Genome-wide chemogenomic screen

The S. cerevisiae MATa yeast DMA (Winzeler et al. 1999), with approximately 4200 strains, was arrayed in duplicate on YPD agar (condensed to 1536 colonies per plate) supplemented with G418 using a Singer RoTor HDA. Using these condensed plates, colonies were pinned onto triplicate YP and YPM agar plates and incubated at 30°. The number of days for incubation depended on when each condensed plate had the lowest difference in average colony size between media, leading to a range of 2–4 days. Images were taken using the Bio-Rad Chemidoc™ XRS system under EPI-white light illumination and growth was assessed using SGAtools (Wagih et al. 2013). Colonies were aligned to gene names using R Suite. Average growth scores on each medium were assessed by comparing strain growth on YPM to YP, and calculated ratios for every strain were ranked on whether they demonstrated increased growth on mucin (i.e., positive impact and larger colonies) or decreased growth on mucin (i.e., negative impact and smaller colonies). Ratios were obtained through two different approaches: (1) by comparing average colony sizes of each strain from YPM to YP, and (2) by comparing each individual pinned colony of each strain from YPM to YP. By combining the top 30 strains from the positive impact group and negative impact group through each approach, these hits were confirmed by conducting dot assays on YP and YPM. Strains were subsequently categorized into two groups: (1) YPM > YP and (2) YPM < YP.