus resulting in an efficient knock down!
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