Thanks Nina and Bob for your replies but I don't believe mRNA degradation
can explain our whole problem. Firstly (I didn't include this info in my
initial messsage) In situ hybridization with riboprobes works even better
in our paraffin sections (5µ) than our frozen sections (15µ), so in
paraffin sections we have 3 times less material but twice the signal. Its
true that PCR requires intact mRNA while ISH doesn't. Secondly we are also
unable to amplify genomic DNA from our paraffin sections. So we think its
more a question of digestion/extraction/accessibility of mRNA molecules.
We're now looking and testing extraction protocoles. We believe RTPCR from
paraffin sections is possible because the only three makers of
microdissection systems : LEICA, ARCTURUS, and PALM claim that it's
feasable. And thats why we bought the da - !$OX ! Somebody, Somebody out
there must know how to do it......