Been thinking a lot about expression in tissue these days. Funny quote in a post from the always quotable Dan Graur: “They looked at the process of transcription in long-dead tissues? Isn’t that like studying the [...] circulation system in sushi?” He also points to this study from Yoav Gilad about RNA degradation, which is really great–wish there were more such studies.
We have been doing a fair amount of RNA FISH in tissues (big thanks to help from Shalev Itzkovitz and Long Cai), and while we haven’t done a formal study, I can say that RNA degradation is a huge problem in tissue. We’ve seen RNA in some tissues disappear literally within minutes after tissue harvest. This seems somewhat correlated with RNase content of the tissue, but it’s still unclear. We’ve also worked in fresh frozen human samples, all collected ostensibly the same way, and found huge variability in RNA recovery, with some samples showing great signals and other, seemingly identical samples showing no RNA whatsoever. This is true even for GAPDH. No clue whether the variability is biological or not, but I'm inclined to think it's technical. Most likely culprit is ischemic time, of which we had no control in the human samples.
We’ve also found that we’ve been able to get decent signals in formaldehyde fixed paraffin embedded samples, even though those are thought to be generally worse than fresh frozen. If I had to guess, I’d say it’s all about sample handling before freezing/fixing. I would be very hesitant to make any strong claims about gene expression without being absolutely certain about the sample quality. Problem is, I don't know what it means to be absolutely certain... :)
Anyway, so far, all we have is the sum of anecdotes, which I share here in case anyone’s interested. We really should do a more formal study of this at some point.