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how to determine copy number in a transgenic pup - (Jul/23/2008 )

I understand that one can determine copy number of a transgene by either Real-time PCR or southern blot. But I am not familiar with either of the techniques.

Can somebody help me in giving me tips how to plan my experiment, if possible a protocol, and precautions to be taken?

Thanks for your help.



I used for copy number varation the Affymetrix Chip. I tested also Real-Time PCR and Illumina Chip. I got the best results from Affymetrix 6.0 Chips. Now I'm trying to make the CNV-Analysis with SNP-Stream assay. the basic is the same as Affymetrix. My collegs tryed to use GeXP which is used for Gene Expression analysis for CNV alalysis but the results were not realy satisfying.

Best regards