Probably, it depends on bacteria. I work with Salmonellae which are very fast-growing bacteria, and from my experience I can say that if ever you have doubts about the normality of growth, stop the experiment right away. What you risk to have at the end is an uncertainty about the actual conditions of the experiment and the validity of comparisons. Naturally, when you analyse a gene expression you try to exclude all extra factors which are likely to influence interpretation. The growth stage is one of such factors.

Hi Alexander,

Yes that was the decision I came to anyway. It is frustrating but I don't want to compromise my experiment.

Thank you for your response.

I agree with both of you (Alexander and Simone). Also, I recommend you consider plating out your stock every time you grow more bacteria for RT-PCR. I suggest you use at least two different media, preferentially differential media and _not_ Luria-Delbrück or other media used for bacteria genetic studies.You may see morphologic changes in colonies that indicate that your stock has gone bad, when otherwise you may think that you mis-measured your growth medium or made another error.

Could you tell me what is your bacteria if you do not mind?