I am isolating synaptoneurosomes and the next step is to check for the quantity of some target RNA; however, 1st i need to show that synapton have more relative quantity of some RNA when compared with the homogenated. For instance, mRNA for PSD95 should be more present when compared with the homogenated preparation.
But, is happening the opposite. The difference is not that much, but still i have more expression of PSD95 in homogenated than in synaptoneurosomes. I have done tha same for protein and did go very well.
I am just guessing that the proportion of RNA in such a small structure when compared with the whole cell is obscuring my results.
Does anyone have a clue?