c Agar, a seaweed extract, has been the standard support matrix for microbial experiments for over a century. Recent developments in high-throughput genetic screens have created a need to reevaluate the suitability of agar for use as colony support, as modern robotic printing systems now routinely spot thousands of colonies within the area of a single microtiter plate. Identifying optimal biophysical, biochemical, and biological properties of the gel support matrix in these extreme experimental conditions is instrumental to achieving the best possible reproducibility and sensitivity. Here we systematically evaluate a range of gelling agents by using the yeast Saccharomyces cerevisiae as a model microbe. We find that carrageenan and Phytagel have superior optical clarity and reduced autofluorescence, crucial for high-resolution imaging and fluorescent reporter screens. Nutrient choice and use of refined Noble agar or pure agarose reduce the effective dose of numerous selective drugs by >50%, potentially enabling large cost savings in genetic screens. Using thousands of mutant yeast strains to compare colony growth between substrates, we found no evidence of significant growth or nutrient biases between gel substrates, indicating that researchers could freely pick and choose the optimal gel for their respective application and experimental condition. Single-cell organisms such as bacteria and yeasts have been used extensively to study genes and genome organization, proteins and protein interactions, biological pathways, and cellular structure and to address numerous other fundamental biological questions (1, 2). Many microbes, especially the species Escherichia coli and Saccharomyces cerevisiae, combine numerous beneficial properties that make them ideal model organisms: easy laboratory cultivation, easy genetic manipulation, short generation time, and safe handling. Microbial cultures can be maintained in liquid growth medium or on solid/semisolid gel substrates (3). Liquid colony maintenance allows the microbial cultures to expand rapidly and is used in screens that rely on optical density measurements to extract kinetic growth parameters or use downstream liquid-based assays such as flow cytometry or high-throughput microscopy (4-7). While throughput in liquid is generally bound to a maximum of 96 or 384 samples per plate, solid-substrate colony maintenance has the advantage that individual cell clones can be readily separated and that colony parameters such as color, shape, structure, and size can be extracted easily using digital image acquisition (8-10). Additionally, advances in robotic pinning devices allow for much higher throughput on solid substrate, with close to 25,000 colonies possible on a single microtiter footprintsized gel plate (11). This much higher density has led to solidsubstrate screening being the method of choice for many current high-throughput applications (12)(13)(14).Historically, agar has been the predominant gelling agent in microbial research. Agar is a mixture of polysaccharides f...

We have developed a highly parallel strategy, systematic gene-to-phenotype arrays (SGPAs), to comprehensively map the genetic landscape driving molecular phenotypes of interest. By this approach, a complete yeast genetic mutant array is crossed with fluorescent reporters and imaged on membranes at high density and contrast. Importantly, SGPA enables quantification of phenotypes that are not readily detectable in ordinary genetic analysis of cell fitness. We benchmark SGPA by examining two fundamental biological phenotypes: first, we explore glucose repression, in which SGPA identifies a requirement for the Mediator complex and a role for the CDK8/kinase module in regulating transcription. Second, we examine selective protein quality control, in which SGPA identifies most known quality control factors along with U tRNA modification, which acts independently of proteasomal degradation to limit misfolded protein production. Integration of SGPA with other fluorescent readouts will enable genetic dissection of a wide range of biological pathways and conditions.