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.

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.

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?

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

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.

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