effects of cell confluency - (Jun/21/2010 )

When I read papers, I noticed that sometimes authors mentioned about the cell confluency. For example, they may isolated RNA for microarray experiments "when cells are about 60% confluency"; they may collect protein lysates (to check phosphorylation level) "when cells are about 80% confluency". Why cell confluency matters? Sometimes to have as much lysates as possible, I let cells grow to almost complete confluency, would that affect my results?

Thanks in advance!

confluency is a rough measure of the growth status of the cells you are using. Cultured cells, like bacteria and yeasts have a standard sigmoidal growth curve, where at low density, growth is slow (lag phase), then at medium density, growth is logarithmic, and finally at high density, growth again slows and plateaus to a steady state. At each of these stages gene expression and cell morphology may vary, which could affect how your cells behave under treatment.
How the density affects your experiments will depend on what you are looking at, but to be comparable, you should only attempt to compare samples from different cell lines that have been harvested at similar densities, so that the cells are the most similar in behaviour.