I am doing colony formation assay using methlycellulose media on RPMI8226 and U266 cells. In the treated samples, number of colonies is reduced compared to the control samples but size of the colonies is increased. Any explanation for this?
Not necessarily- the number of colonies is a more pertinent measure. the size of the colonies could simply be a feature of doubling time or favorable growth conditions. It is possible that all or some of the cells within a colony are resistant but you cannot conclude this from this assay. You would need to pick and reseed the colonies in the presence of the drug.
As Dr, Marie Boyd suggested, there is a great problem whether or not drug resistant phenotype is homogeneously or heterogeneously recognized. Furthermore, you have to keep in mind that in the experiment of colony-formation assay and related experiments, colony size and its numbers should be distinguished and they do not necessarily show the consistent increase/decreased change. In the case of your experiments, the colony of U266 cells is composed of heterogeneous cellular population between central and peripheral region. In addition, the tendency to entry into G0 dormant status in the hypoxic microenvironment as compared with its periphery should be evaluated in terms of cell-cycle analysis of U266 cells in each colony.