I would like to make stable cell line with two different constructs with two different colors. I tried Neon transfection and so far I managed to get the stable cell only with one construct once I transfect it with additional DNA I lost the expression within 3,4 days.
If both plasmids are using the same selection marker, like G418, its going to be very difficult to select for cell populations that have integretated both of your plasmids. You could always clone them by serial diluations or sort dual positive cells by flow cytometry, but it will be tedious and most likely not very effective.
I would recommend to subclone one of your insert (ex. GFP-ProteinX) to a plasmid vector with hygromycin resistance and select your cells with the two antibiotics like g418 and hygro or try to subclone into a vector were you can express multiple cassette into one plasmid .
Good luck!
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