I ran an array based q PCR and obtained data for fold change in genes. I followed this up by running end pint PCR followed by a gel. But the fold change in my end point PCR is not the same as as in my RT PCR. The primer sets are different and conditions were different as the RT PCR was a profiler array from Qiagen. Does this usually happen or should the fold change in RT PCR and end pint PCR be the same?
Thank you
Hi Vasundhara,
The qPCR data and the end-point PCR analysis are two different analyses. The qPCR analysis analysis the progress of amplification of the product in a real-time manner and takes concentration of the product at an early time-point, while the end point data is taken at the end of the reaction. At the end of the amplification many times differentially expressed genes will show similar amount of product. It is also seen in the amplification plot of the qPCR analysis. If you anyway want to do a gel based analysis...do a semi-quantitative PCR where you need to take out samples at different PCR cycles and then run on a gel...
bye
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