I want to design an experiment for 2D-DIGE and I have two types of samples, one: control tissue from healthy individuals and other from patients. besides comparing proteom of patients to control samples, I want to compare patient to patient variations as well. I was thinking ofsome thing like attached experimental design, would you let me know if it is right and works for further analysis using decyder software?
Thank you
Hi Mehdi
Not sure about use with DeCyder - but I'd suggest looking at dye swapping for more accuracy. Ideally you need to ensure that the 3 samples are present in both the Cy3 and Cy5 channels due to the small shift typically seen at low molecular weights.
Also, how were you planning to setup your experiment(s)? Have you accounted for technical replicates?
Michael
Hi Michael,
Thanks for the dye swapping suggestion, I'll be doing each run in three replicates, Just wondering if you had a chance to review my attached file for experimental design, I need to make sure that it is correct,
Thank you
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