Data from: Diverse mechanisms of metaeffector activity in an intracellular bacterial pathogen, Legionella pneumophila

Urbanus ML, Quaile AT, Stogios PJ, Morar M, Rao C, Di Leo R, Evdokimova E, Lam M, Oatway C, Cuff ME, Osipiuk J, Michalska KM, Nocek BP, Taipale M, Savchenko A, Ensminger A

Date Published: December 13, 2016

DOI: http://dx.doi.org/10.5061/dryad.kj666

 

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Title Query strain identities and corresponding screening set.
Downloaded 1 time
Description 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.
Download Array_set_annotation.xls (100.3 Kb)
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Title SGA output for analysis sets 1-10.
Downloaded 3 times
Description 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/). 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 .zip archive includes spreadsheets that encompass the raw SGAtools data output from the paper for analysis sets 1-10.
Download UrbanusMSB_SGA.zip (45.42 Mb)
Download Urbanus_SGA_1-10.zip (13.42 Mb)
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Title SGA output for analysis sets 11-20.
Downloaded 1 time
Description 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/). 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 .zip archive includes spreadsheets that encompass the raw SGAtools data output from the paper for analysis sets 11-20.
Download Urbanus_SGA_11-20.zip (6.456 Mb)
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Title SGA output for analysis sets 21-30.
Downloaded 1 time
Description 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/). 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 .zip archive includes spreadsheets that encompass the raw SGAtools data output from the paper for analysis sets 21-30.
Download Urbanus_SGA_21-30.zip (17.91 Mb)
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Title SGA output for analysis sets 31-37.
Downloaded 2 times
Description 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/). 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 .zip archive includes spreadsheets that encompass the raw SGAtools data output from the paper for analysis sets 31-37.
Download Urbanus_SGA_31-37.zip (9.945 Mb)
Details View File Details

When using this data, please cite the original publication:

Urbanus ML, Quaile AT, Stogios PJ, Morar M, Rao C, Di Leo R, Evdokimova E, Lam M, Oatway C, Cuff ME, Osipiuk J, Michalska KM, Nocek BP, Taipale M, Savchenko A, Ensminger A (2016) Diverse mechanisms of metaeffector activity in an intracellular bacterial pathogen, Legionella pneumophila. Molecular Systems Biology 12: 893. http://dx.doi.org/10.15252/msb.20167381

Additionally, please cite the Dryad data package:

Urbanus ML, Quaile AT, Stogios PJ, Morar M, Rao C, Di Leo R, Evdokimova E, Lam M, Oatway C, Cuff ME, Osipiuk J, Michalska KM, Nocek BP, Taipale M, Savchenko A, Ensminger A (2016) Data from: Diverse mechanisms of metaeffector activity in an intracellular bacterial pathogen, Legionella pneumophila. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.kj666
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