That approach might be feasible using the custom RNA probes designed by eBioscience. They currently make three different color probe sets. This approach was originally designed for the simultaneous detection of RNA and protein at a single-cell analysis.

http://www.ebioscience.com/knowledge-center/application/flowrna/primeflow-rna-assay-principle.htm

Hi Grant, I'm familiar with that method to study endogenous mRNA levels. I'm asking about an approach to transfect synthetic mRNAs into cells that encode GFP and that are also Cy5 labelled. This would allow researchers to interrogate specific mRNA elements and combinations thereof in live cells.

Thanks Holger. This paper seems to indicate that the authors could detect 1800 copies of Histone H4 mRNA with Cy5 labelled probes:

https://www.researchgate.net/publication/21416397_Sensitive_detection_of_RNAs_in_single_cells_by_flow_cytometry

It I'm reading it correctly the authors used nine different 5' end labelled probes. I suspect that uridine labelled mRNAs would then carry much more Cy5 per mRNA. Of course you could transfect in as much as you need to, but there might be a trade-off with physiological relevance.

Article Sensitive detection of RNAs in single cells by flow cytometry