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Details	EV-TRACK ID	Experiment nr.	Species	Sample type	Separation protocol	First author	Year	EV-METRIC
	EV230401	3/24	Pseudomonas aeruginosa	PAO1	(d)(U)C Filtration	Zhang L	2020	57%
Study summary Full title Proteomic Analysis of Vesicle-Producing PAO1 Exposed to X-Ray Irradiation. All authors Zhang L, Zhao SQ, Zhang J, Sun Y, Xie YL, Liu YB, Ma CC, Jiang BG, Liao XY, Li WF, Cheng XJ, Wang ZL Journal Front Microbiol Abstract Ionizing irradiation kills pathogens by destroying nucleic acids without protein structure destructi (show more...)Ionizing irradiation kills pathogens by destroying nucleic acids without protein structure destruction. However, how pathogens respond to irradiation stress has not yet been fully elucidated. Here, we observed that PAO1 could release nucleic acids into the extracellular environment under X-ray irradiation. Using scanning electron microscopy (SEM) and transmission electron microscopy (TEM), X-ray irradiation was observed to induce outer membrane vesicle (OMV) formation in PAO1. The size distribution of the OMVs of the irradiated PAO1 was similar to that of the OMVs of the non-irradiated PAO1 according to nanoparticle tracking analysis (NTA). The pyocin-related proteins are involved in OMV production in PAO1 under X-ray irradiation conditions, and that this is regulated by the key SOS gene . The OMV production was significantly impaired in the irradiated PAO1 Δ mutant, suggesting that Lys endolysin is associated with OMV production in PAO1 upon irradiation stress. Meanwhile, no significant difference in OMV production was observed between PAO1 lacking the , , or genes and the parent strain, demonstrating that the irradiation-induced OMV biosynthesis of was independent of the quinolone signal (PQS). (hide) EV-METRIC 57% (91st percentile of all experiments on the same sample type) Reported Not reported Not applicable EV-enriched proteins Protein analysis: analysis of three or more EV-enriched proteins non EV-enriched protein Protein analysis: assessment of a non-EV-enriched protein qualitative and quantitative analysis Particle analysis: implementation of both qualitative and quantitative methods. For the quantitative method, the reporting of measured EV concentration is expected. electron microscopy images Particle analysis: inclusion of a widefield and close-up electron microscopy image density gradient Separation method: density gradient, at least as validation of results attributed to EVs EV density Separation method: reporting of obtained EV density ultracentrifugation specifics Separation method: reporting of g-forces, duration and rotor type of ultracentrifugation steps antibody specifics Protein analysis: antibody clone/reference number and dilution lysate preparation Protein analysis: lysis buffer composition Study data Sample type Cell culture supernatant Sample origin Control condition Focus vesicles Outer membrane vesicle (OMV) Separation protocol Separation protocol Gives a short, non-chronological overview of the different steps of the separation protocol. dUC = (Differential) (ultra)centrifugation DG = density gradient UF = ultrafiltration SEC = size-exclusion chromatography IAF = immuno-affinity capture (Differential) (ultra)centrifugation Filtration Protein markers EV: None non-EV: None Proteomics yes Show all info Study aim Identification of content (omics approaches) Sample Species Pseudomonas aeruginosa Sample Type Cell culture supernatant EV-producing cells PAO1 EV-harvesting Medium Serum free medium Separation Method (Differential) (ultra)centrifugation dUC: centrifugation steps Between 800 g and 10,000 g Between 10,000 g and 50,000 g Between 100,000 g and 150,000 g Pelleting performed Yes Pelleting: rotor type SW 32 Ti Pelleting: speed (g) 100000 Filtration steps Between 0.22 and 0.45 µm Characterization: Protein analysis Protein Concentration Method BCA Proteomics database No Characterization: Lipid analysis No Characterization: Particle analysis NTA Report type Mean Reported size (nm) 160 EV concentration Yes Particle yield as number of particles per million colony-forming units: 5.00E+11 EM EM-type Transmission-EM Image type Close-up, Wide-field

	EV230401	4/24	Pseudomonas aeruginosa	PAO1	(d)(U)C Filtration	Zhang L	2020	57%
Study summary Full title Proteomic Analysis of Vesicle-Producing PAO1 Exposed to X-Ray Irradiation. All authors Zhang L, Zhao SQ, Zhang J, Sun Y, Xie YL, Liu YB, Ma CC, Jiang BG, Liao XY, Li WF, Cheng XJ, Wang ZL Journal Front Microbiol Abstract Ionizing irradiation kills pathogens by destroying nucleic acids without protein structure destructi (show more...)Ionizing irradiation kills pathogens by destroying nucleic acids without protein structure destruction. However, how pathogens respond to irradiation stress has not yet been fully elucidated. Here, we observed that PAO1 could release nucleic acids into the extracellular environment under X-ray irradiation. Using scanning electron microscopy (SEM) and transmission electron microscopy (TEM), X-ray irradiation was observed to induce outer membrane vesicle (OMV) formation in PAO1. The size distribution of the OMVs of the irradiated PAO1 was similar to that of the OMVs of the non-irradiated PAO1 according to nanoparticle tracking analysis (NTA). The pyocin-related proteins are involved in OMV production in PAO1 under X-ray irradiation conditions, and that this is regulated by the key SOS gene . The OMV production was significantly impaired in the irradiated PAO1 Δ mutant, suggesting that Lys endolysin is associated with OMV production in PAO1 upon irradiation stress. Meanwhile, no significant difference in OMV production was observed between PAO1 lacking the , , or genes and the parent strain, demonstrating that the irradiation-induced OMV biosynthesis of was independent of the quinolone signal (PQS). (hide) EV-METRIC 57% (91st percentile of all experiments on the same sample type) Reported Not reported Not applicable EV-enriched proteins Protein analysis: analysis of three or more EV-enriched proteins non EV-enriched protein Protein analysis: assessment of a non-EV-enriched protein qualitative and quantitative analysis Particle analysis: implementation of both qualitative and quantitative methods. For the quantitative method, the reporting of measured EV concentration is expected. electron microscopy images Particle analysis: inclusion of a widefield and close-up electron microscopy image density gradient Separation method: density gradient, at least as validation of results attributed to EVs EV density Separation method: reporting of obtained EV density ultracentrifugation specifics Separation method: reporting of g-forces, duration and rotor type of ultracentrifugation steps antibody specifics Protein analysis: antibody clone/reference number and dilution lysate preparation Protein analysis: lysis buffer composition Study data Sample type Cell culture supernatant Sample origin irradiated Focus vesicles Outer membrane vesicle (OMV) Separation protocol Separation protocol Gives a short, non-chronological overview of the different steps of the separation protocol. dUC = (Differential) (ultra)centrifugation DG = density gradient UF = ultrafiltration SEC = size-exclusion chromatography IAF = immuno-affinity capture (Differential) (ultra)centrifugation Filtration Protein markers EV: None non-EV: None Proteomics yes Show all info Study aim Identification of content (omics approaches) Sample Species Pseudomonas aeruginosa Sample Type Cell culture supernatant EV-producing cells PAO1 EV-harvesting Medium Serum free medium Separation Method (Differential) (ultra)centrifugation dUC: centrifugation steps Between 800 g and 10,000 g Between 10,000 g and 50,000 g Between 100,000 g and 150,000 g Pelleting performed Yes Pelleting: rotor type SW 32 Ti Pelleting: speed (g) 100000 Filtration steps Between 0.22 and 0.45 µm Characterization: Protein analysis Protein Concentration Method BCA Proteomics database No Characterization: Lipid analysis No Characterization: Particle analysis NTA Report type Mean Reported size (nm) 170 EV concentration Yes Particle yield as number of particles per million colony-forming units: 5.50E+12 EM EM-type Transmission-EM Image type Close-up, Wide-field

	EV230401	1/24	Escherichia coli	K12	(d)(U)C Filtration	Zhang L	2020	14%
Study summary Full title Proteomic Analysis of Vesicle-Producing PAO1 Exposed to X-Ray Irradiation. All authors Zhang L, Zhao SQ, Zhang J, Sun Y, Xie YL, Liu YB, Ma CC, Jiang BG, Liao XY, Li WF, Cheng XJ, Wang ZL Journal Front Microbiol Abstract Ionizing irradiation kills pathogens by destroying nucleic acids without protein structure destructi (show more...)Ionizing irradiation kills pathogens by destroying nucleic acids without protein structure destruction. However, how pathogens respond to irradiation stress has not yet been fully elucidated. Here, we observed that PAO1 could release nucleic acids into the extracellular environment under X-ray irradiation. Using scanning electron microscopy (SEM) and transmission electron microscopy (TEM), X-ray irradiation was observed to induce outer membrane vesicle (OMV) formation in PAO1. The size distribution of the OMVs of the irradiated PAO1 was similar to that of the OMVs of the non-irradiated PAO1 according to nanoparticle tracking analysis (NTA). The pyocin-related proteins are involved in OMV production in PAO1 under X-ray irradiation conditions, and that this is regulated by the key SOS gene . The OMV production was significantly impaired in the irradiated PAO1 Δ mutant, suggesting that Lys endolysin is associated with OMV production in PAO1 upon irradiation stress. Meanwhile, no significant difference in OMV production was observed between PAO1 lacking the , , or genes and the parent strain, demonstrating that the irradiation-induced OMV biosynthesis of was independent of the quinolone signal (PQS). (hide) EV-METRIC 14% (43rd percentile of all experiments on the same sample type) Reported Not reported Not applicable EV-enriched proteins Protein analysis: analysis of three or more EV-enriched proteins non EV-enriched protein Protein analysis: assessment of a non-EV-enriched protein qualitative and quantitative analysis Particle analysis: implementation of both qualitative and quantitative methods. For the quantitative method, the reporting of measured EV concentration is expected. electron microscopy images Particle analysis: inclusion of a widefield and close-up electron microscopy image density gradient Separation method: density gradient, at least as validation of results attributed to EVs EV density Separation method: reporting of obtained EV density ultracentrifugation specifics Separation method: reporting of g-forces, duration and rotor type of ultracentrifugation steps antibody specifics Protein analysis: antibody clone/reference number and dilution lysate preparation Protein analysis: lysis buffer composition Study data Sample type Cell culture supernatant Sample origin Control condition Focus vesicles Outer membrane vesicle (OMV) Separation protocol Separation protocol Gives a short, non-chronological overview of the different steps of the separation protocol. dUC = (Differential) (ultra)centrifugation DG = density gradient UF = ultrafiltration SEC = size-exclusion chromatography IAF = immuno-affinity capture (Differential) (ultra)centrifugation Filtration Protein markers EV: None non-EV: None Proteomics no Show all info Study aim Identification of content (omics approaches) Sample Species Escherichia coli Sample Type Cell culture supernatant EV-producing cells K12 EV-harvesting Medium Serum free medium Separation Method (Differential) (ultra)centrifugation dUC: centrifugation steps Between 800 g and 10,000 g Between 10,000 g and 50,000 g Between 100,000 g and 150,000 g Pelleting performed Yes Pelleting: rotor type SW 32 Ti Pelleting: speed (g) 100000 Filtration steps Between 0.22 and 0.45 µm Characterization: Protein analysis None Protein Concentration Method Not determined Characterization: Lipid analysis No Characterization: Particle analysis NTA EM EM-type Scanning-EM Image type Wide-field

	EV230401	2/24	Escherichia coli	K12	(d)(U)C Filtration	Zhang L	2020	14%
Study summary Full title Proteomic Analysis of Vesicle-Producing PAO1 Exposed to X-Ray Irradiation. All authors Zhang L, Zhao SQ, Zhang J, Sun Y, Xie YL, Liu YB, Ma CC, Jiang BG, Liao XY, Li WF, Cheng XJ, Wang ZL Journal Front Microbiol Abstract Ionizing irradiation kills pathogens by destroying nucleic acids without protein structure destructi (show more...)Ionizing irradiation kills pathogens by destroying nucleic acids without protein structure destruction. However, how pathogens respond to irradiation stress has not yet been fully elucidated. Here, we observed that PAO1 could release nucleic acids into the extracellular environment under X-ray irradiation. Using scanning electron microscopy (SEM) and transmission electron microscopy (TEM), X-ray irradiation was observed to induce outer membrane vesicle (OMV) formation in PAO1. The size distribution of the OMVs of the irradiated PAO1 was similar to that of the OMVs of the non-irradiated PAO1 according to nanoparticle tracking analysis (NTA). The pyocin-related proteins are involved in OMV production in PAO1 under X-ray irradiation conditions, and that this is regulated by the key SOS gene . The OMV production was significantly impaired in the irradiated PAO1 Δ mutant, suggesting that Lys endolysin is associated with OMV production in PAO1 upon irradiation stress. Meanwhile, no significant difference in OMV production was observed between PAO1 lacking the , , or genes and the parent strain, demonstrating that the irradiation-induced OMV biosynthesis of was independent of the quinolone signal (PQS). (hide) EV-METRIC 14% (43rd percentile of all experiments on the same sample type) Reported Not reported Not applicable EV-enriched proteins Protein analysis: analysis of three or more EV-enriched proteins non EV-enriched protein Protein analysis: assessment of a non-EV-enriched protein qualitative and quantitative analysis Particle analysis: implementation of both qualitative and quantitative methods. For the quantitative method, the reporting of measured EV concentration is expected. electron microscopy images Particle analysis: inclusion of a widefield and close-up electron microscopy image density gradient Separation method: density gradient, at least as validation of results attributed to EVs EV density Separation method: reporting of obtained EV density ultracentrifugation specifics Separation method: reporting of g-forces, duration and rotor type of ultracentrifugation steps antibody specifics Protein analysis: antibody clone/reference number and dilution lysate preparation Protein analysis: lysis buffer composition Study data Sample type Cell culture supernatant Sample origin Irradiated Focus vesicles Outer membrane vesicle (OMV) Separation protocol Separation protocol Gives a short, non-chronological overview of the different steps of the separation protocol. dUC = (Differential) (ultra)centrifugation DG = density gradient UF = ultrafiltration SEC = size-exclusion chromatography IAF = immuno-affinity capture (Differential) (ultra)centrifugation Filtration Protein markers EV: None non-EV: None Proteomics no Show all info Study aim Identification of content (omics approaches) Sample Species Escherichia coli Sample Type Cell culture supernatant EV-producing cells K12 EV-harvesting Medium Serum free medium Separation Method (Differential) (ultra)centrifugation dUC: centrifugation steps Between 800 g and 10,000 g Between 10,000 g and 50,000 g Between 100,000 g and 150,000 g Pelleting performed Yes Pelleting: rotor type SW 32 Ti Pelleting: speed (g) 100000 Filtration steps Between 0.22 and 0.45 µm Characterization: Protein analysis None Protein Concentration Method Not determined Characterization: Lipid analysis No Characterization: Particle analysis NTA EM EM-type Scanning-EM Image type Wide-field

	EV230401	5/24	Pseudomonas aeruginosa	PA14	(d)(U)C Filtration	Zhang L	2020	14%
Study summary Full title Proteomic Analysis of Vesicle-Producing PAO1 Exposed to X-Ray Irradiation. All authors Zhang L, Zhao SQ, Zhang J, Sun Y, Xie YL, Liu YB, Ma CC, Jiang BG, Liao XY, Li WF, Cheng XJ, Wang ZL Journal Front Microbiol Abstract Ionizing irradiation kills pathogens by destroying nucleic acids without protein structure destructi (show more...)Ionizing irradiation kills pathogens by destroying nucleic acids without protein structure destruction. However, how pathogens respond to irradiation stress has not yet been fully elucidated. Here, we observed that PAO1 could release nucleic acids into the extracellular environment under X-ray irradiation. Using scanning electron microscopy (SEM) and transmission electron microscopy (TEM), X-ray irradiation was observed to induce outer membrane vesicle (OMV) formation in PAO1. The size distribution of the OMVs of the irradiated PAO1 was similar to that of the OMVs of the non-irradiated PAO1 according to nanoparticle tracking analysis (NTA). The pyocin-related proteins are involved in OMV production in PAO1 under X-ray irradiation conditions, and that this is regulated by the key SOS gene . The OMV production was significantly impaired in the irradiated PAO1 Δ mutant, suggesting that Lys endolysin is associated with OMV production in PAO1 upon irradiation stress. Meanwhile, no significant difference in OMV production was observed between PAO1 lacking the , , or genes and the parent strain, demonstrating that the irradiation-induced OMV biosynthesis of was independent of the quinolone signal (PQS). (hide) EV-METRIC 14% (43rd percentile of all experiments on the same sample type) Reported Not reported Not applicable EV-enriched proteins Protein analysis: analysis of three or more EV-enriched proteins non EV-enriched protein Protein analysis: assessment of a non-EV-enriched protein qualitative and quantitative analysis Particle analysis: implementation of both qualitative and quantitative methods. For the quantitative method, the reporting of measured EV concentration is expected. electron microscopy images Particle analysis: inclusion of a widefield and close-up electron microscopy image density gradient Separation method: density gradient, at least as validation of results attributed to EVs EV density Separation method: reporting of obtained EV density ultracentrifugation specifics Separation method: reporting of g-forces, duration and rotor type of ultracentrifugation steps antibody specifics Protein analysis: antibody clone/reference number and dilution lysate preparation Protein analysis: lysis buffer composition Study data Sample type Cell culture supernatant Sample origin Control condition Focus vesicles Outer membrane vesicle (OMV) Separation protocol Separation protocol Gives a short, non-chronological overview of the different steps of the separation protocol. dUC = (Differential) (ultra)centrifugation DG = density gradient UF = ultrafiltration SEC = size-exclusion chromatography IAF = immuno-affinity capture (Differential) (ultra)centrifugation Filtration Protein markers EV: None non-EV: None Proteomics no Show all info Study aim Identification of content (omics approaches) Sample Species Pseudomonas aeruginosa Sample Type Cell culture supernatant EV-producing cells PA14 EV-harvesting Medium Serum free medium Separation Method (Differential) (ultra)centrifugation dUC: centrifugation steps Between 800 g and 10,000 g Between 10,000 g and 50,000 g Between 100,000 g and 150,000 g Pelleting performed Yes Pelleting: rotor type SW 32 Ti Pelleting: speed (g) 100000 Filtration steps Between 0.22 and 0.45 µm Characterization: Protein analysis None Protein Concentration Method Not determined Protein Yield (µg) as number of particles per million colony-forming units: 2.00E+12 Characterization: Lipid analysis No Characterization: Particle analysis NTA EV concentration Yes Particle yield as number of particles per million colony-forming units: 2.00E+12

	EV230401	6/24	Pseudomonas aeruginosa	PA14	(d)(U)C Filtration	Zhang L	2020	14%
Study summary Full title Proteomic Analysis of Vesicle-Producing PAO1 Exposed to X-Ray Irradiation. All authors Zhang L, Zhao SQ, Zhang J, Sun Y, Xie YL, Liu YB, Ma CC, Jiang BG, Liao XY, Li WF, Cheng XJ, Wang ZL Journal Front Microbiol Abstract Ionizing irradiation kills pathogens by destroying nucleic acids without protein structure destructi (show more...)Ionizing irradiation kills pathogens by destroying nucleic acids without protein structure destruction. However, how pathogens respond to irradiation stress has not yet been fully elucidated. Here, we observed that PAO1 could release nucleic acids into the extracellular environment under X-ray irradiation. Using scanning electron microscopy (SEM) and transmission electron microscopy (TEM), X-ray irradiation was observed to induce outer membrane vesicle (OMV) formation in PAO1. The size distribution of the OMVs of the irradiated PAO1 was similar to that of the OMVs of the non-irradiated PAO1 according to nanoparticle tracking analysis (NTA). The pyocin-related proteins are involved in OMV production in PAO1 under X-ray irradiation conditions, and that this is regulated by the key SOS gene . The OMV production was significantly impaired in the irradiated PAO1 Δ mutant, suggesting that Lys endolysin is associated with OMV production in PAO1 upon irradiation stress. Meanwhile, no significant difference in OMV production was observed between PAO1 lacking the , , or genes and the parent strain, demonstrating that the irradiation-induced OMV biosynthesis of was independent of the quinolone signal (PQS). (hide) EV-METRIC 14% (43rd percentile of all experiments on the same sample type) Reported Not reported Not applicable EV-enriched proteins Protein analysis: analysis of three or more EV-enriched proteins non EV-enriched protein Protein analysis: assessment of a non-EV-enriched protein qualitative and quantitative analysis Particle analysis: implementation of both qualitative and quantitative methods. For the quantitative method, the reporting of measured EV concentration is expected. electron microscopy images Particle analysis: inclusion of a widefield and close-up electron microscopy image density gradient Separation method: density gradient, at least as validation of results attributed to EVs EV density Separation method: reporting of obtained EV density ultracentrifugation specifics Separation method: reporting of g-forces, duration and rotor type of ultracentrifugation steps antibody specifics Protein analysis: antibody clone/reference number and dilution lysate preparation Protein analysis: lysis buffer composition Study data Sample type Cell culture supernatant Sample origin irradiated Focus vesicles Outer membrane vesicle (OMV) Separation protocol Separation protocol Gives a short, non-chronological overview of the different steps of the separation protocol. dUC = (Differential) (ultra)centrifugation DG = density gradient UF = ultrafiltration SEC = size-exclusion chromatography IAF = immuno-affinity capture (Differential) (ultra)centrifugation Filtration Protein markers EV: None non-EV: None Proteomics no Show all info Study aim Identification of content (omics approaches) Sample Species Pseudomonas aeruginosa Sample Type Cell culture supernatant EV-producing cells PA14 EV-harvesting Medium Serum free medium Separation Method (Differential) (ultra)centrifugation dUC: centrifugation steps Between 800 g and 10,000 g Between 10,000 g and 50,000 g Between 100,000 g and 150,000 g Pelleting performed Yes Pelleting: rotor type SW 32 Ti Pelleting: speed (g) 100000 Filtration steps Between 0.22 and 0.45 µm Characterization: Protein analysis None Protein Concentration Method Not determined Protein Yield (µg) as number of particles per million colony-forming units: 5.20E+12 Characterization: Lipid analysis No Characterization: Particle analysis NTA EV concentration Yes Particle yield as number of particles per million colony-forming units: 5.20E+12

	EV230401	7/24	Pseudomonas aeruginosa	PAO1 delta-pqsR	(d)(U)C Filtration	Zhang L	2020	14%
Study summary Full title Proteomic Analysis of Vesicle-Producing PAO1 Exposed to X-Ray Irradiation. All authors Zhang L, Zhao SQ, Zhang J, Sun Y, Xie YL, Liu YB, Ma CC, Jiang BG, Liao XY, Li WF, Cheng XJ, Wang ZL Journal Front Microbiol Abstract Ionizing irradiation kills pathogens by destroying nucleic acids without protein structure destructi (show more...)Ionizing irradiation kills pathogens by destroying nucleic acids without protein structure destruction. However, how pathogens respond to irradiation stress has not yet been fully elucidated. Here, we observed that PAO1 could release nucleic acids into the extracellular environment under X-ray irradiation. Using scanning electron microscopy (SEM) and transmission electron microscopy (TEM), X-ray irradiation was observed to induce outer membrane vesicle (OMV) formation in PAO1. The size distribution of the OMVs of the irradiated PAO1 was similar to that of the OMVs of the non-irradiated PAO1 according to nanoparticle tracking analysis (NTA). The pyocin-related proteins are involved in OMV production in PAO1 under X-ray irradiation conditions, and that this is regulated by the key SOS gene . The OMV production was significantly impaired in the irradiated PAO1 Δ mutant, suggesting that Lys endolysin is associated with OMV production in PAO1 upon irradiation stress. Meanwhile, no significant difference in OMV production was observed between PAO1 lacking the , , or genes and the parent strain, demonstrating that the irradiation-induced OMV biosynthesis of was independent of the quinolone signal (PQS). (hide) EV-METRIC 14% (43rd percentile of all experiments on the same sample type) Reported Not reported Not applicable EV-enriched proteins Protein analysis: analysis of three or more EV-enriched proteins non EV-enriched protein Protein analysis: assessment of a non-EV-enriched protein qualitative and quantitative analysis Particle analysis: implementation of both qualitative and quantitative methods. For the quantitative method, the reporting of measured EV concentration is expected. electron microscopy images Particle analysis: inclusion of a widefield and close-up electron microscopy image density gradient Separation method: density gradient, at least as validation of results attributed to EVs EV density Separation method: reporting of obtained EV density ultracentrifugation specifics Separation method: reporting of g-forces, duration and rotor type of ultracentrifugation steps antibody specifics Protein analysis: antibody clone/reference number and dilution lysate preparation Protein analysis: lysis buffer composition Study data Sample type Cell culture supernatant Sample origin Control condition Focus vesicles Outer membrane vesicle (OMV) Separation protocol Separation protocol Gives a short, non-chronological overview of the different steps of the separation protocol. dUC = (Differential) (ultra)centrifugation DG = density gradient UF = ultrafiltration SEC = size-exclusion chromatography IAF = immuno-affinity capture (Differential) (ultra)centrifugation Filtration Protein markers EV: None non-EV: None Proteomics no Show all info Study aim Identification of content (omics approaches) Sample Species Pseudomonas aeruginosa Sample Type Cell culture supernatant EV-producing cells PAO1 delta-pqsR EV-harvesting Medium Serum free medium Separation Method (Differential) (ultra)centrifugation dUC: centrifugation steps Between 800 g and 10,000 g Between 10,000 g and 50,000 g Between 100,000 g and 150,000 g Pelleting performed Yes Pelleting: rotor type SW 32 Ti Pelleting: speed (g) 100000 Filtration steps Between 0.22 and 0.45 µm Characterization: Protein analysis None Protein Concentration Method Not determined Protein Yield (µg) as number of particles per million colony-forming units: 5.20E+12 Characterization: Lipid analysis No Characterization: Particle analysis NTA Particle yield as number of particles per million colony-forming units: 5.20E+12

	EV230401	8/24	Pseudomonas aeruginosa	PAO1 delta-pqsR	(d)(U)C Filtration	Zhang L	2020	14%
Study summary Full title Proteomic Analysis of Vesicle-Producing PAO1 Exposed to X-Ray Irradiation. All authors Zhang L, Zhao SQ, Zhang J, Sun Y, Xie YL, Liu YB, Ma CC, Jiang BG, Liao XY, Li WF, Cheng XJ, Wang ZL Journal Front Microbiol Abstract Ionizing irradiation kills pathogens by destroying nucleic acids without protein structure destructi (show more...)Ionizing irradiation kills pathogens by destroying nucleic acids without protein structure destruction. However, how pathogens respond to irradiation stress has not yet been fully elucidated. Here, we observed that PAO1 could release nucleic acids into the extracellular environment under X-ray irradiation. Using scanning electron microscopy (SEM) and transmission electron microscopy (TEM), X-ray irradiation was observed to induce outer membrane vesicle (OMV) formation in PAO1. The size distribution of the OMVs of the irradiated PAO1 was similar to that of the OMVs of the non-irradiated PAO1 according to nanoparticle tracking analysis (NTA). The pyocin-related proteins are involved in OMV production in PAO1 under X-ray irradiation conditions, and that this is regulated by the key SOS gene . The OMV production was significantly impaired in the irradiated PAO1 Δ mutant, suggesting that Lys endolysin is associated with OMV production in PAO1 upon irradiation stress. Meanwhile, no significant difference in OMV production was observed between PAO1 lacking the , , or genes and the parent strain, demonstrating that the irradiation-induced OMV biosynthesis of was independent of the quinolone signal (PQS). (hide) EV-METRIC 14% (43rd percentile of all experiments on the same sample type) Reported Not reported Not applicable EV-enriched proteins Protein analysis: analysis of three or more EV-enriched proteins non EV-enriched protein Protein analysis: assessment of a non-EV-enriched protein qualitative and quantitative analysis Particle analysis: implementation of both qualitative and quantitative methods. For the quantitative method, the reporting of measured EV concentration is expected. electron microscopy images Particle analysis: inclusion of a widefield and close-up electron microscopy image density gradient Separation method: density gradient, at least as validation of results attributed to EVs EV density Separation method: reporting of obtained EV density ultracentrifugation specifics Separation method: reporting of g-forces, duration and rotor type of ultracentrifugation steps antibody specifics Protein analysis: antibody clone/reference number and dilution lysate preparation Protein analysis: lysis buffer composition Study data Sample type Cell culture supernatant Sample origin Irradiated Focus vesicles Outer membrane vesicle (OMV) Separation protocol Separation protocol Gives a short, non-chronological overview of the different steps of the separation protocol. dUC = (Differential) (ultra)centrifugation DG = density gradient UF = ultrafiltration SEC = size-exclusion chromatography IAF = immuno-affinity capture (Differential) (ultra)centrifugation Filtration Protein markers EV: None non-EV: None Proteomics no Show all info Study aim Identification of content (omics approaches) Sample Species Pseudomonas aeruginosa Sample Type Cell culture supernatant EV-producing cells PAO1 delta-pqsR EV-harvesting Medium Serum free medium Separation Method (Differential) (ultra)centrifugation dUC: centrifugation steps Between 800 g and 10,000 g Between 10,000 g and 50,000 g Between 100,000 g and 150,000 g Pelleting performed Yes Pelleting: rotor type SW 32 Ti Pelleting: speed (g) 100000 Filtration steps Between 0.22 and 0.45 µm Characterization: Protein analysis None Protein Concentration Method Not determined Protein Yield (µg) as number of particles per million colony-forming units: 4.80E+12 Characterization: Lipid analysis No Characterization: Particle analysis NTA EV concentration Yes Particle yield as number of particles per million colony-forming units: 4.80E+12

	EV230401	9/24	Pseudomonas aeruginosa	PAO1 delta-lasR	(d)(U)C Filtration	Zhang L	2020	14%
Study summary Full title Proteomic Analysis of Vesicle-Producing PAO1 Exposed to X-Ray Irradiation. All authors Zhang L, Zhao SQ, Zhang J, Sun Y, Xie YL, Liu YB, Ma CC, Jiang BG, Liao XY, Li WF, Cheng XJ, Wang ZL Journal Front Microbiol Abstract Ionizing irradiation kills pathogens by destroying nucleic acids without protein structure destructi (show more...)Ionizing irradiation kills pathogens by destroying nucleic acids without protein structure destruction. However, how pathogens respond to irradiation stress has not yet been fully elucidated. Here, we observed that PAO1 could release nucleic acids into the extracellular environment under X-ray irradiation. Using scanning electron microscopy (SEM) and transmission electron microscopy (TEM), X-ray irradiation was observed to induce outer membrane vesicle (OMV) formation in PAO1. The size distribution of the OMVs of the irradiated PAO1 was similar to that of the OMVs of the non-irradiated PAO1 according to nanoparticle tracking analysis (NTA). The pyocin-related proteins are involved in OMV production in PAO1 under X-ray irradiation conditions, and that this is regulated by the key SOS gene . The OMV production was significantly impaired in the irradiated PAO1 Δ mutant, suggesting that Lys endolysin is associated with OMV production in PAO1 upon irradiation stress. Meanwhile, no significant difference in OMV production was observed between PAO1 lacking the , , or genes and the parent strain, demonstrating that the irradiation-induced OMV biosynthesis of was independent of the quinolone signal (PQS). (hide) EV-METRIC 14% (43rd percentile of all experiments on the same sample type) Reported Not reported Not applicable EV-enriched proteins Protein analysis: analysis of three or more EV-enriched proteins non EV-enriched protein Protein analysis: assessment of a non-EV-enriched protein qualitative and quantitative analysis Particle analysis: implementation of both qualitative and quantitative methods. For the quantitative method, the reporting of measured EV concentration is expected. electron microscopy images Particle analysis: inclusion of a widefield and close-up electron microscopy image density gradient Separation method: density gradient, at least as validation of results attributed to EVs EV density Separation method: reporting of obtained EV density ultracentrifugation specifics Separation method: reporting of g-forces, duration and rotor type of ultracentrifugation steps antibody specifics Protein analysis: antibody clone/reference number and dilution lysate preparation Protein analysis: lysis buffer composition Study data Sample type Cell culture supernatant Sample origin Control condition Focus vesicles Outer membrane vesicle (OMV) Separation protocol Separation protocol Gives a short, non-chronological overview of the different steps of the separation protocol. dUC = (Differential) (ultra)centrifugation DG = density gradient UF = ultrafiltration SEC = size-exclusion chromatography IAF = immuno-affinity capture (Differential) (ultra)centrifugation Filtration Protein markers EV: None non-EV: None Proteomics no Show all info Study aim Identification of content (omics approaches) Sample Species Pseudomonas aeruginosa Sample Type Cell culture supernatant EV-producing cells PAO1 delta-lasR EV-harvesting Medium Serum free medium Separation Method (Differential) (ultra)centrifugation dUC: centrifugation steps Between 800 g and 10,000 g Between 10,000 g and 50,000 g Between 100,000 g and 150,000 g Pelleting performed Yes Pelleting: rotor type SW 32 Ti Pelleting: speed (g) 100000 Filtration steps Between 0.22 and 0.45 µm Characterization: Protein analysis None Protein Concentration Method Not determined Protein Yield (µg) as number of particles per million colony-forming units: 4.80E+12 Characterization: Lipid analysis No Characterization: Particle analysis NTA Particle yield as number of particles per million colony-forming units: 4.80E+12

	EV230401	10/24	Pseudomonas aeruginosa	PAO1 delta-lasR	(d)(U)C Filtration	Zhang L	2020	14%
Study summary Full title Proteomic Analysis of Vesicle-Producing PAO1 Exposed to X-Ray Irradiation. All authors Zhang L, Zhao SQ, Zhang J, Sun Y, Xie YL, Liu YB, Ma CC, Jiang BG, Liao XY, Li WF, Cheng XJ, Wang ZL Journal Front Microbiol Abstract Ionizing irradiation kills pathogens by destroying nucleic acids without protein structure destructi (show more...)Ionizing irradiation kills pathogens by destroying nucleic acids without protein structure destruction. However, how pathogens respond to irradiation stress has not yet been fully elucidated. Here, we observed that PAO1 could release nucleic acids into the extracellular environment under X-ray irradiation. Using scanning electron microscopy (SEM) and transmission electron microscopy (TEM), X-ray irradiation was observed to induce outer membrane vesicle (OMV) formation in PAO1. The size distribution of the OMVs of the irradiated PAO1 was similar to that of the OMVs of the non-irradiated PAO1 according to nanoparticle tracking analysis (NTA). The pyocin-related proteins are involved in OMV production in PAO1 under X-ray irradiation conditions, and that this is regulated by the key SOS gene . The OMV production was significantly impaired in the irradiated PAO1 Δ mutant, suggesting that Lys endolysin is associated with OMV production in PAO1 upon irradiation stress. Meanwhile, no significant difference in OMV production was observed between PAO1 lacking the , , or genes and the parent strain, demonstrating that the irradiation-induced OMV biosynthesis of was independent of the quinolone signal (PQS). (hide) EV-METRIC 14% (43rd percentile of all experiments on the same sample type) Reported Not reported Not applicable EV-enriched proteins Protein analysis: analysis of three or more EV-enriched proteins non EV-enriched protein Protein analysis: assessment of a non-EV-enriched protein qualitative and quantitative analysis Particle analysis: implementation of both qualitative and quantitative methods. For the quantitative method, the reporting of measured EV concentration is expected. electron microscopy images Particle analysis: inclusion of a widefield and close-up electron microscopy image density gradient Separation method: density gradient, at least as validation of results attributed to EVs EV density Separation method: reporting of obtained EV density ultracentrifugation specifics Separation method: reporting of g-forces, duration and rotor type of ultracentrifugation steps antibody specifics Protein analysis: antibody clone/reference number and dilution lysate preparation Protein analysis: lysis buffer composition Study data Sample type Cell culture supernatant Sample origin irradiated Focus vesicles Outer membrane vesicle (OMV) Separation protocol Separation protocol Gives a short, non-chronological overview of the different steps of the separation protocol. dUC = (Differential) (ultra)centrifugation DG = density gradient UF = ultrafiltration SEC = size-exclusion chromatography IAF = immuno-affinity capture (Differential) (ultra)centrifugation Filtration Protein markers EV: None non-EV: None Proteomics no Show all info Study aim Identification of content (omics approaches) Sample Species Pseudomonas aeruginosa Sample Type Cell culture supernatant EV-producing cells PAO1 delta-lasR EV-harvesting Medium Serum free medium Separation Method (Differential) (ultra)centrifugation dUC: centrifugation steps Between 800 g and 10,000 g Between 10,000 g and 50,000 g Between 100,000 g and 150,000 g Pelleting performed Yes Pelleting: rotor type SW 32 Ti Pelleting: speed (g) 100000 Filtration steps Between 0.22 and 0.45 µm Characterization: Protein analysis None Protein Concentration Method Not determined Protein Yield (µg) as number of particles per million colony-forming units: 4.90E+12 Characterization: Lipid analysis No Characterization: Particle analysis NTA EV concentration Yes Particle yield as number of particles per million colony-forming units: 4.90E+12

	EV230401	11/24	Pseudomonas aeruginosa	PAO1 delta-rhlR	(d)(U)C Filtration	Zhang L	2020	14%
Study summary Full title Proteomic Analysis of Vesicle-Producing PAO1 Exposed to X-Ray Irradiation. All authors Zhang L, Zhao SQ, Zhang J, Sun Y, Xie YL, Liu YB, Ma CC, Jiang BG, Liao XY, Li WF, Cheng XJ, Wang ZL Journal Front Microbiol Abstract Ionizing irradiation kills pathogens by destroying nucleic acids without protein structure destructi (show more...)Ionizing irradiation kills pathogens by destroying nucleic acids without protein structure destruction. However, how pathogens respond to irradiation stress has not yet been fully elucidated. Here, we observed that PAO1 could release nucleic acids into the extracellular environment under X-ray irradiation. Using scanning electron microscopy (SEM) and transmission electron microscopy (TEM), X-ray irradiation was observed to induce outer membrane vesicle (OMV) formation in PAO1. The size distribution of the OMVs of the irradiated PAO1 was similar to that of the OMVs of the non-irradiated PAO1 according to nanoparticle tracking analysis (NTA). The pyocin-related proteins are involved in OMV production in PAO1 under X-ray irradiation conditions, and that this is regulated by the key SOS gene . The OMV production was significantly impaired in the irradiated PAO1 Δ mutant, suggesting that Lys endolysin is associated with OMV production in PAO1 upon irradiation stress. Meanwhile, no significant difference in OMV production was observed between PAO1 lacking the , , or genes and the parent strain, demonstrating that the irradiation-induced OMV biosynthesis of was independent of the quinolone signal (PQS). (hide) EV-METRIC 14% (43rd percentile of all experiments on the same sample type) Reported Not reported Not applicable EV-enriched proteins Protein analysis: analysis of three or more EV-enriched proteins non EV-enriched protein Protein analysis: assessment of a non-EV-enriched protein qualitative and quantitative analysis Particle analysis: implementation of both qualitative and quantitative methods. For the quantitative method, the reporting of measured EV concentration is expected. electron microscopy images Particle analysis: inclusion of a widefield and close-up electron microscopy image density gradient Separation method: density gradient, at least as validation of results attributed to EVs EV density Separation method: reporting of obtained EV density ultracentrifugation specifics Separation method: reporting of g-forces, duration and rotor type of ultracentrifugation steps antibody specifics Protein analysis: antibody clone/reference number and dilution lysate preparation Protein analysis: lysis buffer composition Study data Sample type Cell culture supernatant Sample origin Control condition Focus vesicles Outer membrane vesicle (OMV) Separation protocol Separation protocol Gives a short, non-chronological overview of the different steps of the separation protocol. dUC = (Differential) (ultra)centrifugation DG = density gradient UF = ultrafiltration SEC = size-exclusion chromatography IAF = immuno-affinity capture (Differential) (ultra)centrifugation Filtration Protein markers EV: None non-EV: None Proteomics no Show all info Study aim Identification of content (omics approaches) Sample Species Pseudomonas aeruginosa Sample Type Cell culture supernatant EV-producing cells PAO1 delta-rhlR EV-harvesting Medium Serum free medium Separation Method (Differential) (ultra)centrifugation dUC: centrifugation steps Between 800 g and 10,000 g Between 10,000 g and 50,000 g Between 100,000 g and 150,000 g Pelleting performed Yes Pelleting: rotor type SW 32 Ti Pelleting: speed (g) 100000 Filtration steps Between 0.22 and 0.45 µm Characterization: Protein analysis None Protein Concentration Method Not determined Protein Yield (µg) as number of particles per million colony-forming units: 4.90E+12 Characterization: Lipid analysis No Characterization: Particle analysis NTA Particle yield as number of particles per million colony-forming units: 4.90E+12

	EV230401	12/24	Pseudomonas aeruginosa	PAO1 delta-rhlR	(d)(U)C Filtration	Zhang L	2020	14%
Study summary Full title Proteomic Analysis of Vesicle-Producing PAO1 Exposed to X-Ray Irradiation. All authors Zhang L, Zhao SQ, Zhang J, Sun Y, Xie YL, Liu YB, Ma CC, Jiang BG, Liao XY, Li WF, Cheng XJ, Wang ZL Journal Front Microbiol Abstract Ionizing irradiation kills pathogens by destroying nucleic acids without protein structure destructi (show more...)Ionizing irradiation kills pathogens by destroying nucleic acids without protein structure destruction. However, how pathogens respond to irradiation stress has not yet been fully elucidated. Here, we observed that PAO1 could release nucleic acids into the extracellular environment under X-ray irradiation. Using scanning electron microscopy (SEM) and transmission electron microscopy (TEM), X-ray irradiation was observed to induce outer membrane vesicle (OMV) formation in PAO1. The size distribution of the OMVs of the irradiated PAO1 was similar to that of the OMVs of the non-irradiated PAO1 according to nanoparticle tracking analysis (NTA). The pyocin-related proteins are involved in OMV production in PAO1 under X-ray irradiation conditions, and that this is regulated by the key SOS gene . The OMV production was significantly impaired in the irradiated PAO1 Δ mutant, suggesting that Lys endolysin is associated with OMV production in PAO1 upon irradiation stress. Meanwhile, no significant difference in OMV production was observed between PAO1 lacking the , , or genes and the parent strain, demonstrating that the irradiation-induced OMV biosynthesis of was independent of the quinolone signal (PQS). (hide) EV-METRIC 14% (43rd percentile of all experiments on the same sample type) Reported Not reported Not applicable EV-enriched proteins Protein analysis: analysis of three or more EV-enriched proteins non EV-enriched protein Protein analysis: assessment of a non-EV-enriched protein qualitative and quantitative analysis Particle analysis: implementation of both qualitative and quantitative methods. For the quantitative method, the reporting of measured EV concentration is expected. electron microscopy images Particle analysis: inclusion of a widefield and close-up electron microscopy image density gradient Separation method: density gradient, at least as validation of results attributed to EVs EV density Separation method: reporting of obtained EV density ultracentrifugation specifics Separation method: reporting of g-forces, duration and rotor type of ultracentrifugation steps antibody specifics Protein analysis: antibody clone/reference number and dilution lysate preparation Protein analysis: lysis buffer composition Study data Sample type Cell culture supernatant Sample origin irradiated Focus vesicles Outer membrane vesicle (OMV) Separation protocol Separation protocol Gives a short, non-chronological overview of the different steps of the separation protocol. dUC = (Differential) (ultra)centrifugation DG = density gradient UF = ultrafiltration SEC = size-exclusion chromatography IAF = immuno-affinity capture (Differential) (ultra)centrifugation Filtration Protein markers EV: None non-EV: None Proteomics no Show all info Study aim Identification of content (omics approaches) Sample Species Pseudomonas aeruginosa Sample Type Cell culture supernatant EV-producing cells PAO1 delta-rhlR EV-harvesting Medium Serum free medium Separation Method (Differential) (ultra)centrifugation dUC: centrifugation steps Between 800 g and 10,000 g Between 10,000 g and 50,000 g Between 100,000 g and 150,000 g Pelleting performed Yes Pelleting: rotor type SW 32 Ti Pelleting: speed (g) 100000 Filtration steps Between 0.22 and 0.45 µm Characterization: Protein analysis None Protein Concentration Method Not determined Protein Yield (µg) as number of particles per million colony-forming units: 4.90E+12 Characterization: Lipid analysis No Characterization: Particle analysis NTA EV concentration Yes Particle yield as number of particles per million colony-forming units: 4.90E+12

	EV230401	13/24	Pseudomonas aeruginosa	PAO1 delta-lys	(d)(U)C Filtration	Zhang L	2020	14%
Study summary Full title Proteomic Analysis of Vesicle-Producing PAO1 Exposed to X-Ray Irradiation. All authors Zhang L, Zhao SQ, Zhang J, Sun Y, Xie YL, Liu YB, Ma CC, Jiang BG, Liao XY, Li WF, Cheng XJ, Wang ZL Journal Front Microbiol Abstract Ionizing irradiation kills pathogens by destroying nucleic acids without protein structure destructi (show more...)Ionizing irradiation kills pathogens by destroying nucleic acids without protein structure destruction. However, how pathogens respond to irradiation stress has not yet been fully elucidated. Here, we observed that PAO1 could release nucleic acids into the extracellular environment under X-ray irradiation. Using scanning electron microscopy (SEM) and transmission electron microscopy (TEM), X-ray irradiation was observed to induce outer membrane vesicle (OMV) formation in PAO1. The size distribution of the OMVs of the irradiated PAO1 was similar to that of the OMVs of the non-irradiated PAO1 according to nanoparticle tracking analysis (NTA). The pyocin-related proteins are involved in OMV production in PAO1 under X-ray irradiation conditions, and that this is regulated by the key SOS gene . The OMV production was significantly impaired in the irradiated PAO1 Δ mutant, suggesting that Lys endolysin is associated with OMV production in PAO1 upon irradiation stress. Meanwhile, no significant difference in OMV production was observed between PAO1 lacking the , , or genes and the parent strain, demonstrating that the irradiation-induced OMV biosynthesis of was independent of the quinolone signal (PQS). (hide) EV-METRIC 14% (43rd percentile of all experiments on the same sample type) Reported Not reported Not applicable EV-enriched proteins Protein analysis: analysis of three or more EV-enriched proteins non EV-enriched protein Protein analysis: assessment of a non-EV-enriched protein qualitative and quantitative analysis Particle analysis: implementation of both qualitative and quantitative methods. For the quantitative method, the reporting of measured EV concentration is expected. electron microscopy images Particle analysis: inclusion of a widefield and close-up electron microscopy image density gradient Separation method: density gradient, at least as validation of results attributed to EVs EV density Separation method: reporting of obtained EV density ultracentrifugation specifics Separation method: reporting of g-forces, duration and rotor type of ultracentrifugation steps antibody specifics Protein analysis: antibody clone/reference number and dilution lysate preparation Protein analysis: lysis buffer composition Study data Sample type Cell culture supernatant Sample origin Control condition Focus vesicles Outer membrane vesicle (OMV) Separation protocol Separation protocol Gives a short, non-chronological overview of the different steps of the separation protocol. dUC = (Differential) (ultra)centrifugation DG = density gradient UF = ultrafiltration SEC = size-exclusion chromatography IAF = immuno-affinity capture (Differential) (ultra)centrifugation Filtration Protein markers EV: None non-EV: None Proteomics no Show all info Study aim Identification of content (omics approaches) Sample Species Pseudomonas aeruginosa Sample Type Cell culture supernatant EV-producing cells PAO1 delta-lys EV-harvesting Medium Serum free medium Separation Method (Differential) (ultra)centrifugation dUC: centrifugation steps Between 800 g and 10,000 g Between 10,000 g and 50,000 g Between 100,000 g and 150,000 g Pelleting performed Yes Pelleting: rotor type SW 32 Ti Pelleting: speed (g) 100000 Filtration steps Between 0.22 and 0.45 µm Characterization: Protein analysis None Protein Concentration Method Not determined Protein Yield (µg) as number of particles per million colony-forming units: 4.90E+12 Characterization: Lipid analysis No Characterization: Particle analysis NTA Particle yield as number of particles per million colony-forming units: 4.90E+12

	EV230401	14/24	Pseudomonas aeruginosa	PAO1 delta-lys	(d)(U)C Filtration	Zhang L	2020	14%
Study summary Full title Proteomic Analysis of Vesicle-Producing PAO1 Exposed to X-Ray Irradiation. All authors Zhang L, Zhao SQ, Zhang J, Sun Y, Xie YL, Liu YB, Ma CC, Jiang BG, Liao XY, Li WF, Cheng XJ, Wang ZL Journal Front Microbiol Abstract Ionizing irradiation kills pathogens by destroying nucleic acids without protein structure destructi (show more...)Ionizing irradiation kills pathogens by destroying nucleic acids without protein structure destruction. However, how pathogens respond to irradiation stress has not yet been fully elucidated. Here, we observed that PAO1 could release nucleic acids into the extracellular environment under X-ray irradiation. Using scanning electron microscopy (SEM) and transmission electron microscopy (TEM), X-ray irradiation was observed to induce outer membrane vesicle (OMV) formation in PAO1. The size distribution of the OMVs of the irradiated PAO1 was similar to that of the OMVs of the non-irradiated PAO1 according to nanoparticle tracking analysis (NTA). The pyocin-related proteins are involved in OMV production in PAO1 under X-ray irradiation conditions, and that this is regulated by the key SOS gene . The OMV production was significantly impaired in the irradiated PAO1 Δ mutant, suggesting that Lys endolysin is associated with OMV production in PAO1 upon irradiation stress. Meanwhile, no significant difference in OMV production was observed between PAO1 lacking the , , or genes and the parent strain, demonstrating that the irradiation-induced OMV biosynthesis of was independent of the quinolone signal (PQS). (hide) EV-METRIC 14% (43rd percentile of all experiments on the same sample type) Reported Not reported Not applicable EV-enriched proteins Protein analysis: analysis of three or more EV-enriched proteins non EV-enriched protein Protein analysis: assessment of a non-EV-enriched protein qualitative and quantitative analysis Particle analysis: implementation of both qualitative and quantitative methods. For the quantitative method, the reporting of measured EV concentration is expected. electron microscopy images Particle analysis: inclusion of a widefield and close-up electron microscopy image density gradient Separation method: density gradient, at least as validation of results attributed to EVs EV density Separation method: reporting of obtained EV density ultracentrifugation specifics Separation method: reporting of g-forces, duration and rotor type of ultracentrifugation steps antibody specifics Protein analysis: antibody clone/reference number and dilution lysate preparation Protein analysis: lysis buffer composition Study data Sample type Cell culture supernatant Sample origin irradiated Focus vesicles Outer membrane vesicle (OMV) Separation protocol Separation protocol Gives a short, non-chronological overview of the different steps of the separation protocol. dUC = (Differential) (ultra)centrifugation DG = density gradient UF = ultrafiltration SEC = size-exclusion chromatography IAF = immuno-affinity capture (Differential) (ultra)centrifugation Filtration Protein markers EV: None non-EV: None Proteomics no Show all info Study aim Identification of content (omics approaches) Sample Species Pseudomonas aeruginosa Sample Type Cell culture supernatant EV-producing cells PAO1 delta-lys EV-harvesting Medium Serum free medium Separation Method (Differential) (ultra)centrifugation dUC: centrifugation steps Between 800 g and 10,000 g Between 10,000 g and 50,000 g Between 100,000 g and 150,000 g Pelleting performed Yes Pelleting: rotor type SW 32 Ti Pelleting: speed (g) 100000 Filtration steps Between 0.22 and 0.45 µm Characterization: Protein analysis None Protein Concentration Method Not determined Protein Yield (µg) as number of particles per million colony-forming units: 2.50E+12 Characterization: Lipid analysis No Characterization: Particle analysis NTA EV concentration Yes Particle yield as number of particles per million colony-forming units: 2.50E+12

	EV230401	15/24	Pseudomonas aeruginosa	PAO1 delta-recA	(d)(U)C Filtration	Zhang L	2020	14%
Study summary Full title Proteomic Analysis of Vesicle-Producing PAO1 Exposed to X-Ray Irradiation. All authors Zhang L, Zhao SQ, Zhang J, Sun Y, Xie YL, Liu YB, Ma CC, Jiang BG, Liao XY, Li WF, Cheng XJ, Wang ZL Journal Front Microbiol Abstract Ionizing irradiation kills pathogens by destroying nucleic acids without protein structure destructi (show more...)Ionizing irradiation kills pathogens by destroying nucleic acids without protein structure destruction. However, how pathogens respond to irradiation stress has not yet been fully elucidated. Here, we observed that PAO1 could release nucleic acids into the extracellular environment under X-ray irradiation. Using scanning electron microscopy (SEM) and transmission electron microscopy (TEM), X-ray irradiation was observed to induce outer membrane vesicle (OMV) formation in PAO1. The size distribution of the OMVs of the irradiated PAO1 was similar to that of the OMVs of the non-irradiated PAO1 according to nanoparticle tracking analysis (NTA). The pyocin-related proteins are involved in OMV production in PAO1 under X-ray irradiation conditions, and that this is regulated by the key SOS gene . The OMV production was significantly impaired in the irradiated PAO1 Δ mutant, suggesting that Lys endolysin is associated with OMV production in PAO1 upon irradiation stress. Meanwhile, no significant difference in OMV production was observed between PAO1 lacking the , , or genes and the parent strain, demonstrating that the irradiation-induced OMV biosynthesis of was independent of the quinolone signal (PQS). (hide) EV-METRIC 14% (43rd percentile of all experiments on the same sample type) Reported Not reported Not applicable EV-enriched proteins Protein analysis: analysis of three or more EV-enriched proteins non EV-enriched protein Protein analysis: assessment of a non-EV-enriched protein qualitative and quantitative analysis Particle analysis: implementation of both qualitative and quantitative methods. For the quantitative method, the reporting of measured EV concentration is expected. electron microscopy images Particle analysis: inclusion of a widefield and close-up electron microscopy image density gradient Separation method: density gradient, at least as validation of results attributed to EVs EV density Separation method: reporting of obtained EV density ultracentrifugation specifics Separation method: reporting of g-forces, duration and rotor type of ultracentrifugation steps antibody specifics Protein analysis: antibody clone/reference number and dilution lysate preparation Protein analysis: lysis buffer composition Study data Sample type Cell culture supernatant Sample origin Control condition Focus vesicles Outer membrane vesicle (OMV) Separation protocol Separation protocol Gives a short, non-chronological overview of the different steps of the separation protocol. dUC = (Differential) (ultra)centrifugation DG = density gradient UF = ultrafiltration SEC = size-exclusion chromatography IAF = immuno-affinity capture (Differential) (ultra)centrifugation Filtration Protein markers EV: None non-EV: None Proteomics no Show all info Study aim Identification of content (omics approaches) Sample Species Pseudomonas aeruginosa Sample Type Cell culture supernatant EV-producing cells PAO1 delta-recA EV-harvesting Medium Serum free medium Separation Method (Differential) (ultra)centrifugation dUC: centrifugation steps Between 800 g and 10,000 g Between 10,000 g and 50,000 g Between 100,000 g and 150,000 g Pelleting performed Yes Pelleting: rotor type SW 32 Ti Pelleting: speed (g) 100000 Filtration steps Between 0.22 and 0.45 µm Characterization: Protein analysis None Protein Concentration Method Not determined Protein Yield (µg) as number of particles per million colony-forming units: 2.50E+12 Characterization: Lipid analysis No Characterization: Particle analysis NTA Particle yield as number of particles per million colony-forming units: 2.50E+12

	EV230401	16/24	Pseudomonas aeruginosa	PAO1 delta-recA	(d)(U)C Filtration	Zhang L	2020	14%
Study summary Full title Proteomic Analysis of Vesicle-Producing PAO1 Exposed to X-Ray Irradiation. All authors Zhang L, Zhao SQ, Zhang J, Sun Y, Xie YL, Liu YB, Ma CC, Jiang BG, Liao XY, Li WF, Cheng XJ, Wang ZL Journal Front Microbiol Abstract Ionizing irradiation kills pathogens by destroying nucleic acids without protein structure destructi (show more...)Ionizing irradiation kills pathogens by destroying nucleic acids without protein structure destruction. However, how pathogens respond to irradiation stress has not yet been fully elucidated. Here, we observed that PAO1 could release nucleic acids into the extracellular environment under X-ray irradiation. Using scanning electron microscopy (SEM) and transmission electron microscopy (TEM), X-ray irradiation was observed to induce outer membrane vesicle (OMV) formation in PAO1. The size distribution of the OMVs of the irradiated PAO1 was similar to that of the OMVs of the non-irradiated PAO1 according to nanoparticle tracking analysis (NTA). The pyocin-related proteins are involved in OMV production in PAO1 under X-ray irradiation conditions, and that this is regulated by the key SOS gene . The OMV production was significantly impaired in the irradiated PAO1 Δ mutant, suggesting that Lys endolysin is associated with OMV production in PAO1 upon irradiation stress. Meanwhile, no significant difference in OMV production was observed between PAO1 lacking the , , or genes and the parent strain, demonstrating that the irradiation-induced OMV biosynthesis of was independent of the quinolone signal (PQS). (hide) EV-METRIC 14% (43rd percentile of all experiments on the same sample type) Reported Not reported Not applicable EV-enriched proteins Protein analysis: analysis of three or more EV-enriched proteins non EV-enriched protein Protein analysis: assessment of a non-EV-enriched protein qualitative and quantitative analysis Particle analysis: implementation of both qualitative and quantitative methods. For the quantitative method, the reporting of measured EV concentration is expected. electron microscopy images Particle analysis: inclusion of a widefield and close-up electron microscopy image density gradient Separation method: density gradient, at least as validation of results attributed to EVs EV density Separation method: reporting of obtained EV density ultracentrifugation specifics Separation method: reporting of g-forces, duration and rotor type of ultracentrifugation steps antibody specifics Protein analysis: antibody clone/reference number and dilution lysate preparation Protein analysis: lysis buffer composition Study data Sample type Cell culture supernatant Sample origin irradiated Focus vesicles Outer membrane vesicle (OMV) Separation protocol Separation protocol Gives a short, non-chronological overview of the different steps of the separation protocol. dUC = (Differential) (ultra)centrifugation DG = density gradient UF = ultrafiltration SEC = size-exclusion chromatography IAF = immuno-affinity capture (Differential) (ultra)centrifugation Filtration Protein markers EV: None non-EV: None Proteomics no Show all info Study aim Identification of content (omics approaches) Sample Species Pseudomonas aeruginosa Sample Type Cell culture supernatant EV-producing cells PAO1 delta-recA EV-harvesting Medium Serum free medium Separation Method (Differential) (ultra)centrifugation dUC: centrifugation steps Between 800 g and 10,000 g Between 10,000 g and 50,000 g Between 100,000 g and 150,000 g Pelleting performed Yes Pelleting: rotor type SW 32 Ti Pelleting: speed (g) 100000 Filtration steps Between 0.22 and 0.45 µm Characterization: Protein analysis None Protein Concentration Method Not determined Protein Yield (µg) as number of particles per million colony-forming units: 1.90E+12 Characterization: Lipid analysis No Characterization: Particle analysis NTA EV concentration Yes Particle yield as number of particles per million colony-forming units: 1.90E+12

	EV230401	17/24	Pseudomonas aeruginosa	PAO1 delta-prtN	(d)(U)C Filtration	Zhang L	2020	14%
Study summary Full title Proteomic Analysis of Vesicle-Producing PAO1 Exposed to X-Ray Irradiation. All authors Zhang L, Zhao SQ, Zhang J, Sun Y, Xie YL, Liu YB, Ma CC, Jiang BG, Liao XY, Li WF, Cheng XJ, Wang ZL Journal Front Microbiol Abstract Ionizing irradiation kills pathogens by destroying nucleic acids without protein structure destructi (show more...)Ionizing irradiation kills pathogens by destroying nucleic acids without protein structure destruction. However, how pathogens respond to irradiation stress has not yet been fully elucidated. Here, we observed that PAO1 could release nucleic acids into the extracellular environment under X-ray irradiation. Using scanning electron microscopy (SEM) and transmission electron microscopy (TEM), X-ray irradiation was observed to induce outer membrane vesicle (OMV) formation in PAO1. The size distribution of the OMVs of the irradiated PAO1 was similar to that of the OMVs of the non-irradiated PAO1 according to nanoparticle tracking analysis (NTA). The pyocin-related proteins are involved in OMV production in PAO1 under X-ray irradiation conditions, and that this is regulated by the key SOS gene . The OMV production was significantly impaired in the irradiated PAO1 Δ mutant, suggesting that Lys endolysin is associated with OMV production in PAO1 upon irradiation stress. Meanwhile, no significant difference in OMV production was observed between PAO1 lacking the , , or genes and the parent strain, demonstrating that the irradiation-induced OMV biosynthesis of was independent of the quinolone signal (PQS). (hide) EV-METRIC 14% (43rd percentile of all experiments on the same sample type) Reported Not reported Not applicable EV-enriched proteins Protein analysis: analysis of three or more EV-enriched proteins non EV-enriched protein Protein analysis: assessment of a non-EV-enriched protein qualitative and quantitative analysis Particle analysis: implementation of both qualitative and quantitative methods. For the quantitative method, the reporting of measured EV concentration is expected. electron microscopy images Particle analysis: inclusion of a widefield and close-up electron microscopy image density gradient Separation method: density gradient, at least as validation of results attributed to EVs EV density Separation method: reporting of obtained EV density ultracentrifugation specifics Separation method: reporting of g-forces, duration and rotor type of ultracentrifugation steps antibody specifics Protein analysis: antibody clone/reference number and dilution lysate preparation Protein analysis: lysis buffer composition Study data Sample type Cell culture supernatant Sample origin Control condition Focus vesicles Outer membrane vesicle (OMV) Separation protocol Separation protocol Gives a short, non-chronological overview of the different steps of the separation protocol. dUC = (Differential) (ultra)centrifugation DG = density gradient UF = ultrafiltration SEC = size-exclusion chromatography IAF = immuno-affinity capture (Differential) (ultra)centrifugation Filtration Protein markers EV: None non-EV: None Proteomics no Show all info Study aim Identification of content (omics approaches) Sample Species Pseudomonas aeruginosa Sample Type Cell culture supernatant EV-producing cells PAO1 delta-prtN EV-harvesting Medium Serum free medium Separation Method (Differential) (ultra)centrifugation dUC: centrifugation steps Between 800 g and 10,000 g Between 10,000 g and 50,000 g Between 100,000 g and 150,000 g Pelleting performed Yes Pelleting: rotor type SW 32 Ti Pelleting: speed (g) 100000 Filtration steps Between 0.22 and 0.45 µm Characterization: Protein analysis None Protein Concentration Method Not determined Protein Yield (µg) as number of particles per million colony-forming units: 1.90E+12 Characterization: Lipid analysis No Characterization: Particle analysis NTA Particle yield as number of particles per million colony-forming units: 1.90E+12

	EV230401	18/24	Pseudomonas aeruginosa	PAO1 delta-prtN	(d)(U)C Filtration	Zhang L	2020	14%
Study summary Full title Proteomic Analysis of Vesicle-Producing PAO1 Exposed to X-Ray Irradiation. All authors Zhang L, Zhao SQ, Zhang J, Sun Y, Xie YL, Liu YB, Ma CC, Jiang BG, Liao XY, Li WF, Cheng XJ, Wang ZL Journal Front Microbiol Abstract Ionizing irradiation kills pathogens by destroying nucleic acids without protein structure destructi (show more...)Ionizing irradiation kills pathogens by destroying nucleic acids without protein structure destruction. However, how pathogens respond to irradiation stress has not yet been fully elucidated. Here, we observed that PAO1 could release nucleic acids into the extracellular environment under X-ray irradiation. Using scanning electron microscopy (SEM) and transmission electron microscopy (TEM), X-ray irradiation was observed to induce outer membrane vesicle (OMV) formation in PAO1. The size distribution of the OMVs of the irradiated PAO1 was similar to that of the OMVs of the non-irradiated PAO1 according to nanoparticle tracking analysis (NTA). The pyocin-related proteins are involved in OMV production in PAO1 under X-ray irradiation conditions, and that this is regulated by the key SOS gene . The OMV production was significantly impaired in the irradiated PAO1 Δ mutant, suggesting that Lys endolysin is associated with OMV production in PAO1 upon irradiation stress. Meanwhile, no significant difference in OMV production was observed between PAO1 lacking the , , or genes and the parent strain, demonstrating that the irradiation-induced OMV biosynthesis of was independent of the quinolone signal (PQS). (hide) EV-METRIC 14% (43rd percentile of all experiments on the same sample type) Reported Not reported Not applicable EV-enriched proteins Protein analysis: analysis of three or more EV-enriched proteins non EV-enriched protein Protein analysis: assessment of a non-EV-enriched protein qualitative and quantitative analysis Particle analysis: implementation of both qualitative and quantitative methods. For the quantitative method, the reporting of measured EV concentration is expected. electron microscopy images Particle analysis: inclusion of a widefield and close-up electron microscopy image density gradient Separation method: density gradient, at least as validation of results attributed to EVs EV density Separation method: reporting of obtained EV density ultracentrifugation specifics Separation method: reporting of g-forces, duration and rotor type of ultracentrifugation steps antibody specifics Protein analysis: antibody clone/reference number and dilution lysate preparation Protein analysis: lysis buffer composition Study data Sample type Cell culture supernatant Sample origin irradiated Focus vesicles Outer membrane vesicle (OMV) Separation protocol Separation protocol Gives a short, non-chronological overview of the different steps of the separation protocol. dUC = (Differential) (ultra)centrifugation DG = density gradient UF = ultrafiltration SEC = size-exclusion chromatography IAF = immuno-affinity capture (Differential) (ultra)centrifugation Filtration Protein markers EV: None non-EV: None Proteomics no Show all info Study aim Identification of content (omics approaches) Sample Species Pseudomonas aeruginosa Sample Type Cell culture supernatant EV-producing cells PAO1 delta-prtN EV-harvesting Medium Serum free medium Separation Method (Differential) (ultra)centrifugation dUC: centrifugation steps Between 800 g and 10,000 g Between 10,000 g and 50,000 g Between 100,000 g and 150,000 g Pelleting performed Yes Pelleting: rotor type SW 32 Ti Pelleting: speed (g) 100000 Filtration steps Between 0.22 and 0.45 µm Characterization: Protein analysis None Protein Concentration Method Not determined Protein Yield (µg) as number of particles per million colony-forming units: 2.00E+12 Characterization: Lipid analysis No Characterization: Particle analysis NTA EV concentration Yes Particle yield as number of particles per million colony-forming units: 2.00E+12

	EV230401	19/24	Pseudomonas aeruginosa	PAO1 delta-PA0634	(d)(U)C Filtration	Zhang L	2020	14%
Study summary Full title Proteomic Analysis of Vesicle-Producing PAO1 Exposed to X-Ray Irradiation. All authors Zhang L, Zhao SQ, Zhang J, Sun Y, Xie YL, Liu YB, Ma CC, Jiang BG, Liao XY, Li WF, Cheng XJ, Wang ZL Journal Front Microbiol Abstract Ionizing irradiation kills pathogens by destroying nucleic acids without protein structure destructi (show more...)Ionizing irradiation kills pathogens by destroying nucleic acids without protein structure destruction. However, how pathogens respond to irradiation stress has not yet been fully elucidated. Here, we observed that PAO1 could release nucleic acids into the extracellular environment under X-ray irradiation. Using scanning electron microscopy (SEM) and transmission electron microscopy (TEM), X-ray irradiation was observed to induce outer membrane vesicle (OMV) formation in PAO1. The size distribution of the OMVs of the irradiated PAO1 was similar to that of the OMVs of the non-irradiated PAO1 according to nanoparticle tracking analysis (NTA). The pyocin-related proteins are involved in OMV production in PAO1 under X-ray irradiation conditions, and that this is regulated by the key SOS gene . The OMV production was significantly impaired in the irradiated PAO1 Δ mutant, suggesting that Lys endolysin is associated with OMV production in PAO1 upon irradiation stress. Meanwhile, no significant difference in OMV production was observed between PAO1 lacking the , , or genes and the parent strain, demonstrating that the irradiation-induced OMV biosynthesis of was independent of the quinolone signal (PQS). (hide) EV-METRIC 14% (43rd percentile of all experiments on the same sample type) Reported Not reported Not applicable EV-enriched proteins Protein analysis: analysis of three or more EV-enriched proteins non EV-enriched protein Protein analysis: assessment of a non-EV-enriched protein qualitative and quantitative analysis Particle analysis: implementation of both qualitative and quantitative methods. For the quantitative method, the reporting of measured EV concentration is expected. electron microscopy images Particle analysis: inclusion of a widefield and close-up electron microscopy image density gradient Separation method: density gradient, at least as validation of results attributed to EVs EV density Separation method: reporting of obtained EV density ultracentrifugation specifics Separation method: reporting of g-forces, duration and rotor type of ultracentrifugation steps antibody specifics Protein analysis: antibody clone/reference number and dilution lysate preparation Protein analysis: lysis buffer composition Study data Sample type Cell culture supernatant Sample origin Control condition Focus vesicles Outer membrane vesicle (OMV) Separation protocol Separation protocol Gives a short, non-chronological overview of the different steps of the separation protocol. dUC = (Differential) (ultra)centrifugation DG = density gradient UF = ultrafiltration SEC = size-exclusion chromatography IAF = immuno-affinity capture (Differential) (ultra)centrifugation Filtration Protein markers EV: None non-EV: None Proteomics no Show all info Study aim Identification of content (omics approaches) Sample Species Pseudomonas aeruginosa Sample Type Cell culture supernatant EV-producing cells PAO1 delta-PA0634 EV-harvesting Medium Serum free medium Separation Method (Differential) (ultra)centrifugation dUC: centrifugation steps Between 800 g and 10,000 g Between 10,000 g and 50,000 g Between 100,000 g and 150,000 g Pelleting performed Yes Pelleting: rotor type SW 32 Ti Pelleting: speed (g) 100000 Filtration steps Between 0.22 and 0.45 µm Characterization: Protein analysis None Protein Concentration Method Not determined Protein Yield (µg) as number of particles per million colony-forming units: 2.00E+12 Characterization: Lipid analysis No Characterization: Particle analysis NTA Particle yield as number of particles per million colony-forming units: 2.00E+12

	EV230401	20/24	Pseudomonas aeruginosa	PAO1 delta-PA0634	(d)(U)C Filtration	Zhang L	2020	14%
Study summary Full title Proteomic Analysis of Vesicle-Producing PAO1 Exposed to X-Ray Irradiation. All authors Zhang L, Zhao SQ, Zhang J, Sun Y, Xie YL, Liu YB, Ma CC, Jiang BG, Liao XY, Li WF, Cheng XJ, Wang ZL Journal Front Microbiol Abstract Ionizing irradiation kills pathogens by destroying nucleic acids without protein structure destructi (show more...)Ionizing irradiation kills pathogens by destroying nucleic acids without protein structure destruction. However, how pathogens respond to irradiation stress has not yet been fully elucidated. Here, we observed that PAO1 could release nucleic acids into the extracellular environment under X-ray irradiation. Using scanning electron microscopy (SEM) and transmission electron microscopy (TEM), X-ray irradiation was observed to induce outer membrane vesicle (OMV) formation in PAO1. The size distribution of the OMVs of the irradiated PAO1 was similar to that of the OMVs of the non-irradiated PAO1 according to nanoparticle tracking analysis (NTA). The pyocin-related proteins are involved in OMV production in PAO1 under X-ray irradiation conditions, and that this is regulated by the key SOS gene . The OMV production was significantly impaired in the irradiated PAO1 Δ mutant, suggesting that Lys endolysin is associated with OMV production in PAO1 upon irradiation stress. Meanwhile, no significant difference in OMV production was observed between PAO1 lacking the , , or genes and the parent strain, demonstrating that the irradiation-induced OMV biosynthesis of was independent of the quinolone signal (PQS). (hide) EV-METRIC 14% (43rd percentile of all experiments on the same sample type) Reported Not reported Not applicable EV-enriched proteins Protein analysis: analysis of three or more EV-enriched proteins non EV-enriched protein Protein analysis: assessment of a non-EV-enriched protein qualitative and quantitative analysis Particle analysis: implementation of both qualitative and quantitative methods. For the quantitative method, the reporting of measured EV concentration is expected. electron microscopy images Particle analysis: inclusion of a widefield and close-up electron microscopy image density gradient Separation method: density gradient, at least as validation of results attributed to EVs EV density Separation method: reporting of obtained EV density ultracentrifugation specifics Separation method: reporting of g-forces, duration and rotor type of ultracentrifugation steps antibody specifics Protein analysis: antibody clone/reference number and dilution lysate preparation Protein analysis: lysis buffer composition Study data Sample type Cell culture supernatant Sample origin irradiated Focus vesicles Outer membrane vesicle (OMV) Separation protocol Separation protocol Gives a short, non-chronological overview of the different steps of the separation protocol. dUC = (Differential) (ultra)centrifugation DG = density gradient UF = ultrafiltration SEC = size-exclusion chromatography IAF = immuno-affinity capture (Differential) (ultra)centrifugation Filtration Protein markers EV: None non-EV: None Proteomics no Show all info Study aim Identification of content (omics approaches) Sample Species Pseudomonas aeruginosa Sample Type Cell culture supernatant EV-producing cells PAO1 delta-PA0634 EV-harvesting Medium Serum free medium Separation Method (Differential) (ultra)centrifugation dUC: centrifugation steps Between 800 g and 10,000 g Between 10,000 g and 50,000 g Between 100,000 g and 150,000 g Pelleting performed Yes Pelleting: rotor type SW 32 Ti Pelleting: speed (g) 100000 Filtration steps Between 0.22 and 0.45 µm Characterization: Protein analysis None Protein Concentration Method Not determined Protein Yield (µg) as number of particles per million colony-forming units: 1.20E+13 Characterization: Lipid analysis No Characterization: Particle analysis NTA EV concentration Yes Particle yield as number of particles per million colony-forming units: 1.20E+13

	EV230401	21/24	Pseudomonas aeruginosa	PAO1 delta-PA0985	(d)(U)C Filtration	Zhang L	2020	14%
Study summary Full title Proteomic Analysis of Vesicle-Producing PAO1 Exposed to X-Ray Irradiation. All authors Zhang L, Zhao SQ, Zhang J, Sun Y, Xie YL, Liu YB, Ma CC, Jiang BG, Liao XY, Li WF, Cheng XJ, Wang ZL Journal Front Microbiol Abstract Ionizing irradiation kills pathogens by destroying nucleic acids without protein structure destructi (show more...)Ionizing irradiation kills pathogens by destroying nucleic acids without protein structure destruction. However, how pathogens respond to irradiation stress has not yet been fully elucidated. Here, we observed that PAO1 could release nucleic acids into the extracellular environment under X-ray irradiation. Using scanning electron microscopy (SEM) and transmission electron microscopy (TEM), X-ray irradiation was observed to induce outer membrane vesicle (OMV) formation in PAO1. The size distribution of the OMVs of the irradiated PAO1 was similar to that of the OMVs of the non-irradiated PAO1 according to nanoparticle tracking analysis (NTA). The pyocin-related proteins are involved in OMV production in PAO1 under X-ray irradiation conditions, and that this is regulated by the key SOS gene . The OMV production was significantly impaired in the irradiated PAO1 Δ mutant, suggesting that Lys endolysin is associated with OMV production in PAO1 upon irradiation stress. Meanwhile, no significant difference in OMV production was observed between PAO1 lacking the , , or genes and the parent strain, demonstrating that the irradiation-induced OMV biosynthesis of was independent of the quinolone signal (PQS). (hide) EV-METRIC 14% (43rd percentile of all experiments on the same sample type) Reported Not reported Not applicable EV-enriched proteins Protein analysis: analysis of three or more EV-enriched proteins non EV-enriched protein Protein analysis: assessment of a non-EV-enriched protein qualitative and quantitative analysis Particle analysis: implementation of both qualitative and quantitative methods. For the quantitative method, the reporting of measured EV concentration is expected. electron microscopy images Particle analysis: inclusion of a widefield and close-up electron microscopy image density gradient Separation method: density gradient, at least as validation of results attributed to EVs EV density Separation method: reporting of obtained EV density ultracentrifugation specifics Separation method: reporting of g-forces, duration and rotor type of ultracentrifugation steps antibody specifics Protein analysis: antibody clone/reference number and dilution lysate preparation Protein analysis: lysis buffer composition Study data Sample type Cell culture supernatant Sample origin Control condition Focus vesicles Outer membrane vesicle (OMV) Separation protocol Separation protocol Gives a short, non-chronological overview of the different steps of the separation protocol. dUC = (Differential) (ultra)centrifugation DG = density gradient UF = ultrafiltration SEC = size-exclusion chromatography IAF = immuno-affinity capture (Differential) (ultra)centrifugation Filtration Protein markers EV: None non-EV: None Proteomics no Show all info Study aim Identification of content (omics approaches) Sample Species Pseudomonas aeruginosa Sample Type Cell culture supernatant EV-producing cells PAO1 delta-PA0985 EV-harvesting Medium Serum free medium Separation Method (Differential) (ultra)centrifugation dUC: centrifugation steps Between 800 g and 10,000 g Between 10,000 g and 50,000 g Between 100,000 g and 150,000 g Pelleting performed Yes Pelleting: rotor type SW 32 Ti Pelleting: speed (g) 100000 Filtration steps Between 0.22 and 0.45 µm Characterization: Protein analysis None Protein Concentration Method Not determined Protein Yield (µg) as number of particles per million colony-forming units: 1.20E+13 Characterization: Lipid analysis No Characterization: Particle analysis NTA Particle yield as number of particles per million colony-forming units: 1.20E+13

	EV230401	22/24	Pseudomonas aeruginosa	PAO1 delta-PA0985	(d)(U)C Filtration	Zhang L	2020	14%
Study summary Full title Proteomic Analysis of Vesicle-Producing PAO1 Exposed to X-Ray Irradiation. All authors Zhang L, Zhao SQ, Zhang J, Sun Y, Xie YL, Liu YB, Ma CC, Jiang BG, Liao XY, Li WF, Cheng XJ, Wang ZL Journal Front Microbiol Abstract Ionizing irradiation kills pathogens by destroying nucleic acids without protein structure destructi (show more...)Ionizing irradiation kills pathogens by destroying nucleic acids without protein structure destruction. However, how pathogens respond to irradiation stress has not yet been fully elucidated. Here, we observed that PAO1 could release nucleic acids into the extracellular environment under X-ray irradiation. Using scanning electron microscopy (SEM) and transmission electron microscopy (TEM), X-ray irradiation was observed to induce outer membrane vesicle (OMV) formation in PAO1. The size distribution of the OMVs of the irradiated PAO1 was similar to that of the OMVs of the non-irradiated PAO1 according to nanoparticle tracking analysis (NTA). The pyocin-related proteins are involved in OMV production in PAO1 under X-ray irradiation conditions, and that this is regulated by the key SOS gene . The OMV production was significantly impaired in the irradiated PAO1 Δ mutant, suggesting that Lys endolysin is associated with OMV production in PAO1 upon irradiation stress. Meanwhile, no significant difference in OMV production was observed between PAO1 lacking the , , or genes and the parent strain, demonstrating that the irradiation-induced OMV biosynthesis of was independent of the quinolone signal (PQS). (hide) EV-METRIC 14% (43rd percentile of all experiments on the same sample type) Reported Not reported Not applicable EV-enriched proteins Protein analysis: analysis of three or more EV-enriched proteins non EV-enriched protein Protein analysis: assessment of a non-EV-enriched protein qualitative and quantitative analysis Particle analysis: implementation of both qualitative and quantitative methods. For the quantitative method, the reporting of measured EV concentration is expected. electron microscopy images Particle analysis: inclusion of a widefield and close-up electron microscopy image density gradient Separation method: density gradient, at least as validation of results attributed to EVs EV density Separation method: reporting of obtained EV density ultracentrifugation specifics Separation method: reporting of g-forces, duration and rotor type of ultracentrifugation steps antibody specifics Protein analysis: antibody clone/reference number and dilution lysate preparation Protein analysis: lysis buffer composition Study data Sample type Cell culture supernatant Sample origin irradiated Focus vesicles Outer membrane vesicle (OMV) Separation protocol Separation protocol Gives a short, non-chronological overview of the different steps of the separation protocol. dUC = (Differential) (ultra)centrifugation DG = density gradient UF = ultrafiltration SEC = size-exclusion chromatography IAF = immuno-affinity capture (Differential) (ultra)centrifugation Filtration Protein markers EV: None non-EV: None Proteomics no Show all info Study aim Identification of content (omics approaches) Sample Species Pseudomonas aeruginosa Sample Type Cell culture supernatant EV-producing cells PAO1 delta-PA0985 EV-harvesting Medium Serum free medium Separation Method (Differential) (ultra)centrifugation dUC: centrifugation steps Between 800 g and 10,000 g Between 10,000 g and 50,000 g Between 100,000 g and 150,000 g Pelleting performed Yes Pelleting: rotor type SW 32 Ti Pelleting: speed (g) 100000 Filtration steps Between 0.22 and 0.45 µm Characterization: Protein analysis None Protein Concentration Method Not determined Protein Yield (µg) as number of particles per million colony-forming units: 9.00E+12 Characterization: Lipid analysis No Characterization: Particle analysis NTA EV concentration Yes Particle yield as number of particles per million colony-forming units: 9.00E+12

	EV230401	23/24	Pseudomonas aeruginosa	PAO1 delta-PA3866	(d)(U)C Filtration	Zhang L	2020	14%
Study summary Full title Proteomic Analysis of Vesicle-Producing PAO1 Exposed to X-Ray Irradiation. All authors Zhang L, Zhao SQ, Zhang J, Sun Y, Xie YL, Liu YB, Ma CC, Jiang BG, Liao XY, Li WF, Cheng XJ, Wang ZL Journal Front Microbiol Abstract Ionizing irradiation kills pathogens by destroying nucleic acids without protein structure destructi (show more...)Ionizing irradiation kills pathogens by destroying nucleic acids without protein structure destruction. However, how pathogens respond to irradiation stress has not yet been fully elucidated. Here, we observed that PAO1 could release nucleic acids into the extracellular environment under X-ray irradiation. Using scanning electron microscopy (SEM) and transmission electron microscopy (TEM), X-ray irradiation was observed to induce outer membrane vesicle (OMV) formation in PAO1. The size distribution of the OMVs of the irradiated PAO1 was similar to that of the OMVs of the non-irradiated PAO1 according to nanoparticle tracking analysis (NTA). The pyocin-related proteins are involved in OMV production in PAO1 under X-ray irradiation conditions, and that this is regulated by the key SOS gene . The OMV production was significantly impaired in the irradiated PAO1 Δ mutant, suggesting that Lys endolysin is associated with OMV production in PAO1 upon irradiation stress. Meanwhile, no significant difference in OMV production was observed between PAO1 lacking the , , or genes and the parent strain, demonstrating that the irradiation-induced OMV biosynthesis of was independent of the quinolone signal (PQS). (hide) EV-METRIC 14% (43rd percentile of all experiments on the same sample type) Reported Not reported Not applicable EV-enriched proteins Protein analysis: analysis of three or more EV-enriched proteins non EV-enriched protein Protein analysis: assessment of a non-EV-enriched protein qualitative and quantitative analysis Particle analysis: implementation of both qualitative and quantitative methods. For the quantitative method, the reporting of measured EV concentration is expected. electron microscopy images Particle analysis: inclusion of a widefield and close-up electron microscopy image density gradient Separation method: density gradient, at least as validation of results attributed to EVs EV density Separation method: reporting of obtained EV density ultracentrifugation specifics Separation method: reporting of g-forces, duration and rotor type of ultracentrifugation steps antibody specifics Protein analysis: antibody clone/reference number and dilution lysate preparation Protein analysis: lysis buffer composition Study data Sample type Cell culture supernatant Sample origin Control condition Focus vesicles Outer membrane vesicle (OMV) Separation protocol Separation protocol Gives a short, non-chronological overview of the different steps of the separation protocol. dUC = (Differential) (ultra)centrifugation DG = density gradient UF = ultrafiltration SEC = size-exclusion chromatography IAF = immuno-affinity capture (Differential) (ultra)centrifugation Filtration Protein markers EV: None non-EV: None Proteomics no Show all info Study aim Identification of content (omics approaches) Sample Species Pseudomonas aeruginosa Sample Type Cell culture supernatant EV-producing cells PAO1 delta-PA3866 EV-harvesting Medium Serum free medium Separation Method (Differential) (ultra)centrifugation dUC: centrifugation steps Between 800 g and 10,000 g Between 10,000 g and 50,000 g Between 100,000 g and 150,000 g Pelleting performed Yes Pelleting: rotor type SW 32 Ti Pelleting: speed (g) 100000 Filtration steps Between 0.22 and 0.45 µm Characterization: Protein analysis None Protein Concentration Method Not determined Protein Yield (µg) as number of particles per million colony-forming units: 9.00E+12 Characterization: Lipid analysis No Characterization: Particle analysis NTA Particle yield as number of particles per million colony-forming units: 9.00E+12

	EV230401	24/24	Pseudomonas aeruginosa	PAO1 delta-PA3866	(d)(U)C Filtration	Zhang L	2020	14%
Study summary Full title Proteomic Analysis of Vesicle-Producing PAO1 Exposed to X-Ray Irradiation. All authors Zhang L, Zhao SQ, Zhang J, Sun Y, Xie YL, Liu YB, Ma CC, Jiang BG, Liao XY, Li WF, Cheng XJ, Wang ZL Journal Front Microbiol Abstract Ionizing irradiation kills pathogens by destroying nucleic acids without protein structure destructi (show more...)Ionizing irradiation kills pathogens by destroying nucleic acids without protein structure destruction. However, how pathogens respond to irradiation stress has not yet been fully elucidated. Here, we observed that PAO1 could release nucleic acids into the extracellular environment under X-ray irradiation. Using scanning electron microscopy (SEM) and transmission electron microscopy (TEM), X-ray irradiation was observed to induce outer membrane vesicle (OMV) formation in PAO1. The size distribution of the OMVs of the irradiated PAO1 was similar to that of the OMVs of the non-irradiated PAO1 according to nanoparticle tracking analysis (NTA). The pyocin-related proteins are involved in OMV production in PAO1 under X-ray irradiation conditions, and that this is regulated by the key SOS gene . The OMV production was significantly impaired in the irradiated PAO1 Δ mutant, suggesting that Lys endolysin is associated with OMV production in PAO1 upon irradiation stress. Meanwhile, no significant difference in OMV production was observed between PAO1 lacking the , , or genes and the parent strain, demonstrating that the irradiation-induced OMV biosynthesis of was independent of the quinolone signal (PQS). (hide) EV-METRIC 14% (43rd percentile of all experiments on the same sample type) Reported Not reported Not applicable EV-enriched proteins Protein analysis: analysis of three or more EV-enriched proteins non EV-enriched protein Protein analysis: assessment of a non-EV-enriched protein qualitative and quantitative analysis Particle analysis: implementation of both qualitative and quantitative methods. For the quantitative method, the reporting of measured EV concentration is expected. electron microscopy images Particle analysis: inclusion of a widefield and close-up electron microscopy image density gradient Separation method: density gradient, at least as validation of results attributed to EVs EV density Separation method: reporting of obtained EV density ultracentrifugation specifics Separation method: reporting of g-forces, duration and rotor type of ultracentrifugation steps antibody specifics Protein analysis: antibody clone/reference number and dilution lysate preparation Protein analysis: lysis buffer composition Study data Sample type Cell culture supernatant Sample origin irradiated Focus vesicles Outer membrane vesicle (OMV) Separation protocol Separation protocol Gives a short, non-chronological overview of the different steps of the separation protocol. dUC = (Differential) (ultra)centrifugation DG = density gradient UF = ultrafiltration SEC = size-exclusion chromatography IAF = immuno-affinity capture (Differential) (ultra)centrifugation Filtration Protein markers EV: None non-EV: None Proteomics no Show all info Study aim Identification of content (omics approaches) Sample Species Pseudomonas aeruginosa Sample Type Cell culture supernatant EV-producing cells PAO1 delta-PA3866 EV-harvesting Medium Serum free medium Separation Method (Differential) (ultra)centrifugation dUC: centrifugation steps Between 800 g and 10,000 g Between 10,000 g and 50,000 g Between 100,000 g and 150,000 g Pelleting performed Yes Pelleting: rotor type SW 32 Ti Pelleting: speed (g) 100000 Filtration steps Between 0.22 and 0.45 µm Characterization: Protein analysis None Protein Concentration Method Not determined Characterization: Lipid analysis No Characterization: Particle analysis NTA EV concentration Yes Particle yield as number of particles per million colony-forming units: 1.25E+13

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EV-TRACK ID	EV230401
species	Pseudomonas aeruginosa	Pseudomonas aeruginosa	Escherichia coli	Escherichia coli	Pseudomonas aeruginosa	Pseudomonas aeruginosa	Pseudomonas aeruginosa	Pseudomonas aeruginosa	Pseudomonas aeruginosa	Pseudomonas aeruginosa	Pseudomonas aeruginosa	Pseudomonas aeruginosa	Pseudomonas aeruginosa	Pseudomonas aeruginosa	Pseudomonas aeruginosa	Pseudomonas aeruginosa	Pseudomonas aeruginosa	Pseudomonas aeruginosa	Pseudomonas aeruginosa	Pseudomonas aeruginosa	Pseudomonas aeruginosa	Pseudomonas aeruginosa	Pseudomonas aeruginosa	Pseudomonas aeruginosa
sample type	Cell culture	Cell culture	Cell culture	Cell culture	Cell culture	Cell culture	Cell culture	Cell culture	Cell culture	Cell culture	Cell culture	Cell culture	Cell culture	Cell culture	Cell culture	Cell culture	Cell culture	Cell culture	Cell culture	Cell culture	Cell culture	Cell culture	Cell culture	Cell culture
cell type	PAO1	PAO1	K12	K12	PA14	PA14	PAO1 delta-pqsR	PAO1 delta-pqsR	PAO1 delta-lasR	PAO1 delta-lasR	PAO1 delta-rhlR	PAO1 delta-rhlR	PAO1 delta-lys	PAO1 delta-lys	PAO1 delta-recA	PAO1 delta-recA	PAO1 delta-prtN	PAO1 delta-prtN	PAO1 delta-PA0634	PAO1 delta-PA0634	PAO1 delta-PA0985	PAO1 delta-PA0985	PAO1 delta-PA3866	PAO1 delta-PA3866
condition	Control condition	irradiated	Control condition	Irradiated	Control condition	irradiated	Control condition	Irradiated	Control condition	irradiated	Control condition	irradiated	Control condition	irradiated	Control condition	irradiated	Control condition	irradiated	Control condition	irradiated	Control condition	irradiated	Control condition	irradiated
separation protocol	dUC/ Filtration	dUC/ Filtration	dUC/ Filtration	dUC/ Filtration	dUC/ Filtration	dUC/ Filtration	dUC/ Filtration	dUC/ Filtration	dUC/ Filtration	dUC/ Filtration	dUC/ Filtration	dUC/ Filtration	dUC/ Filtration	dUC/ Filtration	dUC/ Filtration	dUC/ Filtration	dUC/ Filtration	dUC/ Filtration	dUC/ Filtration	dUC/ Filtration	dUC/ Filtration	dUC/ Filtration	dUC/ Filtration	dUC/ Filtration
Exp. nr.	3	4	1	2	5	6	7	8	9	10	11	12	13	14	15	16	17	18	19	20	21	22	23	24
EV-METRIC %	57	57	14	14	14	14	14	14	14	14	14	14	14	14	14	14	14	14	14	14	14	14	14	14

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