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Details	EV-TRACK ID	Experiment nr.	Species	Sample type	Separation protocol	First author	Year	EV-METRIC
	EV240113	1/6	Escherichia coli	E44Δ	(d)(U)C UF Dialysis	Allahghadry T	2022	33%
Study summary Full title Clarification of large-volume bacterial cultures using a centrifuge-free protocol. All authors Allahghadry T, Bojesen AM, Whitehead BJ, Antenucci F Journal J Appl Microbiol Abstract To provide a reliable, reproducible and centrifuge-free filtration protocol for clarification of lar (show more...)To provide a reliable, reproducible and centrifuge-free filtration protocol for clarification of large volumes of bacterial cultures. (hide) EV-METRIC 33% (74th 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 mutant strain (ST117 O78:H4) Focus vesicles Outer Membrane Vesicle 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 Ultrafiltration Dialysis Protein markers EV: None non-EV: None Proteomics no Show all info Study aim Technical analysis comparing/optimizing EV-related methods Sample Species Escherichia coli Sample Type Cell culture supernatant EV-producing cells E44Δ EV-harvesting Medium Serum free medium Separation Method (Differential) (ultra)centrifugation dUC: centrifugation steps Between 800 g and 10,000 g Pelleting performed No Ultra filtration Cut-off size (kDa) 100 Membrane type Polyethersulfone (PES) Other Name other separation method Dialysis Characterization: Protein analysis Protein Concentration Method Fluorometric assay Protein Yield (µg) per microliter of starting sample Detected EV-associated proteins None Not detected EV-associated proteins None Detected contaminants None Not detected contaminants None Characterization: Lipid analysis No Characterization: Particle analysis NTA Report type Mean Reported size (nm) 95.9 (±1.0) and 90.4 (±0.9) EV concentration Yes Particle yield particles per milliliter of starting sample: 2.64 × 10^12 (±8.6 × 10^10) and 1.44 × 10^12 (±1.4 × 10^11) EM EM-type Cryo-EM Image type Wide-field Extra information - filtration step of separation protocol: The pore size of the filter was 0.45 µm, I reported this as ‘between 0.22 and 0.45 µm’.

	EV240113	2/6	Escherichia coli	E44Δ	Filtration UF Dialysis Prefiltration treatment: diatomaceous earth (20 g/L)	Allahghadry T	2022	33%
Study summary Full title Clarification of large-volume bacterial cultures using a centrifuge-free protocol. All authors Allahghadry T, Bojesen AM, Whitehead BJ, Antenucci F Journal J Appl Microbiol Abstract To provide a reliable, reproducible and centrifuge-free filtration protocol for clarification of lar (show more...)To provide a reliable, reproducible and centrifuge-free filtration protocol for clarification of large volumes of bacterial cultures. (hide) EV-METRIC 33% (74th 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 mutant strain (ST117 O78:H4) Focus vesicles Outer Membrane Vesicle 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 Filtration Ultrafiltration Dialysis Prefiltration treatment: diatomaceous earth (20 g/L) Protein markers EV: None non-EV: None Proteomics no Show all info Study aim Technical analysis comparing/optimizing EV-related methods Sample Species Escherichia coli Sample Type Cell culture supernatant EV-producing cells E44Δ EV-harvesting Medium Serum free medium Separation Method Filtration steps 0.45µm > x > 0.22µm, Ultra filtration Cut-off size (kDa) 100 Membrane type Polyethersulfone (PES) Other Name other separation method Dialysis Other Name other separation method Prefiltration treatment: diatomaceous earth (20 g/L) Characterization: Protein analysis Protein Concentration Method Fluorometric assay Protein Yield (µg) per microliter of starting sample Detected EV-associated proteins None Not detected EV-associated proteins None Detected contaminants None Not detected contaminants None Characterization: Lipid analysis No Characterization: Particle analysis NTA Report type Mean Reported size (nm) 96.0 (±1.6) and 96.2 (±1.2) EV concentration Yes Particle yield particles per milliliter of starting sample: 2.32 × 10^12 (±3.2 × 10^11) and 3.32 × 10^12 (±2.2 × 10^11) EM EM-type Cryo-EM Image type Wide-field

	EV240113	3/6	Escherichia coli	E44Δ	Filtration UF Dialysis Prefiltration treatment: diatomaceous earth (40 g/L)	Allahghadry T	2022	33%
Study summary Full title Clarification of large-volume bacterial cultures using a centrifuge-free protocol. All authors Allahghadry T, Bojesen AM, Whitehead BJ, Antenucci F Journal J Appl Microbiol Abstract To provide a reliable, reproducible and centrifuge-free filtration protocol for clarification of lar (show more...)To provide a reliable, reproducible and centrifuge-free filtration protocol for clarification of large volumes of bacterial cultures. (hide) EV-METRIC 33% (74th 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 mutant strain (ST117 O78:H4) Focus vesicles Outer Membrane Vesicle 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 Filtration Ultrafiltration Dialysis Prefiltration treatment: diatomaceous earth (40 g/L) Protein markers EV: None non-EV: None Proteomics no Show all info Study aim Technical analysis comparing/optimizing EV-related methods Sample Species Escherichia coli Sample Type Cell culture supernatant EV-producing cells E44Δ EV-harvesting Medium Serum free medium Separation Method Filtration steps 0.45µm > x > 0.22µm, Ultra filtration Cut-off size (kDa) 100 Membrane type Polyethersulfone (PES) Other Name other separation method Dialysis Other Name other separation method Prefiltration treatment: diatomaceous earth (40 g/L) Characterization: Protein analysis Protein Concentration Method Fluorometric assay Protein Yield (µg) per microliter of starting sample Detected EV-associated proteins None Not detected EV-associated proteins None Detected contaminants None Not detected contaminants None Characterization: Lipid analysis No Characterization: Particle analysis NTA Report type Mean Reported size (nm) 91.3 (±0.8) and 115.1 (±4.1) EV concentration Yes Particle yield particles per milliliter of starting sample: 2.67 × 10^12 (±1.5 × 10^11) and 2.49 × 10^12 (±3.9 × 10^11) EM EM-type Cryo-EM Image type Wide-field

	EV240113	4/6	Escherichia coli	E44Δ	Filtration UF Dialysis Prefiltration treatment: diatomaceous earth (40 g/L)	Allahghadry T	2022	33%
Study summary Full title Clarification of large-volume bacterial cultures using a centrifuge-free protocol. All authors Allahghadry T, Bojesen AM, Whitehead BJ, Antenucci F Journal J Appl Microbiol Abstract To provide a reliable, reproducible and centrifuge-free filtration protocol for clarification of lar (show more...)To provide a reliable, reproducible and centrifuge-free filtration protocol for clarification of large volumes of bacterial cultures. (hide) EV-METRIC 33% (74th 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 mutant strain (ST117 O78:H4) Focus vesicles Outer Membrane Vesicle 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 Filtration Ultrafiltration Dialysis Prefiltration treatment: diatomaceous earth (40 g/L) Protein markers EV: None non-EV: None Proteomics no Show all info Study aim Technical analysis comparing/optimizing EV-related methods Sample Species Escherichia coli Sample Type Cell culture supernatant EV-producing cells E44Δ EV-harvesting Medium Serum free medium Separation Method Filtration steps 0.22µm or 0.2µm Ultra filtration Cut-off size (kDa) 100 Membrane type Polyethersulfone (PES) Other Name other separation method Dialysis Other Name other separation method Prefiltration treatment: diatomaceous earth (40 g/L) Characterization: Protein analysis Protein Concentration Method Fluorometric assay Protein Yield (µg) per microliter of starting sample Detected EV-associated proteins None Not detected EV-associated proteins None Detected contaminants None Not detected contaminants None Characterization: Lipid analysis No Characterization: Particle analysis NTA Report type Mean EV concentration Yes Particle yield particles per milliliter of starting sample: 4.47 × 10^12 (±3.6 × 10^11) EM EM-type Cryo-EM Image type Wide-field

	EV240113	5/6	Escherichia coli	E44Δ	Filtration UF Dialysis Prefiltration treatment: diatomaceous earth (80 g/L)	Allahghadry T	2022	33%
Study summary Full title Clarification of large-volume bacterial cultures using a centrifuge-free protocol. All authors Allahghadry T, Bojesen AM, Whitehead BJ, Antenucci F Journal J Appl Microbiol Abstract To provide a reliable, reproducible and centrifuge-free filtration protocol for clarification of lar (show more...)To provide a reliable, reproducible and centrifuge-free filtration protocol for clarification of large volumes of bacterial cultures. (hide) EV-METRIC 33% (74th 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 mutant strain (ST117 O78:H4) Focus vesicles Outer Membrane Vesicle 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 Filtration Ultrafiltration Dialysis Prefiltration treatment: diatomaceous earth (80 g/L) Protein markers EV: None non-EV: None Proteomics no Show all info Study aim Technical analysis comparing/optimizing EV-related methods Sample Species Escherichia coli Sample Type Cell culture supernatant EV-producing cells E44Δ EV-harvesting Medium Serum free medium Separation Method Filtration steps 0.22µm or 0.2µm Ultra filtration Cut-off size (kDa) 100 Membrane type Polyethersulfone (PES) Other Name other separation method Dialysis Other Name other separation method Prefiltration treatment: diatomaceous earth (80 g/L) Characterization: Protein analysis Protein Concentration Method Fluorometric assay Protein Yield (µg) per microliter of starting sample Detected EV-associated proteins None Not detected EV-associated proteins None Detected contaminants None Not detected contaminants None Characterization: Lipid analysis No Characterization: Particle analysis NTA Report type Mean EV concentration Yes Particle yield particles per milliliter of starting sample: 4.04 × 10^12 (±2.5 × 10^11) EM EM-type Cryo-EM Image type Wide-field

	EV240113	6/6	Escherichia coli	E44Δ	Filtration UF Dialysis Prefiltration treatment: diatomaceous earth (80 g/L)	Allahghadry T	2022	33%
Study summary Full title Clarification of large-volume bacterial cultures using a centrifuge-free protocol. All authors Allahghadry T, Bojesen AM, Whitehead BJ, Antenucci F Journal J Appl Microbiol Abstract To provide a reliable, reproducible and centrifuge-free filtration protocol for clarification of lar (show more...)To provide a reliable, reproducible and centrifuge-free filtration protocol for clarification of large volumes of bacterial cultures. (hide) EV-METRIC 33% (74th 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 mutant strain (ST117 O78:H4) Focus vesicles Outer Membrane Vesicle 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 Filtration Ultrafiltration Dialysis Prefiltration treatment: diatomaceous earth (80 g/L) Protein markers EV: None non-EV: None Proteomics no Show all info Study aim Technical analysis comparing/optimizing EV-related methods Sample Species Escherichia coli Sample Type Cell culture supernatant EV-producing cells E44Δ EV-harvesting Medium Serum free medium Separation Method Filtration steps 0.22µm or 0.2µm Ultra filtration Cut-off size (kDa) 10 Membrane type Regenerated cellulose Other Name other separation method Dialysis Other Name other separation method Prefiltration treatment: diatomaceous earth (80 g/L) Characterization: Protein analysis Protein Concentration Method Fluorometric assay Protein Yield (µg) per microliter of starting sample Detected EV-associated proteins None Not detected EV-associated proteins None Detected contaminants None Not detected contaminants None Characterization: Lipid analysis No Characterization: Particle analysis NTA Report type Mean EV concentration Yes Particle yield particles per milliliter of starting sample: 3.59 × 10^12 (±1.7 × 10^11) EM EM-type Cryo-EM Image type Wide-field

	EV240113	7/6	NA	NA	NA	Allahghadry T	2022	0%
Study summary Full title Clarification of large-volume bacterial cultures using a centrifuge-free protocol. All authors Allahghadry T, Bojesen AM, Whitehead BJ, Antenucci F Journal J Appl Microbiol Abstract To provide a reliable, reproducible and centrifuge-free filtration protocol for clarification of lar (show more...)To provide a reliable, reproducible and centrifuge-free filtration protocol for clarification of large volumes of bacterial cultures. (hide) EV-METRIC 0% (median: 14% 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 NA Sample origin NA Focus vesicles 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 NA Protein markers EV: None non-EV: None Proteomics no Show all info Study aim Technical analysis comparing/optimizing EV-related methods Sample Species NA Sample Type NA Separation Method Other Name other separation method NA Characterization: Lipid analysis No

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EV-TRACK ID	EV240113
species	Escherichia coli	Escherichia coli	Escherichia coli	Escherichia coli	Escherichia coli	Escherichia coli	NA
sample type	Cell culture	Cell culture	Cell culture	Cell culture	Cell culture	Cell culture	NA

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