We found a very low expression of β-Actin gene in HeLa cells in one cell culture relative to the expression of GFP despite it being a housekeeping gene and is expected to have a high espression.
Can you explain what you mean by low expression, and how you determined it? By qPCR, western blot, etc? qPCR could be explained by bad B-actin primers, (poor efficiency), western blot could be explained by a bad antibody / poor western techniques. Etc. More info would help us to troubleshoot your observations.
By qPCR, but is there anything that has to do with the cell culture nature?
If I were you, I'd check the qPCR protocol first, esp. for primer specificity as Craig pointed out. If You had already done that and no problem was found, then you can question your culture conditions. Keep in mind that the gene being housekeeping gene doesn't mean it is highly expressed , it means its expression is almost the same across tissues (i.e: not tissue specific). So, simply the other gene (GFP) could be over-expressed.
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