Transfection was used to insert transgenes for a few different lines of fish. PCR was used to verify uptake of the transgenes and they performed mostly as expected in the P1 and to some degree in the F1 generation. However, few individuals are showing up as positive as generations continue (F2, F3, etc.) and the consistency of the PCR seems less reliable in latter generation. In order to figure out way this is happening (i.e. formation of concatemers, unstable integration, selection against the transgene, etc.) I want to test for integration of the transgene and potentially determine where the transgenes are integrating. Does anyone with experience in this area have any suggestions for a simple and affordable method for doing this (i.e. TAIL-PCR, inverse PCR, ligation-mediated PCR, Southern blot, probe capture, etc.) that has worked for them?

Best Regards