Data package for "Widespread Genetic Incompatibilities Between First-Step Mutations During Parallel Adaptation of Saccharomyces cerevisiae to a Common Environment" Jasmine Ono, Aleeza C. Gerstein and Sarah P. Otto in PLOS Biology (2016) --------------------- General Notes: --------------------- ######### Nystatin Beneficial Mutation (NBM) ######### Unpublished strain numbers from the original experiment (NBM) are used throughout the data files and R scripts. The translation of these strain numbers into those from the original paper (Gerstein et al. (2012) - BMN) and the corresponding ERG gene mutation are as follows: NBM8 = BMN9 = erg6 NBM12 = BMN1 = erg7 NBM45 = BMN32 = erg3 NBM58 = BMN35 = erg5 ######### Throughout, OD is used in place of “optical density”. ######### ######### Contrast Translation ######### Whenever performing pairwise comparisons, the data files (“XContrasts.csv”) will contain codes like “w,w,w,w - m,w,w,w”, where the two sets refer to wildtype (“w”), mutant (“m”) or heterozygous (“t”) at each of the four genes (erg6, erg7, erg3, erg5), in that order. So, for example: “w,m,w,w - w,m,w,m” in Nys2HapsContrasts.csv compares haploids that are erg7 mutants versus erg7 erg5 double mutants. “w,t,m,w - w,m,m,w” in Nys2DipsTContrasts.csv compares diploids that are erg7/+ erg3/erg3 versus erg7/erg7 erg3/erg3 double mutants. --------------------- Files: --------------------- The following files are included in the Dryad package. The data needed for each script is specified in the script file (read.csv() commands will automatically read in the correct data if the working directory is set to this folder). ######### “DSC2” - Folder containing analyses of the effect of the mutation in DSC2 on the interpretation of the growth rate assays. ######### * “data_output” - Folder containing data files created by the R script looking at the effect of the mutation in DSC2. - Nys2DSC2Contrasts.csv - Data file that contains the statistics calculated for each desired pairwise comparison of maximum growth rates between haploid strains in nystatin2 when including the allele status at DSC2. Created by DSC2effect.R. (See “Contrast Translation” above.) - Nys2DSC2Means.csv - Data file that contains fitted least-squares means of maximum growth rates and their 95% confidence intervals for all haploid strains in nystatin2 when including the allele status at DSC2. Created by DSC2effect.R. - Nys2NoDSC2Contrasts.csv - Data file that contains the statistics calculated for each desired pairwise comparison of maximum growth rates between haploid strains in nystatin2 when excluding strains containing mutations in DSC2. Created by DSC2effect.R. - Nys2NoDSC2Means.csv - Data file that contains fitted least-squares means of maximum growth rates and their 95% confidence intervals for all haploid strains in nystatin2 when excluding strains containing mutations in DSC2. Created by DSC2effect.R. - YPDDSC2Contrasts.csv - Data file that contains the statistics calculated for each desired pairwise comparison of maximum growth rates between haploid strains in YPD when including the allele status at DSC2. Created by DSC2effect.R. - YPDDSC2Means.csv - Data file that contains fitted least-squares means of maximum growth rates and their 95% confidence intervals for all haploid strains in YPD when including the allele status at DSC2. Created by DSC2effect.R. - YPDNoDSC2Contrasts.csv - Data file that contains the statistics calculated for each desired pairwise comparison of maximum growth rates between haploid strains in YPD when excluding strains containing mutations in DSC2. Created by DSC2effect.R. - YPDNoDSC2Means.csv - Data file that contains fitted least-squares means of maximum growth rates and their 95% confidence intervals for all haploid strains in YPD when excluding strains containing mutations in DSC2. Created by DSC2effect.R. * DSC2effect.R - R script used to run t-tests between strains with and without the mutation in DSC2, run mixed-effects models and subsequent pairwise comparisons, and plot the results. Creates Nys2DSC2Means.csv, Nys2DSC2Contrasts.csv, YPDDSC2Means.csv, YPDDSC2Contrasts.csv, Nys2NoDSC2Means.csv, Nys2NoDSC2Contrasts.csv, YPDNoDSC2Means.csv, YPDNoDSC2Contrasts.csv, HapGRPlotDSC2.pdf, and HapGRPlotNoDSC2.pdf. * “plots” - Folder where plots will be created if DSC2effect.R is run. - HapGRPlotDSC2.pdf - Plot similar to Fig 3 that separates strains with different alleles at DSC2. Created by DSC2effect.R. - HapGRPlotNoDSC2.pdf - Plot similar to Fig 3 that excludes strains containing mutations in DSC2. Created by DSC2effect.R. ######### “Figures” - Folder where figures will be created if scripts are run. ######### * DipGRPlot.Fig4.pdf - Fig 4. Created by TablePlot.R. * DipGRPlot.OutIn.S7Fig.pdf - S7 Fig. Created by TablePlot.OutIn.R. * DipMTolPlot.S3Fig.pdf - S3 Fig. Created by TolerancePlot.R. * DipODPlot.S2Fig.pdf - S2 Fig. Created by TablePlot.OD.R. * DipTTolPlot.S5Fig.pdf - S5 Fig. Created by TolerancePlot.R. * HapGRPlot.Fig3.pdf - Fig 3. Created by TablePlot.R. * HapGRPlot.OutIn.S6Fig.pdf - S6 Fig. Created by TablePlot.OutIn.R. * HapODPlot.S1Fig.pdf - S1 Fig. Created by TablePlot.OD.R. * HapTolPlot.Fig5.pdf - Fig 5. Created by TolerancePlot.R. * Heatmap35.S4Fig.pdf - Subplot of combination erg3 - erg5 for S4 Fig. Created by DipHeatmaps.R. * Heatmap36.S4Fig.pdf - Subplot of combination erg3 - erg6 for S4 Fig. Created by DipHeatmaps.R. * Heatmap37.S4Fig.pdf - Subplot of combination erg3 - erg7 for S4 Fig. Created by DipHeatmaps.R. * Heatmap56.S4Fig.pdf - Subplot of combination erg5 - erg6 for S4 Fig. Created by DipHeatmaps.R. * Heatmap57.S4Fig.pdf - Subplot of combination erg5 - erg7 for S4 Fig. Created by DipHeatmaps.R. * Heatmap67.S4Fig.pdf - Subplot of combination erg6 - erg7 for S4 Fig. Created by DipHeatmaps.R. * HeatmapLegend.S4Fig.pdf - Legend for S4 Fig. Created by DipHeatmaps.R. * SterolPlot.Fig6.pdf - Fig 6. Created by SterolPlot.R. ######### “GR.ExcludeOne” - Folder containing analyses of the growth rate assays when outliers are included in the analysis except for one outlier for erg3 in nystatin2. ######### * HapNys2GRPlot.ExclOne.pdf - Plot similar to Fig 3 for analysis of haploid strains in nystatin2 when including all outliers except for one outlier for erg3. Created by TablePlot.ExclOne.R. * LM_Nys2.ExclOne.R - R script used to run the mixed-effects model, and subsequent pairwise comparisons, on the haploid strains in nystatin2 when including all outliers except for one outlier for erg3. Creates Nys2HapsMeans.ExclOne.csv and Nys2HapsContrasts.ExclOne.csv. * Nys2HapsContrasts.ExclOne.csv - Data file that contains the statistics calculated for each desired pairwise comparison of maximum growth rates between haploid strains in nystatin2 when including all outliers except for one outlier for erg3. Created by LM_Nys2.ExclOne.R. * Nys2HapsMeans.ExclOne.csv - Data file that contains fitted least-squares means of maximum growth rates and their 95% confidence intervals for all haploid strains in nystatin2 when including all outliers except for one outlier for erg3. Created by LM_Nys2.ExclOne.R. * TablePlot.ExclOne.R - R script used to create plot similar to Fig 3 for analysis of haploid strains in nystatin2 when including all outliers except for one outlier for erg3. Creates HapNys2GRPlot.ExclOne.pdf. ######### “GR.OpticalDensity” - Folder containing analyses of the OD after 24 hours where data comes from the growth rate assays. ######### * “data_output” - Folder containing data files created by the R scripts analyzing the OD data. - Nys2DipsMContrasts.OD.csv - Data file that contains the statistics calculated for each desired pairwise comparison of log(OD) between homozygous diploid strains in nystatin2. Created by LM_DipNys2.OD.R. - Nys2DipsMMeans.OD.csv - Data file that contains fitted least-squares means of log(OD) and their 95% confidence intervals for all homozygous diploid strains in nystatin2. Created by LM_DipNys2.OD.R. - Nys2DipsTContrasts.OD.csv - Data file that contains the statistics calculated for each desired pairwise comparison of log(OD) between diploid strains in nystatin2. Created by LM_DipNys2.OD.R. - Nys2DipsTMeans.OD.csv - Data file that contains fitted least-squares means of log(OD) and their 95% confidence intervals for all diploid strains in nystatin2. Created by LM_DipNys2.OD.R. - Nys2HapsContrasts.OD.csv - Data file that contains the statistics calculated for each desired pairwise comparison of log(OD) between haploid strains in nystatin2. Created by LM_HapNys2.OD.R. - Nys2HapsMeans.OD.csv - Data file that contains fitted least-squares means of log(OD) and their 95% confidence intervals for all haploid strains in nystatin2. Created by LM_HapNys2.OD.R. - YPDDipsMContrasts.OD.csv - Data file that contains the statistics calculated for each desired pairwise comparison of log(OD) between homozygous diploid strains in YPD. Created by LM_DipYPD.OD.R. - YPDDipsMMeans.OD.csv - Data file that contains fitted least-squares means of log(OD) and their 95% confidence intervals for all homozygous diploid strains in YPD. Created by LM_DipYPD.OD.R. - YPDDipsTContrasts.OD.csv - Data file that contains the statistics calculated for each desired pairwise comparison of log(OD) between diploid strains in YPD. Created by LM_DipYPD.OD.R. - YPDDipsTMeans.OD.csv - Data file that contains fitted least-squares means of log(OD) and their 95% confidence intervals for all diploid strains in YPD. Created by LM_DipYPD.OD.R. - YPDHapsContrasts.OD.csv - Data file that contains the statistics calculated for each desired pairwise comparison of log(OD) between haploid strains in YPD. Created by LM_HapYPD.OD.R. - YPDHapsMeans.OD.csv - Data file that contains fitted least-squares means of log(OD) and their 95% confidence intervals for all haploid strains in YPD. Created by LM_HapYPD.OD.R. * LM_DipNys2.OD.R - R script used to run mixed-effects models, and subsequent pairwise comparisons, on the OD data for diploid strains in nystatin2. Creates Nys2DipsMMeans.OD.csv, Nys2DipsMContrasts.OD.csv, Nys2DipsTMeans.OD.csv, and Nys2DipsTContrasts.OD.csv. * LM_DipYPD.OD.R - R script used to run mixed-effects models, and subsequent pairwise comparisons, on the OD data for diploid strains in YPD. Creates YPDDipsMMeans.OD.csv, YPDDipsMContrasts.OD.csv, YPDDipsTMeans.OD.csv, and YPDDipsTContrasts.OD.csv. * LM_HapNys2.OD.R - R script used to run the mixed-effects models, and subsequent pairwise comparisons, on the OD data for haploid strains in nystatin2. Creates Nys2HapsMeans.OD.csv and Nys2HapsContrasts.OD.csv. * LM_HapYPD.OD.R - R script used to run the mixed-effects models, and subsequent pairwise comparisons, on the OD data for haploid strains in YPD. Creates YPDHapsMeans.OD.csv and YPDHapsContrasts.OD.csv. * TablePlot.OD.R - R script used to create S1 Fig and S2 Fig. Creates HapODPlot.S1Fig.pdf and DipODPlot.S2Fig.pdf. ######### “GR.OutliersIncluded” - Folder containing analyses of the growth rate assays when outliers are included in the analysis. ######### * “data_output” - Folder containing data files created by the R scripts when including all outliers. - Nys2DipsMContrasts.OutIn.csv - Data file that contains the statistics calculated for each desired pairwise comparison of maximum growth rates between homozygous diploid strains in nystatin2 when including all outliers. Created by LM_DipNys2.OutIn.R. - Nys2DipsMMeans.OutIn.csv - Data file that contains fitted least-squares means of maximum growth rates and their 95% confidence intervals for all homozygous diploid strains in nystatin2 when including all outliers. Created by LM_DipNys2.OutIn.R. - Nys2DipsTContrasts.OutIn.csv - Data file that contains the statistics calculated for each desired pairwise comparison of maximum growth rates between diploid strains in nystatin2 when including all outliers. Created by LM_DipNys2.OutIn.R. - Nys2DipsTMeans.OutIn.csv - Data file that contains fitted least-squares means of maximum growth rates and their 95% confidence intervals for all diploid strains in nystatin2 when including all outliers. Created by LM_DipNys2.OutIn.R. - Nys2HapsContrasts.OutIn.csv - Data file that contains the statistics calculated for each desired pairwise comparison of maximum growth rates between haploid strains in nystatin2 when including all outliers. Created by LM_HapNys2.OutIn.R. - Nys2HapsMeans.OutIn.csv - Data file that contains fitted least-squares means of maximum growth rates and their 95% confidence intervals for all haploid strains in nystatin2 when including all outliers. Created by LM_HapNys2.OutIn.R. - YPDDipsMContrasts.OutIn.csv - Data file that contains the statistics calculated for each desired pairwise comparison of maximum growth rates between homozygous diploid strains in YPD when including all outliers. Created by LM_DipYPD.OutIn.R. - YPDDipsMMeans.OutIn.csv - Data file that contains fitted least-squares means of maximum growth rates and their 95% confidence intervals for all homozygous diploid strains in YPD when including all outliers. Created by LM_DipYPD.OutIn.R. - YPDDipsTContrasts.OutIn.csv - Data file that contains the statistics calculated for each desired pairwise comparison of maximum growth rates between diploid strains in YPD when including all outliers. Created by LM_DipYPD.OutIn.R. - YPDDipsTMeans.OutIn.csv - Data file that contains fitted least-squares means of maximum growth rates and their 95% confidence intervals for all diploid strains in YPD when including all outliers. Created by LM_DipYPD.OutIn.R. - YPDHapsContrasts.OutIn.csv - Data file that contains the statistics calculated for each desired pairwise comparison of maximum growth rates between haploid strains in YPD when including all outliers. Created by LM_HapYPD.OutIn.R. - YPDHapsMeans.OutIn.csv - Data file that contains fitted least-squares means of maximum growth rates and their 95% confidence intervals for all haploid strains in YPD when including all outliers. Created by LM_HapYPD.OutIn.R. * LM_DipNys2.OutIn.R - R script used to run mixed-effects models, and subsequent pairwise comparisons, on the diploid strains in nystatin2 when including all outliers. Creates Nys2DipsMMeans.OutIn.csv, Nys2DipsMContrasts.OutIn.csv, Nys2DipsTMeans.OutIn.csv, and Nys2DipsTContrasts.OutIn.csv. * LM_DipYPD.OutIn.R - R script used to run mixed-effects models, and subsequent pairwise comparisons, on the diploid strains in YPD when including all outliers. Creates YPDDipsMMeans.OutIn.csv, YPDDipsMContrasts.OutIn.csv, YPDDipsTMeans.OutIn.csv, and YPDDipsTContrasts.OutIn.csv. * LM_HapNys2.OutIn.R - R script used to run the mixed-effects models, and subsequent pairwise comparisons, on the haploid strains in nystatin2 when including all outliers. Creates Nys2HapsMeans.OutIn.csv and Nys2HapsContrasts.OutIn.csv. * LM_HapYPD.OutIn.R - R script used to run the mixed-effects models, and subsequent pairwise comparisons, on the haploid strains in YPD when including all outliers. Creates YPDHapsMeans.OutIn.csv and YPDHapsContrasts.OutIn.csv. * TablePlot.OutIn.R - R script used to create S6 Fig and S7 Fig. Creates HapGRPlot.OutIn.S6Fig.pdf and DipGRPlot.OutIn.S7Fig.pdf. ######### “GrowthRateAssays” - Folder containing analyses of the growth rate assays. ######### * “data” - Folder containing raw data files and maps. - Assay1_wells.csv - Raw wells file needed to map the raw data to specific lines and media from Assay 1. - Assay1Pl1.csv - Raw OD data measured by the Bioscreen C for the lines measured in Plate 1 of Assay 1. - Assay1Pl2.csv - Raw OD data measured by the Bioscreen C for the lines measured in Plate 2 of Assay 1. - Assay2_wells.csv - Raw wells file needed to map the raw data to specific lines and media from Assay 2. - Assay2Pl1.csv - Raw OD data measured by the Bioscreen C for the lines measured in Plate 1 of Assay 2. - Assay2Pl2.csv - Raw OD data measured by the Bioscreen C for the lines measured in Plate 2 of Assay 2. - Assay3_wells.csv - Raw wells file needed to map the raw data to specific lines and media from Assay 3. - Assay3Pl1.csv - Raw OD data measured by the Bioscreen C for the lines measured in Plate 1 of Assay 3. - Assay3Pl2.csv - Raw OD data measured by the Bioscreen C for the lines measured in Plate 2 of Assay 3. - Assay4_wells.csv - Raw wells file needed to map the raw data to specific lines and media from Assay 4. - Assay4Pl3.csv - Raw OD data measured by the Bioscreen C for the lines measured in Plate 3 of Assay 4. - Assay4Pl12 - Raw OD data measured by the Bioscreen C for the lines measured in Plates 1 and 2 of Assay 4. - Assay5_wells.csv - Raw wells file needed to map the raw data to specific lines and media from Assay 5. - Assay5Pl3.csv - Raw OD data measured by the Bioscreen C for the lines measured in Plate 3 of Assay 5. - Assay6_wells.csv - Raw wells file needed to map the raw data to specific lines and media from Assay 6. - Assay6Pl3.csv - Raw OD data measured by the Bioscreen C for the lines measured in Plate 3 of Assay 6. - Assay6Pl12.csv - Raw OD data measured by the Bioscreen C for the lines measured in Plates 1 and 2 of Assay 6. - Assay7_wells.csv - Raw wells file needed to map the raw data to specific lines and media from Assay 7. - Assay7Pl1.csv - Raw OD data measured by the Bioscreen C for the lines measured in Plate 1 of Assay 7. * “data_output” - Folder containing data files created by the R scripts. - lgrNys2Dips.csv - Data file that contains maximum growth rate, OD after 24 hours, normalized maximum growth rate, whether a well should be omitted or is an outlier, and genotype information for each well containing a diploid strain in the analysis from all growth rate assays in nystatin2. Created by LM_HapNys2.R. - lgrNys2Haps.csv - Data file that contains maximum growth rate, OD after 24 hours, normalized maximum growth rate, whether a well should be omitted or is an outlier, and genotype information for each well containing a haploid strain in the analysis from all growth rate assays in nystatin2. Created by LM_HapNys2.R. - lgrYPDDips.csv - Data file that contains maximum growth rate, OD after 24 hours, normalized maximum growth rate, whether a well should be omitted or is an outlier, and genotype information for each well containing a diploid strain in the analysis from all growth rate assays in YPD. Created by LM_HapYPD.R. - lgrYPDHaps.csv - Data file that contains maximum growth rate, OD after 24 hours, normalized maximum growth rate, whether a well should be omitted or is an outlier, and genotype information for each well containing a haploid strain in the analysis from all growth rate assays in YPD. Created by LM_HapYPD.R. - NormalizedNys2.csv - Data file that contains maximum growth rate, OD after 24 hours, and normalized maximum growth rate of each well included in the analysis from all growth rate assays in nystatin2. Created by Normalization.R. - NormalizedYPD.csv - Data file that contains maximum growth rate, OD after 24 hours, and normalized maximum growth rate of each well included in the analysis from all growth rate assays in YPD. Created by Normalization.R. - Nys2DipsMContrasts.csv - Data file that contains the statistics calculated for each desired pairwise comparison of maximum growth rates between homozygous diploid strains in nystatin2. Created by LM_DipNys2.R. - Nys2DipsMMeans.csv - Data file that contains fitted least-squares means of maximum growth rates and their 95% confidence intervals for all homozygous diploid strains in nystatin2. Created by LM_DipNys2.R. - Nys2DipsTContrasts.csv - Data file that contains the statistics calculated for each desired pairwise comparison of maximum growth rates between diploid strains in nystatin2. Created by LM_DipNys2.R. - Nys2DipsTMeans.csv - Data file that contains fitted least-squares means of maximum growth rates and their 95% confidence intervals for all diploid strains in nystatin2. Created by LM_DipNys2.R. - Nys2HapsContrasts.csv - Data file that contains the statistics calculated for each desired pairwise comparison of maximum growth rates between haploid strains in nystatin2. Created by LM_HapNys2.R. Used in Table 1. - Nys2HapsMeans.csv - Data file that contains fitted least-squares means of maximum growth rates and their 95% confidence intervals for all haploid strains in nystatin2. Created by LM_HapNys2.R. - OmitOutlierNys2.csv - Data file that contains maximum growth rate, OD after 24 hours, and normalized maximum growth rate of each well included in the analysis from all growth rate assays in nystatin2, as well as information about whether the well should be omitted due to standardization problems or is considered to be an outlier. Created by RmOutliers.R. - OmitOutlierYPD.csv - Data file that contains maximum growth rate, OD after 24 hours, and normalized maximum growth rate of each well included in the analysis from all growth rate assays in YPD, as well as information about whether the well should be omitted due to standardization problems or is considered to be an outlier. Created by RmOutliers.R. - YPDDipsMContrasts.csv - Data file that contains the statistics calculated for each desired pairwise comparison of maximum growth rates between homozygous diploid strains in YPD. Created by LM_DipYPD.R. - YPDDipsMMeans.csv - Data file that contains fitted least-squares means of maximum growth rates and their 95% confidence intervals for all homozygous diploid strains in YPD. Created by LM_DipYPD.R. - YPDDipsTContrasts.csv - Data file that contains the statistics calculated for each desired pairwise comparison of maximum growth rates between diploid strains in YPD. Created by LM_DipYPD.R. - YPDDipsTMeans.csv - Data file that contains fitted least-squares means of maximum growth rates and their 95% confidence intervals for all diploid strains in YPD. Created by LM_DipYPD.R. - YPDHapsContrasts.csv - Data file that contains the statistics calculated for each desired pairwise comparison of maximum growth rates between haploid strains in YPD. Created by LM_HapYPD.R. - YPDHapsMeans.csv - Data file that contains fitted least-squares means of maximum growth rates and their 95% confidence intervals for all haploid strains in YPD. Created by LM_HapYPD.R. * DipHeatmaps.R - R script used to create S4 Fig. Creates HeatmapLegend.S4Fig.pdf, Heatmap35.S4Fig.pdf, Heatmap36.S4Fig.pdf, Heatmap37.S4Fig.pdf, Heatmap56.S4Fig.pdf, Heatmap57.S4Fig.pdf, and Heatmap67.S4Fig.pdf. * LM_DipNys2.R - R script used to run mixed-effects models, and subsequent pairwise comparisons, on the diploid strains in nystatin2. Creates Nys2DipsMMeans.csv, Nys2DipsMContrasts.csv, Nys2DipsTMeans.csv, and Nys2DipsTContrasts.csv. * LM_DipYPD.R - R script used to run mixed-effects models, and subsequent pairwise comparisons, on the diploid strains in YPD. Creates YPDDipsMMeans.csv, YPDDipsMContrasts.csv, YPDDipsTMeans.csv, and YPDDipsTContrasts.csv. * LM_HapNys2.R - R script used to format the data for analysis with mixed-effects models. Also used to run the mixed-effects models, and subsequent pairwise comparisons, on the haploid strains in nystatin2. Includes models of mating types analyzed separately. Creates lgrNys2Haps.csv, lgrNys2Dips.csv, Nys2HapsMeans.csv, and Nys2HapsContrasts.csv. Creates the data for Table 1. * LM_HapYPD.R - R script used to format the data for analysis with mixed-effects models. Also used to run the mixed-effects models, and subsequent pairwise comparisons, on the haploid strains in YPD. Includes models of mating types analyzed separately. Creates lgrYPDHaps.csv, lgrYPDDips.csv, YPDHapsMeans.csv, and YPDHapsContrasts.csv. * Normalization.R - R script used to take the raw data and find the maximum growth rate, OD after 24 hours, and normalized maximum growth rate of each well included in the analysis from all growth rate assays. Creates NormalizedNys.csv and NormalizedYPD.csv. * PreGrowthMediumTest.R - R script used to investigate the potential effect of pre-growth medium on growth rate assay results. Includes sign test and paired t-test comparing assays pre-grown in YPD or 0.5 uM nystatin. * RmOutliers.R - R script used to take the normalized maximum growth rate of each well included in the analysis from all growth rate assays and determine whether there are outliers for each strain in each medium type. Also adds information about wells that should be omitted due to standardization problems. Creates OmitOutlierNys2.csv and OmitOutlierYPD.csv. * TablePlot.R - R script used to create Fig 3 and Fig 4. Creates HapGRPlot.Fig3.pdf and DipGRPlot.Fig4.pdf. ######### “SterolAssay” - Folder containing analyses of sterol profiles. ######### * SterolAbs.csv - Raw absorbance data measured in the sterol assay. * SterolPlot.R - R script used to create Fig 6. Creates SterolPlot.Fig6.pdf. ######### “ToleranceAssay” - Folder containing analyses of OD after 24 hours measured in a range of concentrations of nystatin. ######### * Tolerance_sorted.csv - Data file that contains the OD data after 24 hours of growth in the tolerance assay, sorted by strain and medium type. Also contains information about whether the well should be omitted and the OD of the culture after correction for the OD of the medium. * Tolerance_wells.csv - Raw wells file needed to map the raw data to specific lines and media from the tolerance assay. * ToleranceOD24.csv - Raw OD data measured after 24 hours of growth in the tolerance assay * TolerancePlot.R - R script used to format the tolerance data for analysis and to create Fig 5, S3 Fig, and S5 Fig. Creates Tolerance_sorted.csv, HapTolPlot.Fig5.pdf, DipMTolPlot.S3Fig.pdf, and DipTTolPlot.S5Fig.pdf. --------------------- Figures: --------------------- The following scripts were used to generate the figures. The data needed for each script is specified in the script file (read.csv() commands will automatically read in the correct data if the working directory is set to this folder). ######### Fig 3: Maximum growth rate of haploid strains in nystatin2 (above diagonal) and YPD (below diagonal). AND Fig 4: Maximum growth rate of diploid strains in nystatin2 (above diagonal) and YPD (below diagonal). ######### * "GrowthRateAssays" - TablePlot.R (makes the figures) * “Figures” - HapGRPlot.Fig3.pdf (Fig 3) * “Figures” - DipGRPlot.Fig4.pdf (Fig 4) ######### Fig 5: Optical density after 24 hours of growth for haploid strains in a range of concentrations of nystatin. ######### * "ToleranceAssay" - TolerancePlot.R (makes the figure) * “Figures” - HapTolPlot.Fig5.pdf (Fig 5) ######### Fig 6: Sterol profiles of all MATa haploid strains as measured using a spectrophotometry-based assay. ######### * “SterolAssay” - SterolPlot.R (makes the figure) * “Figures” - SterolPlot.Fig6.pdf (Fig 6) ######### S1 Fig: Optical density after 24 hours of growth for haploid strains in nystatin2 (above diagonal) and YPD (below diagonal), plotted on a log scale. AND S2 Fig: Optical density after 24 hours of growth for diploid strains in nystatin2 (above diagonal) and YPD (below diagonal), plotted on a log scale. ######### * "GR.OpticalDensity" - TablePlot.OD.R (makes the figures) * “Figures” - HapODPlot.S1Fig.pdf (S1 Fig) * “Figures” - DipODPlot.S2Fig.pdf (S2 Fig) ######### S3 Fig: Optical density after 24 hours of growth for homozygous diploids in a range of concentrations of nystatin. ######### * "ToleranceAssay" - TolerancePlot.R (makes the figure) * “Figures” - DipMTolPlot.S3Fig.pdf (S3 Fig) ######### S4 Fig: Maximum growth rate of diploid strains for each gene combination in nystatin2. ######### Was created from these components: * "GrowthRateAssays" - DipHeatmaps.R (makes components of the figure) * “Figures” - HeatmapLegend.S4Fig.pdf * “Figures” - Heatmap35.S4Fig.pdf * “Figures” - Heatmap36.S4Fig.pdf * “Figures” - Heatmap37.S4Fig.pdf * “Figures” - Heatmap56.S4Fig.pdf * “Figures” - Heatmap57.S4Fig.pdf * “Figures” - Heatmap67.S4Fig.pdf ######### S5 Fig: Optical density after 24 hours of growth for diploid strains in a range of concentrations of nystatin. ######### * "ToleranceAssay" - TolerancePlot.R (makes the figure) * “Figures” - DipTTolPlot.S5Fig.pdf (S5 Fig) ######### S6 Fig: Maximum growth rate of haploid strains in nystatin2 (above diagonal) and YPD (below diagonal) when including outliers. AND S7 Fig: Maximum growth rate of diploid strains in nystatin2 (above diagonal) and YPD (below diagonal) when including outliers. ######### * "GR.OutliersIncluded" - TablePlot.OutIn.R (makes the figures) * “Figures” - HapGRPlot.OutIn.S6Fig.pdf (S6 Fig) * “Figures” - DipGRPlot.OutIn.S7Fig.pdf (S7 Fig) --------------------- Tables: --------------------- The following scripts were used to generate the tables. The data needed for each script is specified in the script file (read.csv() commands will automatically read in the correct data if the working directory is set to this folder). ######### Table 1: Results from a mixed-effects model run on all genes using the haploid maximum growth rate data in nystatin2. ######### * “GrowthRateAssays” - LM_HapNys2.R (script that runs the mixed effects models and pairwise comparisons) * “GrowthRateAssays” - “data_output” - Nys2HapsContrasts.csv (results file) ######### Table 2: Results from a mixed-effects model run on all genes using the homozygous diploid maximum growth rate data in nystatin2. ######### * “GrowthRateAssays” - LM_DipNys2.R (script that runs the mixed effects models and pairwise comparisons) * “GrowthRateAssays” - “data_output” - Nys2DipsMContrasts.csv (results file) ######### Table 3: Results from a mixed-effects model run on all genes using the haploid maximum growth rate data in YPD. ######### * “GrowthRateAssays” - LM_HapYPD.R (script that runs the mixed effects models and pairwise comparisons) * “GrowthRateAssays” - “data_output” - YPDHapsContrasts.csv (results file) ######### Table 4: Results from a mixed-effects model run on all genes using the homozygous diploid maximum growth rate data in YPD. ######### * “GrowthRateAssays” - LM_DipYPD.R (script that runs the mixed effects models and pairwise comparisons) * “GrowthRateAssays” - “data_output” - YPDDipsMContrasts.csv (results file) --------------------- Other things by section: --------------------- ######### Inclusion of Outliers ######### * “GrowthRateAssays” - RmOutliers.R (script to mark outliers and plot them) All notes of differences between the analysis with and without outlier removal are found by comparing the files in “GrowthRateAssays” to those in “GR.OutliersIncluded”. For details of what each file contains, see the descriptions above. Analysis of the exclusion of a single outlier for erg3. * “GR.ExcludeOne” - LM_Nys2.ExclOne.R (script to run linear model and pairwise comparisons) * “GR.ExcludeOne” - TablePlot.ExclOne.R (script to plot the results) * “GR.ExcludeOne” - HapNys2GRPlot.ExclOne.pdf (plot similar to Fig 3 that excludes only one outlier) ######### RESULTS - “Tolerance across a range of nystatin” ######### Linear model of the effects of mating type, concentration of nystatin and strain identity on OD. * “ToleranceAssay” - TolerancePlot.R (script to run the linear model) ######### S1 FILE - “Segregating mutation in DSC2” ######### Two sample t-tests of strains that differ in their status at DSC2 between mating types. * “DSC2” - DSC2effect.R (script to run the t-tests) Differences in the results when including information about DSC2 (or excluding dsc2 mutants altogether). * “DSC2” - DSC2effect.R (script to run linear models, pairwise comparisons and plot the results) * “DSC2” - HapGRPlotDSC2.pdf (plot similar to Fig 3 separating strains by genotype at DSC2.) * “DSC2” - HapGRPlotNoDSC2.pdf - (plot similar to Fig 3 that excludes strains containing mutations in DSC2) ######### S1 FILE - “Preparing stocks for growth rate assays” ######### Sign test and paired t-test comparing assays pre-grown in YPD or 0.5 uM nystatin. * “GrowthRateAssays” - PreGrowthMediumTest.R (script to run the tests) ######### S1 FILE - “Analysis including outliers” ######### Comparison between erg3 erg6 and erg6 in nystatin2. See contrast “m,w,w,w - m,w,m,w” in files: * “GrowthRateAssays” - “data_output” - Nys2HapsContrasts.csv (comparisons in haploids when excluding all outliers) * “GR.OutliersIncluded” - “data_output” - Nys2HapsContrasts.OutIn.csv (comparisons in haploids when including all outliers) * “GR.ExcludeOne” - Nys2HapsContrasts.ExclOne.csv (comparisons in haploids when excluding one outlier for erg3) * “GrowthRateAssays” - “data_output” - Nys2DipsMContrasts.csv (comparisons in diploids when excluding all outliers) * “GR.OutliersIncluded” - “data_output” - Nys2DipsMContrasts.OutIn (comparisons in diploids when including all outliers)