Heparin is water soluble and will be in the serum layer, plus without information on RNA isolation kit. nothing can be concluded properly. how many cells, are you using heparin (negatively charged) to precipitate RNA (negatively charged), glycogen is better alternative (neutral). did you ran the RNA on a formaldhehhyde agarose to see 18S and 8S RNA bands. again without more details it is difficult to provide proper answer