You always have to test different housekeeper candidates for your experimental settings before you start your qPCR analysis. We use normally 5 different candidates and test with geNORM, which is the best candidate. 18S is not a good candidate as the stability of a rRNA is different from a mRNA. ACTB, GAPDH, HPRT1, B2M; GNB2L, RPL23, RPL 27 etc are good housekeepers.

Hi, this page will help you a lot: http://normalisation.gene-quantification.info/

Cheers, Nadine

By Q-PCR, what do you mean?  Are you trying to measure expression of particular genes or are you trying to assess copies of a particular gDNA.

Assuming you want to measure gene expression, there is no one size fits all reference target and generally you need at least 5 for meaningful results.

Since Q-PCR can only compare levels of expression of the pancreatic cells in state A to state B, unless your experimental conditions exactly match state A and state B, you can't just assume a reference target is valid because the literature says so.

You need to pick a number of targets and actually measure expression levels to see if they are relatively invariant.

As a side note, Dr Pierre Thibault from  Université de Montréal has a working system to measure the phosphorylation state of all the proteins in a given cell line simultaneously and in real time, which is another way to ask and answer the questions you may have.

GAPDH or beta-Actin

Which is your model organism? Human? and how do you synthesize your cDNA? using oligo dT or random hexamers?

If you're going to be rigorous about it, take a panel of 8 (or more) candidates, and determine the best two or three reference genes empirically., via geNorm, Normfinder or bestkeeper.

For instance, GAPDH and beta-actin turn out to be absolutely TERRIBLE for normalising differentiating muscle cells, but in mature muscle tissue, GAPDH is pretty good.

It's definitely worth investing the time and money to get it right before you analyse your sample data.

We use GAPDH, Beta Actin, 18S rRNA and HPRT as standards. You need at least 3 standards (preferably 4-5) for QPCR. These are well established in the literature

the control gene to be analyzed for Q-PCR may be species, tissue, cell-type specific. That is why people use 2-3 genes for normalization for Q-PCR.

Any gene you choose, you have to test it whith your own specie, tissue and experimental conditions.

Dear Friends,

My sample is "pancreatic tissue" from "Human" and I want to analyse the expression of some pancreatic tissue specific genes only. So what should be the best pancreatic tissue specific control gene should i use for Q-PCR validation?

18S rRNA is a good candidate.

You can use GAPDH, 18s or TBP and other...

http://www.plosone.org/article/fetchObject.action?uri=info:doi/10.1371/journal.pone.0059180&representation=PDF

I am using Beta actin for my work. ACTB, GAPDH, HPRT1, and B2M- these are the  housekeeping (HK gene) which are used generally and  RPS13, RPL27, RPS20 and OAZ1 were found to be a novel house keeping genes in 2007. So better refer the article "Evidence Based Selection of Housekeeping Genes" published in PLos one and select which is more suitable for your work. 

You always have to test different housekeeper candidates for your experimental settings before you start your qPCR analysis. We use normally 5 different candidates and test with geNORM, which is the best candidate. 18S is not a good candidate as the stability of a rRNA is different from a mRNA. ACTB, GAPDH, HPRT1, B2M; GNB2L, RPL23, RPL 27 etc are good housekeepers.

As others have said you have to fiddle around and find which control works best with your specific experiment. For the work I do it's looking at levels of human protein in mouse cells so I tend to use either human 18s or human GAPDH as my housekeeping controls. I find my results are better with 18s, but it could be different for yours.

Hi,

I see many good candidates in the answers you have already. Nevertheless, I tell you my favorite one: RPL32. It is very stable in almost any condition I have tryed (both in mammalian cells and tissues).

Good luck!

It's depend, for expression studies: if your gene of interest has high expression GAPDH is OK, however if the gene of interest has low expression and PBMCs are the target B2 microglobulin looks better. for very low expression like transcription factors please have a look in literature and find something fit with your work. please note it is not reliable for a gene with low expression to use something like Beta actin or GAPDH. 

Highly-expressed “housekeeping” markers such as beta-actin (ActB), GAPDH or 18S ribosomal RNA are widely employed, with the assumption that these markers remain constant for any given mRNA population within an experiment.

For getting further interesting informations you can follow the link below:-

http://currents.plos.org/md/article/identification-and-validation-of-quantitative-pcr-reference-genes-suitable-for-normalizing-expression-in-normal-and-dystrophic-cell-culture-models-of-myogenesis/

For lymphocyte and low expression genes Beta 2- macroglobulin.