Should I use the SureSilencing shRNA Plasmids with the neomycin-resistance marker, the puromycin-resistance marker, or the GFP reporter gene?
FAQ ID -2882

Use the SureSilencing shRNA Plasmids with the neomycin (or the puromycin) resistance marker for stable transfection to achieve long-term knock down (a cell line permanently suppressing expression of the gene of interest). The neomycin and puromycin resistance markers also provide an alternative marker for cell lines that are already neomycin or puromycin resistant from a previous stable transfection of exogenous nucleic acid. The puromycin selection process is typically quicker than the neomycin selection process. Use the SureSilencing shRNA Plasmids with GFP for transient transfections and gene function assays that can be performed with the cells quickly (within 48 hours post-transfection). For best results when using the GFP-carrying plasmids, it is critical that you enrich for transfected cells via flow cytometry, prior to carrying out knock down validation studies and functional assays.