Why do you use trizol and chloroform extraction? I suggest you try to instantly freeze the tissues in liquid nitrogen post harvesting, then do RNA purification with RNeasy kit. Liquid nitrogen stops RNA disgestion by RNases, it worked for me with colon sections, in which no rRNA bands were seen by direct purification of samples.

Thanks for your suggestion Ido. We received this protocol from another lab from a person who is working with pig sceletal muscle. And for her it works this way.

Try to run your samples on simple agarose gel, to exclude a problem in your TAPE station.

Thanks Ido, we did that already - same result :-(. Is it possible to isolate only the 18S RNA and no 28S RNA?

When you have RNA degradation, the first peak that starts to disappear is that of 28S. Post your gel image if you have it, denaturation can be visulaized by multiple (possibly faded) bands.