snap frozen vs formaldehyde-fixed paraffin tissue samples

[hammerberlin]

dear all,

I would like to know if somebody here has experience with formaldehyde-fixed paraffin tissue samples in terms of sequencing? We have access to a tumor paraffin archive and we would like to do RNA-Seq (Solexa or Solid) with these samples. Thus my question is how high would be the correlation of snap frozen versus paraffin tissue sample in terms of RNA-Seq with next generation sequencing? Are there any information/papers out?

I could imagine that the correlation of the results would be high because the RNA is still present in the paraffin sample. Ok the RNA is fragmented by degradation but the first step of the library construction is fragmentation. So I could think that there is not so high difference between snap-frozen and paraffin samples or???

any comments would be great!

thanks
paul

[cyril]

Hi Hammerberlin,

I am starting a project where I need to fix my samples before performing any further experiment. I see that you posted more than one year ago.
Have you tried this experiment ?

Thanks

Cyril