I would appreciate any comments as to which loading control is generally used for cytoplasmic lysates: alpha actin or beta actin. What are the reasons for why you prefer the one over the other?
The most common used loading control proteins are beta-actin and GAPDH. The first because is the stable actin form. You will find many other loading control cyto proteins but be careful that they will not change in expression in your model.
For all my Westerns I use GAPDH as internal standard. In normal cases (short term treatments) it does not vary that much. In case of conflicting with the molecular weight of your target you can switch to b-actin. Both are well established and both are easy to do.
Without knowing your platform, I would say neither. Actin is a notoriously poor loading control for many tissues and cell types. See PMID: 16688701. Structural proteins in general are a bad choice due to age or treatment-dependent alterations in cellular architecture. The propensity for actin to saturate can be easily observed when performing densitometric analyses of blots as it does not follow target protein expression in a linear fashion.
Why not use a total protein dye or find a platform-specific loading control instead of assuming actin works because others do it?
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