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To compare normal and cancer tissue - (Mar/06/2007 )

I need to compare expression of a set of genes between normal tissue and cancer tissue. What we have planned is 3 sets of experiments for 3 different normal tissues and 3 or more tumor tissues and then compare between average values of normal tissue as control and tumors as test.. Is this necessary or is it possible (easier) that I pool RNA from 3 different normal tissues and synthesize cDNA followed by Real Time PCR? Thank you.

-Calvin*-

in my opinion, it's better to run the 3 tissues separately and take an average afterwards. this allows you to do more in the way of statistical analysis.

-aimikins-

The normal tissue samples where we do not anticipate changes between different tissues act as a control for comparison with tumor. So even then pooling would not be an option?

-Calvin*-

well, it's up to you. but I would expect a certain amount of variation between tissues from 3 different individuals; the epxression pattern should be similar but not identical. perhaps run a handful of 'normal' tissues for your GOI and see how much variability you can expect

-aimikins-

I don't think you should pool your data/samples at this stage. Keep them saperate. You'll have much more data that way and thus can later decide to pool the figures or not.

-perneseblue-

By pooling, you reduce the probability of seeing something statisticaly significant. Use every sample seperately.

-kr├╝melmonster-