Whole-cell pipettes with positive pressure are attached on cell membrane, through which you can remove cell debris from cell surface without pipette contamination. Since your control pipettes were contaminated by the suction of pipettes in tissues, this way is not a good control.  By the way, please read my papers to find answers from there.

Dear Elizabeth,

I suggest you also look at the controls in the publications from James Eberwine's lab at U Penn, or Diane O'Dowd at UC Irvine.  I do not have access to PubMed at the moment, so I can't get you the PDFs. 

Unfortunately, I have only tried this in vitro, so it is much cleaner and easier to patch the neurons.

Good Luck!

Jill 

 Dear Elizabeth,

It may be that it is difficult have negative controls with sucking the extracellular fluid that is probably full of various RNA molecules due to tissue damage and leakage in to the extracellular fluid/matrix during slicing and electrode penetration. Given the sensitivity of amplification process, even a few copies will give you positive results. Therefore it may be better to suck into your electrode just the bath solution, without going into the tissue. Another option will be to do PCR of dissociated cells. We have in the past succesfully performed single cell RT-PCR for TRPC channels in isolated/dissociated  hair cells from the cochlea. For details please see the following publication.

Best wishes, Refik

Article TRPC-like conductance mediates restoration of intracellular ...