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I have to perform an RNA extraction that should start with 900 uL of 2%SDS bacterial solution. The problem is that the sample is in 900 uL of PBS.

I thought about centrifugation of the sample at 5ºC, remove PBS and then add the 2%SDS.

DO you think bacterial RNA quantities will vary?

Thanks!

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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.

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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 medium or buffer by centrifugation is pretty easy and should just work. But if at any of your previous steps you already lysed your bacteria, this won't work because the cells aren't intact anymore.

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