Genotype specific phenotypic behaviour of auxotrophic and prototrophic gene deletion collections

To systematically characterize the phenotypic behavior of two 'prototrophic' version of the Yeast Knockout (YKO) gene deletion collection, we compared genome-wide finess assays across a diverse set of drug and environmental conditions. This analysis uncovered experimental liabilities in the the prototrophic collections distinct from the YKO auxotrophies that shows that auxotrophic repair (regardless of methodology) does not restore wildtype behaviour. We compared the YKO auxotrophic deletion collection to 2 prototrophic collections in 15 media conditions and 4 drug conditions, in triplicate, resulting in 236 total Affymetrix Chips, as well as 37 Bar-seq samples for comparison to the microarray data. We compared both the deletion strain content of these collections as well as their quantitative fitness profiles.