The choice between transient or stable transfection will usually depend on your goals, cell type and the facilities available to you. In short, transient transfection exerts a temporary influence on your cells, whereas stable transfection leads to permanent genetic changes that are usually passed on to future cell progeny. More details on both transient and stable transfection are provided below.
For most transfection applications, a transient influence on gene expression or cell function is necessary, sufficient or preferred. Examples of such applications include short-term gene expression studies, gene knockdown studies and small-scale protein production. To achieve transient transfection, you must use factors that will not be incorporated in the host cell’s genome. This can include using DNA, proteins, mRNA or non-coding RNAs, all of which will degrade over time or will be diluted out through cell division. As such, transient transfection only influences your cells over a short time window spanning a few hours to a few days.
To achieve stable transfection, you must use genetic constructs that will be incorporated into the genome of the host cells (either into the chromosomes themselves, or as extra-chromosomal episomes), so that they will pass these new genes onto their offspring. The constructs must also carry selection markers, so that you can identify which cells have been successfully transfected. Stable transfection is often required for large-scale protein production, research into long-term gene regulation, the generation of stable cell lines, and for gene therapy. As the method requires successful DNA integration into the host genome, it is often much harder to achieve than transient transfection, and typically has lower transfection efficiency. Stable integration can occur randomly with plasmids, actively at random sites with help of transposases or viruses, or site-specifically when using genome editing tools like CRISPR.