I want to clone PPAR-gamma together with GFP genes into my rat bone marrow stem cells to induce the lipofibrolastic differentiation.
Would you please which vector is more simple and reliable to my experiments? As to the protocols, I would recommend the "PCR based molecular cloning protocols" http://www.lab-manual.com/lm_177.htm

Any advice related to PCR based molecular cloning is welcome. Thank you in advance.

When you say PCR cloning of PPAR and GFPs, do you mean construction of fusion genes or do you want to express each as a separate polypeptide?

I'm biased but right now I'd say that there's not much that would beat a lentiviral vector and size of the expression cassette shouldn't be a problem.

Is it a rat stem cell line or primary cells you are using?