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I want to extract RNA from various tissue samples, liver, gut etc, in different treatment groups. Due to the large amount of samples I will extract in sets. I am wondering, in reducing the potential for contamination whether it will be better to extract by tissue type or by treatment?

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What you do not want to do is prep all your control samples on one day, and all your treated samples on another day, because you will not be able to separate differences caused by treatment from differences caused by batch effect. I'd worry more about that than from cross contamination. Since you probably aren't comparing the different tissues to each other, batch effect between tissues won't be much of a problem. So do all your spleen samples, treated and untreated, on one day, all your kidney samples the next, etc.

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