Query strain identities and corresponding screening set.

In order to obtain an IDTS-wide genetic interaction map, we modified the automated, high-density replica plating approaches previously developed for analyzing S. cerevisiae double mutants through Synthetic Genetic Array (SGA) analysis (Tong AH, Evangelista M, Parsons AB, Xu H, Bader GD, Page N, Robinson M, Raghibizadeh S, Hogue CW, Bussey H, Andrews B, Tyers M, Boone C (2001) Systematic genetic analysis with ordered arrays of yeast deletion mutants. Science 294: 2364-2368). Instead of looking at double mutants, however, we used yeast genetics to systematically assess the effects of Legionella effector co-expression on yeast growth. Query strains that express one effector were mated to an array of ~330 effectors in groups of ~10 queries at a time ("Analysis Set"). The arrays were then imaged using a high-resolution camera and the spot sizes were quantified using SGAtools (http://sgatools.ccbr.utoronto.ca/) (Wagih O, Usaj M, Baryshnikova A, VanderSluis B, Kuzmin E, Costanzo M, Myers CL, Andrews BJ, Boone CM, Parts L (2013) SGAtools: One-stop analysis and visualization of array-based genetic interaction screens. Nucleic acids research 41: W591-596). Outlier spot sizes flagged by the Jackknife filter (JK) in SGAtools were removed and the average and standard deviation of the remaining values were calculated and normalized to the average empty vector control. This spreadsheet lists all query strains and links them to one or more specific analysis set.为获取覆盖全IDTS范围的遗传互作图谱，我们对此前基于合成遗传阵列（Synthetic Genetic Array, SGA）分析酿酒酵母（S. cerevisiae）双突变体的自动化高密度影印铺板方法进行了改良，该原始方法由Tong AH等人于2001年发表（Tong AH, Evangelista M, Parsons AB, Xu H, Bader GD, Page N, Robinson M, Raghibizadeh S, Hogue CW, Bussey H, Andrews B, Tyers M, Boone C (2001) Systematic genetic analysis with ordered arrays of yeast deletion mutants. Science 294: 2364-2368）。与既往研究聚焦双突变体不同，本研究借助酵母遗传学手段，系统评估军团菌效应蛋白共表达对酵母生长的影响。实验中，携带单种效应蛋白的查询菌株将与约330种效应蛋白组成的阵列进行杂交，每次以约10个查询菌株组成一组，称为“分析集（Analysis Set）”。随后通过高分辨率相机对培养阵列进行成像，并利用SGAtools（http://sgatools.ccbr.utoronto.ca/）对菌落斑点尺寸进行定量分析，该工具由Wagih O等人于2013年推出（Wagih O, Usaj M, Baryshnikova A, VanderSluis B, Kuzmin E, Costanzo M, Myers CL, Andrews BJ, Boone CM, Parts L (2013) SGAtools: One-stop analysis and visualization of array-based genetic interaction screens. Nucleic acids research 41: W591-596）。我们移除了SGAtools中通过刀切法过滤器（Jackknife filter, JK）标记的异常斑点尺寸数据，对剩余数值计算平均值与标准差，并以空载对照的平均信号值为基准进行标准化处理。本电子表格列出了所有查询菌株，并将其与一个或多个特定分析集相关联。