Housekeeping gene - acceptable variation?

[marcin]

We are trying to compare expression levels of certain genes among four types of tissue. We currently are looking for a good houskeeping gene for this experiment. We found out that actin expression differs a lot in one of the tissue, whereas is quite constant in others. So we tried 28S. The same tissue also shows lower level of 28S expression. The difference of Ct is just 1 cycle - is that acceptable?

[moe]

Hi
To my knowledge, all housekeeping genes including 18s and 28s vary (i don't think you will get constant expression).
As long as you normalise your gene of interest with your housekeeping gene from the same tissue and interpret with normalised ratio, that's fine.
But check with your PI first.
Hope this helps.
moe

[rashmi singh]

Hi moe
Does this mean that despite there is variation in the expression levels of endogenous controls in two different groups, one can normalize with that housekeeping gene within that group and then compare the two groups?

[moe]

Hi Rashmi,

Yes I think so.
(btw) I am talking about RT-PCR (real time or semi-quantitative). It's very hard to get exactly same expression level.
But if you are doing western/northern blotting, your house keeping gene level should be same (in your photo).
End of the day, if your PI or your reviewer agrees with you, that's fine.