what is the best way to express the western blot data. mostly it is expressed as relative to sample control, but i also found some papers where the data was expressed as Realtive to beta actin. i personally want to express it as relative to beta actin. what would be the best way to do so?
It (protein of interest) should be normalized to a loading contol (i.e. beta-actin). But make sure that beta-actin is stably expressed in all groups where it is used as a loading control (by looking at raw signal). Total protein expression is also another robust method.
Yes, you can use Beta-Actin or GAPDH or any other housekeeping gene but, if you are working with a nuclear protein, you should use Lamin B or any other house keeping gene specific for nucleus. Sometimes, the condition of your research plan may affect GAPDH expression. In this condition, you must use beta-Actin. The bone of contention is that the expression of this control must be almost the same for all your samples irrespective of the changes expressed in the text groups. Once your choice of control is not fulfilling this purpose, you are not using the right housekeeping gene. I hope this helps.
I would suggest at first to normalize all samples according to beta-actin, and then if you wish you may normalize to the sample control.
Do both. First normalise the intensity of each band to that of housekeeping protei, then you can express your results as a fraction of the control sample.
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