Should I use the SureSilencing shRNA Plasmids with the GFP, neomycin, or hygromycin, or puromycin resistance marker?
FAQ ID -2900

Use the SureSilencing shRNA Plasmids with the neomycin, hygromycin or puromycin resistance marker for stable transfection to achieve long-term knockdown (a cell line with permanently knockdown of the gene of interest) and to perform gene function assays in cells for a long period of time. Neomycin tends to be the more popular choice, but some researchers prefer puromycin because the time needed for selection of puromycin resistance is typically shorter than neomycin resistance. Puromycin and hygromycin resistance may also be used to stably transfect SureSilencing shRNA into cells that are already neomycin resistant due to a previous stable transfection with other exogenous nucleic acid. Use the SureSilencing shRNA Plasmids with GFP for transient transfections and gene function assays that can be performed with the cells quickly (in less than a day), but only if you have access to flow cytometry.