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Details	EV-TRACK ID	Experiment nr.	Species	Sample type	Separation protocol	First author	Year	EV-METRIC
	EV250039	1/2	Homo sapiens	Stool	DG Filtration (d)(U)C SEC (commercial) UF	Mishra S	2025	50%
Study summary Full title Gut microbiome-derived bacterial extracellular vesicles in patients with solid tumours. All authors Mishra S, Tejesvi MV, Hekkala J, Turunen J, Kandikanti N, Kaisanlahti A, Suokas M, Leppä S, Vihinen P, Kuitunen H, Sunela K, Koivunen J, Jukkola A, Kalashnikov I, Auvinen P, Kääriäinen OS, Peñate Medina T, Peñate Medina O, Saarnio J, Meriläinen S, Rautio T, Aro R, Häivälä R, Suojanen J, Laine M, Erawijattari PP, Lahti L, Karihtala P, Ruuska TS, Reunanen J Journal J Adv Res Abstract Gut microbiome-derived nanoparticles, known as bacterial extracellular vesicles (bEVs), have garnere (show more...)Gut microbiome-derived nanoparticles, known as bacterial extracellular vesicles (bEVs), have garnered interest as promising tools for studying the link between the gut microbiome and human health. The diverse composition of bEVs, including their proteins, mRNAs, metabolites, and lipids, makes them useful for investigating diseases such as cancer. However, conventional approaches for studying gut microbiome composition alone may not be accurate in deciphering host-gut microbiome communication. In clinical microbiome research, there is a gap in the knowledge on the role of bEVs in solid tumor patients. (hide) EV-METRIC 50% (76th 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 Stool Sample origin Patients with solid tumor Focus vesicles extracellular 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 Density gradient Filtration (Differential) (ultra)centrifugation Size-exclusion chromatography (commercial) Ultrafiltration Protein markers EV: None non-EV: None Proteomics yes EV density (g/ml) - Show all info Study aim Identification of content (omics approaches) Sample Species Homo sapiens Sample Type Stool Separation Method (Differential) (ultra)centrifugation dUC: centrifugation steps Between 10,000 g and 50,000 g Pelleting performed No Density gradient Type Discontinuous Number of initial discontinuous layers 4 Lowest density fraction 5% Highest density fraction 40% Total gradient volume, incl. sample (mL) 10 Sample volume (mL) 0.2 Orientation Top-down Speed (g) 100000 Duration (min) 1080 Fraction volume (mL) 1 Fraction processing Centrifugation Pelleting: volume per fraction 10 Pelleting: speed (g) 100000 Filtration steps Larger than 0.45 µm/ Between 0.22 and 0.45 µm Ultra filtration Cut-off size (kDa) 10 Membrane type Regenerated cellulose Other Name other separation method Size-exclusion chromatography (commercial) Characterization: Protein analysis Protein Concentration Method Not determined Proteomics database PRIDE Characterization: Lipid analysis No Characterization: Particle analysis NTA Report type Mean Reported size (nm) 202 EV concentration Yes Particle yield particles per milliliter of starting sample: 1.08E+08 EM EM-type Transmission-EM Image type Wide-field

	EV250039	2/2	Homo sapiens	Stool	DG Filtration (d)(U)C SEC (commercial)	Mishra S	2025	50%
Study summary Full title Gut microbiome-derived bacterial extracellular vesicles in patients with solid tumours. All authors Mishra S, Tejesvi MV, Hekkala J, Turunen J, Kandikanti N, Kaisanlahti A, Suokas M, Leppä S, Vihinen P, Kuitunen H, Sunela K, Koivunen J, Jukkola A, Kalashnikov I, Auvinen P, Kääriäinen OS, Peñate Medina T, Peñate Medina O, Saarnio J, Meriläinen S, Rautio T, Aro R, Häivälä R, Suojanen J, Laine M, Erawijattari PP, Lahti L, Karihtala P, Ruuska TS, Reunanen J Journal J Adv Res Abstract Gut microbiome-derived nanoparticles, known as bacterial extracellular vesicles (bEVs), have garnere (show more...)Gut microbiome-derived nanoparticles, known as bacterial extracellular vesicles (bEVs), have garnered interest as promising tools for studying the link between the gut microbiome and human health. The diverse composition of bEVs, including their proteins, mRNAs, metabolites, and lipids, makes them useful for investigating diseases such as cancer. However, conventional approaches for studying gut microbiome composition alone may not be accurate in deciphering host-gut microbiome communication. In clinical microbiome research, there is a gap in the knowledge on the role of bEVs in solid tumor patients. (hide) EV-METRIC 50% (76th 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 Stool Sample origin Control condition Focus vesicles extracellular 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 Density gradient Filtration (Differential) (ultra)centrifugation Size-exclusion chromatography (commercial) Protein markers EV: None non-EV: None Proteomics yes EV density (g/ml) - Show all info Study aim Identification of content (omics approaches) Sample Species Homo sapiens Sample Type Stool Separation Method (Differential) (ultra)centrifugation dUC: centrifugation steps Between 10,000 g and 50,000 g Pelleting performed No Density gradient Type Discontinuous Number of initial discontinuous layers 4 Lowest density fraction 5% Highest density fraction 40% Total gradient volume, incl. sample (mL) 10 Sample volume (mL) 0.2 Orientation Top-down Speed (g) 100000 Duration (min) 1080 Fraction volume (mL) 1 Fraction processing Centrifugation Pelleting: volume per fraction 10 Pelleting: speed (g) 100000 Filtration steps Larger than 0.45 µm/ Between 0.22 and 0.45 µm Ultra filtration Cut-off size (kDa) 10 Membrane type Regenerated cellulose Other Name other separation method Size-exclusion chromatography (commercial) Characterization: Protein analysis Protein Concentration Method Not determined Proteomics database PRIDE Characterization: Lipid analysis No Characterization: Particle analysis NTA Report type Mean Reported size (nm) 168.9 EV concentration Yes Particle yield particles per milliliter of starting sample: 2.52E+08 EM EM-type Transmission-EM Image type Wide-field

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EV-TRACK ID	EV250039
species	Homo sapiens
sample type	Stool
condition	Patients with solid tumor	Control condition
separation protocol	Density gradient/ Filtration/ dUC/ Size-exclusion chromatography (commercial)/ Ultrafiltration	Density gradient/ Filtration/ dUC/ Size-exclusion chromatography (commercial)
Exp. nr.	1	2
EV-METRIC %	50	50