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

<b>Images metadata (file</b><b>)</b>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.<b>Images (zipped folder)</b>This folder contains all of the phenotyping images obtained in this study.<b>Sequenced mutants dataset (zipped folder)</b>Includes two items:1) Sulfite phenotyping of haploid mutants of <i>S. cerevisiae</i> and <i>S. paradoxus</i> chosen as candidates for sequencing.2) Copper phenotyping of haploid mutants of <i>S. cerevisiae </i>and <i>S. paradoxus</i> 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.<b>Diploid dataset (zipped folder)</b>This dataset includes images and colony size measurements from several phenotyping experiments: Copper phenotyping of diploid mutants of <i>S. cerevisiae</i> and <i>S. paradoxus</i> with elevated resistance.Sulfite phenotyping of diploid mutants of <i>S. cerevisiae</i> and <i>S. paradoxus</i> 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.<b>Haploid dataset (zipped folder)</b>This dataset includes images and colony size measurements from several phenotyping experiments: Copper phenotyping of haploid mutants of <i>S. cerevisiae</i> and <i>S. paradoxus</i> 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).<b>Processed data used to generate figures (zipped folder)</b>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 <i>S. paradoxus</i> counts.YJF4464_CUP1.csv contained coverage data at the <i>CUP1</i> locus for <i>S. paradoxus</i> copper mutant YJF4464

**图像元数据文件**：`Image_metadata.xlsx` 是用于指定本项目中每张图像文件所关联的实验信息、培养天数、胁迫/培养基条件以及胁迫因子浓度的表格文件。
**图像（压缩文件夹）**：本文件夹包含本研究中获取的全部表型成像图片。
**测序突变体数据集（压缩文件夹）**：本数据集包含两项内容：1）针对筛选出的拟测序酿酒酵母（*S. cerevisiae*）和帕拉普酵母（*S. paradoxus*）单倍体突变体的亚硫酸盐表型分析；2）针对筛选出的拟测序酿酒酵母（*S. cerevisiae*）和帕拉普酵母（*S. paradoxus*）单倍体突变体的铜离子表型分析。
针对亚硫酸盐表型数据，提供的文件包含如下信息：
`Raw_data_positions_sulfite.txt`：记录每个平板上各位置的菌落尺寸。
`Raw_data_strains_sulfite.csv`：经处理的原始数据，用于将菌落尺寸测量结果与特定菌株的技术重复样本进行关联；每个平板的亚硫酸盐浓度亦可在该文件的最右侧列中查询。
`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`：用于将平板上的成像位置与突变体的数字编号进行关联。
`YJF_key_triplicate_sulfite.csv`：用于将本研究中拟测序突变体的YJF编号与其实验内数字ID进行关联。
针对铜离子表型数据，共有两个文件包含全部相关信息：
`4_13_21_seqed_coppermutsreplicatedphenod3_ColonyData_AllPlates.txt`：包含本数据集所有成像平板中各位置的全部菌落尺寸数据。
`Copper_design_YJFdesignations.csv`：用于指定每个平板位置上各菌株的YJF编号。
**二倍体数据集（压缩文件夹）**：本数据集包含多项表型实验的成像结果与菌落尺寸测量数据，具体包括：具有高抗性的酿酒酵母（*S. cerevisiae*）和帕拉普酵母（*S. paradoxus*）二倍体突变体的铜离子表型分析、具有高抗性的酿酒酵母（*S. cerevisiae*）和帕拉普酵母（*S. paradoxus*）二倍体突变体的亚硫酸盐表型分析，以及上述突变体在许可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尺寸测量数据，以及与每个样本对应的采集元数据，包括相对尺寸、菌落颜色、恢复浓度、圆度、突变类型（自发/诱导）。
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的成像位置。
**单倍体数据集（压缩文件夹）**：本数据集包含多项表型实验的成像结果与菌落尺寸测量数据，具体包括：具有高抗性的酿酒酵母（*S. cerevisiae*）和帕拉普酵母（*S. paradoxus*）单倍体突变体的铜离子表型分析、具有高抗性的酿酒酵母（*S. cerevisiae*）和帕拉普酵母（*S. paradoxus*）单倍体突变体的亚硫酸盐表型分析，以及上述突变体在许可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尺寸测量数据，以及与每个样本对应的采集元数据，包括相对尺寸、菌落颜色、恢复浓度、圆度、突变类型（自发/诱导）。
**用于生成论文图表的处理后数据（压缩文件夹）**：本文件夹内的文件包含用于生成相关论文中图表的全部数据，具体如下：
`canavanine2.csv`：包含两种酵母在三种瓜氨酸浓度下、两种处理方式（诱变处理与mock诱变处理）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；该文件新增了用于在`ggplot2`中指定线条连接与水平点偏移的列。
`copper3.csv`：包含两种酵母在两种处理方式下的铜离子总突变率，该文件包含用于`ggplot2`绘图水平偏移的列。
`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合度成本数据。
`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，并包含用于按类别对突变体进行分组的列。
`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，并按物种进行分组统计。
`KSP1_muts.csv`、`PMA1_muts.csv`、`RTS1_muts.csv`、`REG1_muts.csv`：包含本研究中分离得到的突变体的位置与序列信息，可用于绘制条形图；其中负值用于表示帕拉普酵母（*S. paradoxus*）的计数数据。
`YJF4464_CUP1.csv`：包含帕拉普酵母（*S. paradoxus*）铜离子突变体YJF4464的*CUP1*基因座的测序覆盖度数据。