Fig. 1

Development and optimization of the pipeline for genome-wide screening for light-sensitive mutants. a The spectrum of the UV-filtered fluorescent lamp, Osram L 940 with the warm white color code 830, in comparison to the spectrum of a normal fluorescent lamp in the lab. Inset shows an enlargement of the 350–450 nm range. Note that the peak in the UV range at ~ 360 nm in the normal lamp is absent for the UV filtered Osram L 940. b Experimental design of the set-up for the genome-wide screen of the light sensitivity of the deletion mutants. The agar plates are placed on wooden sticks to maximize air-flow and cooling. The lamp could be adjusted to various heights to optimize the scoring of light sensitivity. c Both light intensity and the initial cell density affect the light sensitivity of yeast strains, seen on wild type and yap1∆ mutant strains. d Schematic drawing that exemplifies the methodological challenge, with all strains being light sensitive at lower initial cell densities, and none at high initial cell densities. In between, there is an analytical window which is to be used for scoring light-sensitive mutants. e Images show the contrast in growth between the wild type and the positive control yap1∆ using the same procedure and format (384 colonies/plate) as in the genome-wide screening experiments. f Example of the variation in cell density at day 0 directly after pinning. g Image analysis procedure for the estimation of light sensitivity of the deletion mutants. Illustration of how the cell density was estimated by measuring the intensity over each colony in the image. Both a background intensity value and a colony intensity value were extracted and the difference in intensity was taken as the cell density estimate (CDE). h Experimental distribution of the 1064 control strains present at 76 copies per plate. An asymmetrical distribution of the control cells is clearly apparent, with colonies with a CDE at day 0 ≥ 121 (dotted line) showing 100% growth response during light exposure (day 6 data). At a CDE day 0 < 121, the light sensitivities of the control strains are clearly much more variable. High confidence set (light shaded box) and moderate confidence set (dark shaded box) are indicated (scoring criterium I). i The light sensitivity distribution of the mutants. High confidence set (light shaded box) and moderate confidence set (dark shaded box). j Schematic growth curves of light-sensitive and not light-sensitive mutants according to the scoring procedure used taking both slow growth in light as well as in the dark into account (scoring criterium II)