I am growing A. thaliana roots on agar plates and trying to extract RNA to use for gene expression analysis. Currently, I can't seem to get a concentration above about 15 ng/ul, and even then, it's not very pure. I'm using a Qiagen RNEasy Plant Mini Kit, as well as a drill with a plastic pestle attached to grind up the tiny root tissue in a micro centrifuge tube. I'm almost positive my method of breaking up the root tissue is causing the problem. I'm debating trying the common mortar and pestle method, but the arabidopsis roots are so small. Does anyone have any tips or experience on the best mechanical method to break up the tissue and maintain a good enough RNA yield to carryout PCR? Anything would be appreciated.