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图像元数据文件（file）Image_metadata.xlsx：用于明确本项目中所有图像文件对应的实验信息、微生物培养天数、胁迫/培养基条件以及胁迫因子浓度。 图像压缩文件夹（zipped folder）：内含本研究获取的所有表型成像图像。 候选测序突变体数据集（zipped folder）：该压缩文件夹包含两项内容：1. 酿酒酵母（S. cerevisiae）与帕拉酵母（S. paradoxus）单倍体候选测序突变体的亚硫酸盐表型分析；2. 酿酒酵母（S. cerevisiae）与帕拉酵母（S. paradoxus）单倍体候选测序突变体的铜离子表型分析。 亚硫酸盐表型分析相关文件说明如下： - Raw_data_positions_sulfite.txt：记录各平板每个位置的菌落大小数据； - Raw_data_strains_sulfite.csv：经过预处理的原始数据，用于将菌落大小测量值与对应菌株的技术重复样本进行关联，各平板的亚硫酸盐浓度亦可在该文件最右侧列中查询； - ANC_key_triplicate_sulfite.csv：用于将突变体的数字编号与其祖先菌株进行关联； - positions_key_triplicate_sulfite.csv：用于将平板上的菌落位置与突变体的数字编号进行关联； - YJF_key_triplicate_sulfite.csv：用于将本实验中入选测序的突变体的YJF编号与其本次实验的数字ID进行关联。 铜离子表型分析相关文件包含以下两份核心数据： - 4_13_21_seqed_coppermutsreplicatedphenod3_ColonyData_AllPlates.txt：包含所有平板各位置的菌落大小数据； - Copper_design_YJFdesignations.csv：明确了每个平板位置对应菌株的YJF编号。 二倍体突变体数据集（zipped folder）：该压缩数据集包含多项表型实验的成像图像与菌落大小测量数据，具体包括：1. 高抗性酿酒酵母（S. cerevisiae）与帕拉酵母（S. paradoxus）二倍体突变体的铜离子表型分析；2. 高抗性酿酒酵母（S. cerevisiae）与帕拉酵母（S. paradoxus）二倍体突变体的亚硫酸盐表型分析；3. 上述突变体在适宜培养条件下的表型分析。 文件diploid_colony_size_dataset.csv包含从本文件夹图像中提取的菌落大小测量数据，以及每个样本对应的采集元数据，包括相对大小、菌落颜色、恢复浓度、圆度、自发突变/诱导突变类型。请注意该文件中的"mutnumericid_techreps"列，该列用于定义属于同一突变体/菌株的技术重复样本位置。 单倍体突变体数据集（zipped folder）：该压缩数据集包含多项表型实验的成像图像与菌落大小测量数据，具体包括：1. 高抗性酿酒酵母（S. cerevisiae）与帕拉酵母（S. paradoxus）单倍体突变体的铜离子表型分析；2. 高抗性酿酒酵母（S. cerevisiae）与帕拉酵母（S. paradoxus）单倍体突变体的亚硫酸盐表型分析；3. 上述突变体在适宜培养条件下的表型分析。 文件haploid_colony_size_dataset.csv包含从本文件夹图像中提取的菌落大小测量数据，以及每个样本对应的采集元数据，包括相对大小、菌落颜色、恢复浓度、圆度、自发突变/诱导突变类型。 用于生成论文插图的处理后数据集（zipped folder）：该压缩文件夹包含用于生成相关发表论文插图的全部处理后数据，各文件说明如下： - canavanine2.csv：包含两种酵母在三种胍氨酸浓度下、两种处理方式（诱变与模拟诱变）的突变率及其标准差； - copper2.csv：包含两种酵母在两种处理方式下、各铜离子浓度对应的突变率及其标准差，新增了用于ggplot2绘图中线型连接与横向点偏移的列； - copper3.csv：包含两种酵母在两种处理方式下的铜离子总突变率，新增了用于ggplot2绘图横向偏移的列； - hapcop.csv、dipcop.csv、hapsul.csv、dipsul.csv：包含两种酵母中所有经表型分析的非逃逸菌株的效应量数据； - hapcopc.csv、dipcopc.csv、hapsulc.csv、dipsulc.csv：包含两种酵母中所有经表型分析的非逃逸菌株的适应度成本数据； - rc_da_cop.csv与rc_da_sul.csv：包含测序突变体的ΔAUC值与成本测量数据，新增了用于按类别划分突变体的列； - Incidence.csv：包含本研究中分离得到的主要突变类别的发生率数据，按酵母物种进行分组统计； - KSP1_muts.csv、PMA1_muts.csv、RTS1_muts.csv、REG1_muts.csv：记录了本研究中分离得到的突变体的位置与类型，可用于绘制柱状图，其中负值代表帕拉酵母（S. paradoxus）的计数； - YJF4464_CUP1.csv：包含帕拉酵母（S. paradoxus）铜离子突变体YJF4464的CUP1基因座覆盖度数据。