In  order to make a good standarization,  one should have the same number of bacteria from different conditions tested to examine the expression of the reference genes?  is there any other way I might not taking notice of?

I'm thinking about to do a direct counting with a Petroff Hausser chamber , and when the bacteria reach the mid log phase  do dilutions to have the same number in both conditions, extract RNA , convert to cDNA and carry the qPCR.

I would like to know some recommendations to do this task  and to appeal to your experience. 

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