To find out the integration site of a transgene - (Mar/13/2006 )
How could I find out the integration site of a transgene inside the genome ?
I am working on transgenic cotton varieties - its molecular characterization, structural and funtional stability analysis. I am trying to find out the adjoining gene sequences of a transgene inserted in to the cotton genome.
I read about vectorette PCR see here although this was in relation with one project that is frozen (at -70C...) right at this moment. And I haven't tryed it myself.
Maybe try a TAIL-PCR (Thermal assymetric interlaced PCR)? (it's normally performed for finding where T-DNA from agrobacterium has integrated, but probably can be adjusted for any integration).
Do a google search for "TAIL-PCR" or check out http://preuss.bsd.uchicago.edu/protocols/tail.html as a start.