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Will RNAlater solution denature the proteins in the cell pellets?

Yes. RNAlater® Solution denatures proteins. 
As a result, proteins isolated from PromoCell cell pellets stored in RNAlater are suitable for applications, such as
  • Western blotting
  • 2‑D gel electrophoresis
and  not suitable for applications requiring native (functional) protein conformation, such as enzyme activity assays or protein–protein interaction studies.

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