Raw and processed data for Longan and Fay 2024 (copper and sulfite mutagenesis of S. cerevisiae and S. paradoxus)

Images metadata (file)Image_metadata.xlsx is a file which specifies the experiment, days of growth, stress/media, and stressor concentration associated with each image file included in this project.Images (zipped folder)This folder contains all of the phenotyping images obtained in this study.Sequenced mutants dataset (zipped folder)Includes two items:1) Sulfite phenotyping of haploid mutants of S. cerevisiae and S. paradoxus chosen as candidates for sequencing.2) Copper phenotyping of haploid mutants of S. cerevisiae and S. paradoxus chosen as candidates for sequencing.For sulfite the files provided contain the following info: Raw_data_positions_sulfite.txt = colony sizes at each position for each plate. Raw_data_strains_sulfite.csv = The raw data processed to link the colony size measurements with a technical replicate of a particular strain. Sulfite concentrations of each plate can also be found in the rightmost column. ANC_key_triplicate_sulfite.csv = Link the numeric designations of the mutants to their ancestors. positions_key_triplicate_sulfite.csv = links the positions on the plates to the numeric designations of the mutants. YJF_key_triplicate_sulfite.csv = YJF designations for the mutants that were chosen for sequencing linked to their numeric id in this experiment.For copper, two files contain all of the information. 4_13_21_seqed_coppermutsreplicatedphenod3_ColonyData_AllPlates.txt contains all of the colony sizes for each position in the images. Copper_design_YJFdesignations.csv specifies the YJF designations of each strain in each position.Diploid dataset (zipped folder)This dataset includes images and colony size measurements from several phenotyping experiments: Copper phenotyping of diploid mutants of S. cerevisiae and S. paradoxus with elevated resistance.Sulfite phenotyping of diploid mutants of S. cerevisiae and S. paradoxus with elevated resistance.Phenotyping these mutants in permissive conditions.The file diploid_colony_size_dataset.csv contains colony size measurements derived from the images in this item along with the collection metadata associated with each sample (relative size, color, recovery concentration, circularity, spontaneous/induced).Note the column "mutnumericid_techreps" in this file, which defines the positions that are technical replicates of the same mutant/strain.Haploid dataset (zipped folder)This dataset includes images and colony size measurements from several phenotyping experiments: Copper phenotyping of haploid mutants of S. cerevisiae and S. paradoxus with elevated resistance.Sulfite phenotyping of haploid mutants of S. cerevisiae and S. paradoxus with elevated resistance.Phenotyping these mutants in permissive conditions.The file haploid_colony_size_dataset.csv contains colony size measurements derived from the images in this item along with the collection metadata associated with each sample (relative size, color, recovery concentration, circularity, spontaneous/induced).Processed data used to generate figures (zipped folder)The following files contain the data used to generate the figures in the associated publication:canavanine2.csv = mutation rates and standard deviations of those rates for the three concentrations of canavanine used for both species for each treatment (mutagenized and mock mutagenized)copper2.csv = mutation rates and standard deviations for each copper concentration for both species for both treatments. Columns are added that were used to specify line connections and horizontal point offset in ggplot2.copper3.csv = Total mutation rates for copper for both species for both treatments. Includes a column used for horizontal offset in ggplot2.hapcop.csv, dipcop,csv, hapsul.csv, dipsul.csv contain effect size data for all the nonescapee strains that were phenotyped for both species.hapcopc.csv, dipcopc,csv, hapsulc.csv, dipsulc.csv contain costs data for all the nonescapee strains that were phenotyped for both species.rc_da_cop.csv and rc_da_sul.csv contain delta AUC values and costs measurements for the sequenced mutants and contain columns to split the mutants by category.Incidence.csv contains the incidence of the major mutant classes recovered in this study split between species.KSP1_muts.csv, PMA1_muts.csv, RTS1_muts.csv, REG1_muts.csv, encodes the position and identity of mutants recovered in this study such that they can be visualized as bar charts. Negative values are used for S. paradoxus counts.YJF4464_CUP1.csv contained coverage data at the CUP1 locus for S. paradoxus copper mutant YJF4464