Functional genomic screens can be divided into arrayed and pooled formats. In arrayed screens, each gene is perturbed in an individual well containing one or more cells. In contrast, in pooled screens, sets of genes are perturbed individually in a population of cells that is propagated in large culture flasks or dishes.

Many assay types are compatible with both screening formats. For example, screens based on changes in cell fitness (proliferation and/or cell death) or for changes in the per cell level of a fluorescent reporter can be performed in both screening formats. However, subcellular phenotypes and cell-cell interactions based on paracrine signaling have been mostly restricted to the arrayed screening format. That said, recent advances in the development of optical screening technologies that make use of, for example, photo-activable reporters, will also enable screening of such phenotypes in the pooled format. In addition, there are many factors that influence the choice of screening format such as the availability of tools such as liquid handling robotics and high-throughput, high-content imaging microscopes, as well as assay performance and cost.