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I think it is relatively unlikely that the RNA will degrade under this conditions. For the future, I would handle this differently: You can centrifuge the cells and snap freeze them in an appropriate buffer in liquid nitrogen and then store them at -80°C. I would not freeze the dry pellet, as these are often hard to re-dissolve after freezing. ...


PBS is isotonic to most cells, so in this buffer your bacterial cells are intact. Centrifuging them to remove PBS won't harm them it is quite standard procedure. You have to be careful after adding 2% SDS because it will lyse your cells and then the RNA contained within them will become "free" and RNAs are fragile molecules.


I'm assuming that you have a solution of bacteria in your buffer directly after growing them for some time, and without performing a lysis step yet. The 2% SDS step looks like it is for lysis of your cells. In that case, centrifuging the bacteria and resuspending them in lysis buffer is a very common step in many protocols. Separating whole bacteria from ...

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