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Details	EV-TRACK ID	Experiment nr.	Species	Sample type	Separation protocol	First author	Year	EV-METRIC
	EV220300	3/18	Homo sapiens	MCF7	UF (d)(U)C Filtration DG SEC (non-commercial)	Pinheiro C	2024	100%
Study summary Full title Identification and validation of extracellular vesicle reference genes for the normalization of RT-qPCR data. All authors Pinheiro C, Guilbert N, Lippens L, Roux Q, Boiy R, Fischer S, Van Dorpe S, De Craene B, Berx G, Boterberg T, Sys G, Denys H, Miinalainen I, Mestdagh P, Vandesompele J, De Wever O, Hendrix A Journal J Extracell Vesicles Abstract Extracellular vesicles (EVs) contain a plethora of biomolecules, including nucleic acids, with diver (show more...)Extracellular vesicles (EVs) contain a plethora of biomolecules, including nucleic acids, with diverse diagnostic and therapeutic application potential. Although reverse transcription-quantitative PCR (RT-qPCR) is the most widely applied laboratory technique to evaluate gene expression, its applicability in EV research is challenged by the lack of universal and stably present reference genes (RGs). In this study, we identify, validate and establish SNRPG, OST4, TOMM7 and NOP10 as RGs for the normalization of EV-associated genes by RT-qPCR. We show the stable presence of SNRPG, OST4, TOMM7 and NOP10 in multiple cell lines and their secreted EVs (n = 12) under different (patho)physiological conditions as well as in human-derived biofluids (n = 3). Enzymatic treatments confirm the presence of SNRPG, OST4, TOMM7 and NOP10 inside EVs. In addition, the four EV-associated RGs are stably detected in a size-range of EV subpopulations. RefFinder analysis reveals that SNRPG, OST4, TOMM7 and NOP10 are more stable compared to RGs established specifically for cultured cells or tissues such as HMBS, YWHAZ, SDHA and GAPDH. In summary, we present four universal and stably present EV-associated RGs to enable normalization and thus steer the implementation of RT-qPCR for the analysis of EV-associated RNA cargo for research or clinical applications. (hide) EV-METRIC 100% (99th 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 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 Ultrafiltration (Differential) (ultra)centrifugation Filtration Density gradient Size-exclusion chromatography (non-commercial) Protein markers EV: Alix/ CD9/ Flotillin-1/ TSG101/ Syntenin non-EV: Argonaute 2 Proteomics no EV density (g/ml) 1.09-1.11 Show all info Study aim Validation of standards Sample Species Homo sapiens Sample Type Cell culture supernatant EV-producing cells MCF7 EV-harvesting Medium EV-depleted medium Preparation of EDS >=18h at >= 100,000g Cell viability (%) 96 Cell count 4.43e8 Separation Method (Differential) (ultra)centrifugation dUC: centrifugation steps Below or equal to 800 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) 15.5 Sample volume (mL) 1 Orientation Top-down Speed (g) 100000 Duration (min) 1080 Fraction volume (mL) 1 Fraction processing Centrifugation Pelleting: volume per fraction 16 Pelleting: speed (g) 100000 Filtration steps Between 0.22 and 0.45 _m Ultra filtration Cut-off size (kDa) 10 kDa Membrane type Regenerated cellulose Size-exclusion chromatography Resin type EV-subtype Distinction between multiple subtypes Size Used subtypes 120-250 Characterization: Protein analysis Protein Concentration Method Not determined Protein Yield (µg) particles per milliliter of starting sample: 1.54E11-2.60E11 Western Blot Detected EV-associated proteins Alix/ CD9/ Flotillinð1/ TSG101/ Syntenin Not detected contaminants Argonauteð2 Characterization: RNA analysis RNA analysis Type (RT)(q)PCR Proteinase treatment Yes Moment of Proteinase treatment After Proteinase type Proteinase K Proteinase concentration 2 RNAse treatment Yes RNAse type RNase A RNAse concentration 8 Characterization: Lipid analysis No Characterization: Particle analysis NTA Report type Mean Reported size (nm) 125.7-134.7 EV concentration Yes Particle yield particles per milliliter of starting sample: 1.54E11-2.60E11 EM EM-type Transmission-EM Image type Wide-field

	EV220300	4/18	Homo sapiens	A549	UF (d)(U)C Filtration DG	Pinheiro C	2024	89%
Study summary Full title Identification and validation of extracellular vesicle reference genes for the normalization of RT-qPCR data. All authors Pinheiro C, Guilbert N, Lippens L, Roux Q, Boiy R, Fischer S, Van Dorpe S, De Craene B, Berx G, Boterberg T, Sys G, Denys H, Miinalainen I, Mestdagh P, Vandesompele J, De Wever O, Hendrix A Journal J Extracell Vesicles Abstract Extracellular vesicles (EVs) contain a plethora of biomolecules, including nucleic acids, with diver (show more...)Extracellular vesicles (EVs) contain a plethora of biomolecules, including nucleic acids, with diverse diagnostic and therapeutic application potential. Although reverse transcription-quantitative PCR (RT-qPCR) is the most widely applied laboratory technique to evaluate gene expression, its applicability in EV research is challenged by the lack of universal and stably present reference genes (RGs). In this study, we identify, validate and establish SNRPG, OST4, TOMM7 and NOP10 as RGs for the normalization of EV-associated genes by RT-qPCR. We show the stable presence of SNRPG, OST4, TOMM7 and NOP10 in multiple cell lines and their secreted EVs (n = 12) under different (patho)physiological conditions as well as in human-derived biofluids (n = 3). Enzymatic treatments confirm the presence of SNRPG, OST4, TOMM7 and NOP10 inside EVs. In addition, the four EV-associated RGs are stably detected in a size-range of EV subpopulations. RefFinder analysis reveals that SNRPG, OST4, TOMM7 and NOP10 are more stable compared to RGs established specifically for cultured cells or tissues such as HMBS, YWHAZ, SDHA and GAPDH. In summary, we present four universal and stably present EV-associated RGs to enable normalization and thus steer the implementation of RT-qPCR for the analysis of EV-associated RNA cargo for research or clinical applications. (hide) EV-METRIC 89% (99th 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 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 Ultrafiltration (Differential) (ultra)centrifugation Filtration Density gradient Protein markers EV: Alix/ CD9/ TSG101 non-EV: None Proteomics no EV density (g/ml) 1.09-1.11 Show all info Study aim Validation of standards Sample Species Homo sapiens Sample Type Cell culture supernatant EV-producing cells A549 EV-harvesting Medium EV-depleted medium Preparation of EDS >=18h at >= 100,000g Cell viability (%) 93 Cell count 1.09e8 Separation Method (Differential) (ultra)centrifugation dUC: centrifugation steps Below or equal to 800 g Between 100,000 g and 150,000 g Pelleting performed Yes Pelleting: rotor type SW32.1 Ti Pelleting: speed (g) 100000 Density gradient Type Discontinuous Number of initial discontinuous layers 4 Lowest density fraction 5% Highest density fraction 40% Total gradient volume, incl. sample (mL) 15.5 Sample volume (mL) 1 Orientation Top-down Speed (g) 100000 Duration (min) 1080 Fraction volume (mL) 1 Fraction processing Centrifugation Pelleting: volume per fraction 16 Pelleting: speed (g) 100000 Filtration steps Between 0.22 and 0.45 _m Ultra filtration Cut-off size (kDa) 10 kDa Membrane type Regenerated cellulose Size-exclusion chromatography Resin type Characterization: Protein analysis Protein Concentration Method Not determined Protein Yield (µg) particles per milliliter of starting sample: 9.88E10 Western Blot Detected EV-associated proteins Alix/ CD9/ TSG101 Characterization: RNA analysis RNA analysis Type (RT)(q)PCR Proteinase treatment No RNAse treatment No Characterization: Lipid analysis No Characterization: Particle analysis NTA Report type Mean Reported size (nm) 186.1 EV concentration Yes Particle yield particles per milliliter of starting sample: 9.88E10 EM EM-type Transmission-EM Image type Close-up, Wide-field

	EV220300	7/18	Homo sapiens	CT5.3hTeRT	UF (d)(U)C Filtration DG SEC (non-commercial)	Pinheiro C	2024	63%
Study summary Full title Identification and validation of extracellular vesicle reference genes for the normalization of RT-qPCR data. All authors Pinheiro C, Guilbert N, Lippens L, Roux Q, Boiy R, Fischer S, Van Dorpe S, De Craene B, Berx G, Boterberg T, Sys G, Denys H, Miinalainen I, Mestdagh P, Vandesompele J, De Wever O, Hendrix A Journal J Extracell Vesicles Abstract Extracellular vesicles (EVs) contain a plethora of biomolecules, including nucleic acids, with diver (show more...)Extracellular vesicles (EVs) contain a plethora of biomolecules, including nucleic acids, with diverse diagnostic and therapeutic application potential. Although reverse transcription-quantitative PCR (RT-qPCR) is the most widely applied laboratory technique to evaluate gene expression, its applicability in EV research is challenged by the lack of universal and stably present reference genes (RGs). In this study, we identify, validate and establish SNRPG, OST4, TOMM7 and NOP10 as RGs for the normalization of EV-associated genes by RT-qPCR. We show the stable presence of SNRPG, OST4, TOMM7 and NOP10 in multiple cell lines and their secreted EVs (n = 12) under different (patho)physiological conditions as well as in human-derived biofluids (n = 3). Enzymatic treatments confirm the presence of SNRPG, OST4, TOMM7 and NOP10 inside EVs. In addition, the four EV-associated RGs are stably detected in a size-range of EV subpopulations. RefFinder analysis reveals that SNRPG, OST4, TOMM7 and NOP10 are more stable compared to RGs established specifically for cultured cells or tissues such as HMBS, YWHAZ, SDHA and GAPDH. In summary, we present four universal and stably present EV-associated RGs to enable normalization and thus steer the implementation of RT-qPCR for the analysis of EV-associated RNA cargo for research or clinical applications. (hide) EV-METRIC 63% (93rd 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 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 Ultrafiltration (Differential) (ultra)centrifugation Filtration Density gradient Size-exclusion chromatography (non-commercial) Protein markers EV: Alix/ TSG101/ Flotillin-1/ Syntenin-1/ CD9 non-EV: None Proteomics no EV density (g/ml) 1.09-1.11 Show all info Study aim Validation of standards Sample Species Homo sapiens Sample Type Cell culture supernatant EV-producing cells CT5.3hTeRT EV-harvesting Medium EV-depleted medium Preparation of EDS >=18h at >= 100,000g Separation Method (Differential) (ultra)centrifugation dUC: centrifugation steps Below or equal to 800 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) 15.5 Sample volume (mL) 1 Orientation Top-down Speed (g) 100000 Duration (min) 1080 Fraction volume (mL) 1 Fraction processing Centrifugation Pelleting: volume per fraction 16 Pelleting: speed (g) 100000 Filtration steps Between 0.22 and 0.45 _m Ultra filtration Cut-off size (kDa) 10 kDa Membrane type Regenerated cellulose Size-exclusion chromatography Total column volume (mL) 10 Sample volume/column (mL) 2 Resin type Sepharose CL-2B Characterization: Protein analysis Protein Concentration Method Not determined Protein Yield (µg) particles per milliliter of starting sample: 2.10E10-8.93E10 Characterization: RNA analysis RNA analysis Type (RT)(q)PCR Proteinase treatment No RNAse treatment No Characterization: Lipid analysis No Characterization: Particle analysis NTA Report type Mean Reported size (nm) 139.6-150.4 EV concentration Yes Particle yield particles per milliliter of starting sample: 2.10E10-8.93E10

	EV220300	8/18	Homo sapiens	CT5.3hTeRT	UF (d)(U)C Filtration DG SEC (non-commercial)	Pinheiro C	2024	63%
Study summary Full title Identification and validation of extracellular vesicle reference genes for the normalization of RT-qPCR data. All authors Pinheiro C, Guilbert N, Lippens L, Roux Q, Boiy R, Fischer S, Van Dorpe S, De Craene B, Berx G, Boterberg T, Sys G, Denys H, Miinalainen I, Mestdagh P, Vandesompele J, De Wever O, Hendrix A Journal J Extracell Vesicles Abstract Extracellular vesicles (EVs) contain a plethora of biomolecules, including nucleic acids, with diver (show more...)Extracellular vesicles (EVs) contain a plethora of biomolecules, including nucleic acids, with diverse diagnostic and therapeutic application potential. Although reverse transcription-quantitative PCR (RT-qPCR) is the most widely applied laboratory technique to evaluate gene expression, its applicability in EV research is challenged by the lack of universal and stably present reference genes (RGs). In this study, we identify, validate and establish SNRPG, OST4, TOMM7 and NOP10 as RGs for the normalization of EV-associated genes by RT-qPCR. We show the stable presence of SNRPG, OST4, TOMM7 and NOP10 in multiple cell lines and their secreted EVs (n = 12) under different (patho)physiological conditions as well as in human-derived biofluids (n = 3). Enzymatic treatments confirm the presence of SNRPG, OST4, TOMM7 and NOP10 inside EVs. In addition, the four EV-associated RGs are stably detected in a size-range of EV subpopulations. RefFinder analysis reveals that SNRPG, OST4, TOMM7 and NOP10 are more stable compared to RGs established specifically for cultured cells or tissues such as HMBS, YWHAZ, SDHA and GAPDH. In summary, we present four universal and stably present EV-associated RGs to enable normalization and thus steer the implementation of RT-qPCR for the analysis of EV-associated RNA cargo for research or clinical applications. (hide) EV-METRIC 63% (93rd 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 10Gy single dose 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 Ultrafiltration (Differential) (ultra)centrifugation Filtration Density gradient Size-exclusion chromatography (non-commercial) Protein markers EV: Alix/ TSG101/ Flotillin-1/ Syntenin-1/ CD9 non-EV: None Proteomics no EV density (g/ml) 1.09-1.11 Show all info Study aim Validation of standards Sample Species Homo sapiens Sample Type Cell culture supernatant EV-producing cells CT5.3hTeRT EV-harvesting Medium EV-depleted medium Preparation of EDS >=18h at >= 100,000g Separation Method (Differential) (ultra)centrifugation dUC: centrifugation steps Below or equal to 800 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) 15.5 Sample volume (mL) 1 Orientation Top-down Speed (g) 100000 Duration (min) 1080 Fraction volume (mL) 1 Fraction processing Centrifugation Pelleting: volume per fraction 16 Pelleting: speed (g) 100000 Filtration steps Between 0.22 and 0.45 _m Ultra filtration Cut-off size (kDa) 10 kDa Membrane type Regenerated cellulose Size-exclusion chromatography Total column volume (mL) 10 Sample volume/column (mL) 2 Resin type Sepharose CL-2B Characterization: Protein analysis Protein Concentration Method Not determined Protein Yield (µg) particles per milliliter of starting sample: 2.10E10-8.93E10 Characterization: RNA analysis RNA analysis Type (RT)(q)PCR Proteinase treatment No RNAse treatment No Characterization: Lipid analysis No Characterization: Particle analysis NTA Report type Mean Reported size (nm) 139.6-150.4 EV concentration Yes Particle yield particles per milliliter of starting sample: 2.10E10-8.93E10

	EV220300	12/18	Homo sapiens	PANC1	UF (d)(U)C Filtration DG	Pinheiro C	2024	57%
Study summary Full title Identification and validation of extracellular vesicle reference genes for the normalization of RT-qPCR data. All authors Pinheiro C, Guilbert N, Lippens L, Roux Q, Boiy R, Fischer S, Van Dorpe S, De Craene B, Berx G, Boterberg T, Sys G, Denys H, Miinalainen I, Mestdagh P, Vandesompele J, De Wever O, Hendrix A Journal J Extracell Vesicles Abstract Extracellular vesicles (EVs) contain a plethora of biomolecules, including nucleic acids, with diver (show more...)Extracellular vesicles (EVs) contain a plethora of biomolecules, including nucleic acids, with diverse diagnostic and therapeutic application potential. Although reverse transcription-quantitative PCR (RT-qPCR) is the most widely applied laboratory technique to evaluate gene expression, its applicability in EV research is challenged by the lack of universal and stably present reference genes (RGs). In this study, we identify, validate and establish SNRPG, OST4, TOMM7 and NOP10 as RGs for the normalization of EV-associated genes by RT-qPCR. We show the stable presence of SNRPG, OST4, TOMM7 and NOP10 in multiple cell lines and their secreted EVs (n = 12) under different (patho)physiological conditions as well as in human-derived biofluids (n = 3). Enzymatic treatments confirm the presence of SNRPG, OST4, TOMM7 and NOP10 inside EVs. In addition, the four EV-associated RGs are stably detected in a size-range of EV subpopulations. RefFinder analysis reveals that SNRPG, OST4, TOMM7 and NOP10 are more stable compared to RGs established specifically for cultured cells or tissues such as HMBS, YWHAZ, SDHA and GAPDH. In summary, we present four universal and stably present EV-associated RGs to enable normalization and thus steer the implementation of RT-qPCR for the analysis of EV-associated RNA cargo for research or clinical applications. (hide) EV-METRIC 57% (92nd 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 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 Ultrafiltration (Differential) (ultra)centrifugation Filtration Density gradient Protein markers EV: None non-EV: None Proteomics no EV density (g/ml) 1.09-1.11 Show all info Study aim Validation of standards Sample Species Homo sapiens Sample Type Cell culture supernatant EV-producing cells PANC1 EV-harvesting Medium EV-depleted medium Preparation of EDS >=18h at >= 100,000g Cell viability (%) 92 Cell count 2.06e8 Separation Method (Differential) (ultra)centrifugation dUC: centrifugation steps Below or equal to 800 g Between 100,000 g and 150,000 g Pelleting performed Yes Pelleting: rotor type SW32.1 Ti Pelleting: speed (g) 100000 Density gradient Type Discontinuous Number of initial discontinuous layers 4 Lowest density fraction 5% Highest density fraction 40% Total gradient volume, incl. sample (mL) 15.5 Sample volume (mL) 1 Orientation Top-down Speed (g) 100000 Duration (min) 1080 Fraction volume (mL) 1 Fraction processing Centrifugation Pelleting: volume per fraction 16 Pelleting: speed (g) 100000 Filtration steps Between 0.22 and 0.45 _m Ultra filtration Cut-off size (kDa) 10 kDa Membrane type Regenerated cellulose Size-exclusion chromatography Resin type EV-subtype Distinction between multiple subtypes Size Characterization: Protein analysis None Protein Concentration Method Fluorometric assay Protein Yield (µg) per microliter Characterization: RNA analysis RNA analysis Type (RT)(q)PCR Proteinase treatment No RNAse treatment No Characterization: Lipid analysis No Characterization: Particle analysis EM EM-type Transmission-EM Image type Close-up, Wide-field Report size (nm) 50-90

	EV220300	13/18	Homo sapiens	T47D	UF (d)(U)C Filtration DG	Pinheiro C	2024	57%
Study summary Full title Identification and validation of extracellular vesicle reference genes for the normalization of RT-qPCR data. All authors Pinheiro C, Guilbert N, Lippens L, Roux Q, Boiy R, Fischer S, Van Dorpe S, De Craene B, Berx G, Boterberg T, Sys G, Denys H, Miinalainen I, Mestdagh P, Vandesompele J, De Wever O, Hendrix A Journal J Extracell Vesicles Abstract Extracellular vesicles (EVs) contain a plethora of biomolecules, including nucleic acids, with diver (show more...)Extracellular vesicles (EVs) contain a plethora of biomolecules, including nucleic acids, with diverse diagnostic and therapeutic application potential. Although reverse transcription-quantitative PCR (RT-qPCR) is the most widely applied laboratory technique to evaluate gene expression, its applicability in EV research is challenged by the lack of universal and stably present reference genes (RGs). In this study, we identify, validate and establish SNRPG, OST4, TOMM7 and NOP10 as RGs for the normalization of EV-associated genes by RT-qPCR. We show the stable presence of SNRPG, OST4, TOMM7 and NOP10 in multiple cell lines and their secreted EVs (n = 12) under different (patho)physiological conditions as well as in human-derived biofluids (n = 3). Enzymatic treatments confirm the presence of SNRPG, OST4, TOMM7 and NOP10 inside EVs. In addition, the four EV-associated RGs are stably detected in a size-range of EV subpopulations. RefFinder analysis reveals that SNRPG, OST4, TOMM7 and NOP10 are more stable compared to RGs established specifically for cultured cells or tissues such as HMBS, YWHAZ, SDHA and GAPDH. In summary, we present four universal and stably present EV-associated RGs to enable normalization and thus steer the implementation of RT-qPCR for the analysis of EV-associated RNA cargo for research or clinical applications. (hide) EV-METRIC 57% (92nd 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 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 Ultrafiltration (Differential) (ultra)centrifugation Filtration Density gradient Protein markers EV: None non-EV: None Proteomics no EV density (g/ml) 1.09-1.11 Show all info Study aim Validation of standards Sample Species Homo sapiens Sample Type Cell culture supernatant EV-producing cells T47D EV-harvesting Medium EV-depleted medium Preparation of EDS >=18h at >= 100,000g Separation Method (Differential) (ultra)centrifugation dUC: centrifugation steps Below or equal to 800 g Between 100,000 g and 150,000 g Pelleting performed Yes Pelleting: rotor type SW32.1 Ti Pelleting: speed (g) 100000 Density gradient Type Discontinuous Number of initial discontinuous layers 4 Lowest density fraction 5% Highest density fraction 40% Total gradient volume, incl. sample (mL) 15.5 Sample volume (mL) 1 Orientation Top-down Speed (g) 100000 Duration (min) 1080 Fraction volume (mL) 1 Fraction processing Centrifugation Pelleting: volume per fraction 16 Pelleting: speed (g) 100000 Filtration steps Between 0.22 and 0.45 _m Ultra filtration Cut-off size (kDa) 10 kDa Membrane type Regenerated cellulose Size-exclusion chromatography Resin type Characterization: Protein analysis None Protein Concentration Method Fluorometric assay Protein Yield (µg) per microliter Characterization: RNA analysis RNA analysis Type (RT)(q)PCR Proteinase treatment No RNAse treatment No Characterization: Lipid analysis No Characterization: Particle analysis EM EM-type Transmission-EM Image type Close-up, Wide-field Report size (nm) 90-120

	EV220300	14/18	Homo sapiens	U87MG	UF (d)(U)C Filtration DG	Pinheiro C	2024	57%
Study summary Full title Identification and validation of extracellular vesicle reference genes for the normalization of RT-qPCR data. All authors Pinheiro C, Guilbert N, Lippens L, Roux Q, Boiy R, Fischer S, Van Dorpe S, De Craene B, Berx G, Boterberg T, Sys G, Denys H, Miinalainen I, Mestdagh P, Vandesompele J, De Wever O, Hendrix A Journal J Extracell Vesicles Abstract Extracellular vesicles (EVs) contain a plethora of biomolecules, including nucleic acids, with diver (show more...)Extracellular vesicles (EVs) contain a plethora of biomolecules, including nucleic acids, with diverse diagnostic and therapeutic application potential. Although reverse transcription-quantitative PCR (RT-qPCR) is the most widely applied laboratory technique to evaluate gene expression, its applicability in EV research is challenged by the lack of universal and stably present reference genes (RGs). In this study, we identify, validate and establish SNRPG, OST4, TOMM7 and NOP10 as RGs for the normalization of EV-associated genes by RT-qPCR. We show the stable presence of SNRPG, OST4, TOMM7 and NOP10 in multiple cell lines and their secreted EVs (n = 12) under different (patho)physiological conditions as well as in human-derived biofluids (n = 3). Enzymatic treatments confirm the presence of SNRPG, OST4, TOMM7 and NOP10 inside EVs. In addition, the four EV-associated RGs are stably detected in a size-range of EV subpopulations. RefFinder analysis reveals that SNRPG, OST4, TOMM7 and NOP10 are more stable compared to RGs established specifically for cultured cells or tissues such as HMBS, YWHAZ, SDHA and GAPDH. In summary, we present four universal and stably present EV-associated RGs to enable normalization and thus steer the implementation of RT-qPCR for the analysis of EV-associated RNA cargo for research or clinical applications. (hide) EV-METRIC 57% (92nd 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 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 Ultrafiltration (Differential) (ultra)centrifugation Filtration Density gradient Protein markers EV: None non-EV: None Proteomics no EV density (g/ml) 1.09-1.11 Show all info Study aim Validation of standards Sample Species Homo sapiens Sample Type Cell culture supernatant EV-producing cells U87MG EV-harvesting Medium EV-depleted medium Preparation of EDS >=18h at >= 100,000g Cell viability (%) 94 Cell count 6.52e8 Separation Method (Differential) (ultra)centrifugation dUC: centrifugation steps Below or equal to 800 g Between 100,000 g and 150,000 g Pelleting performed Yes Pelleting: rotor type SW32.1 Ti Pelleting: speed (g) 100000 Density gradient Type Discontinuous Number of initial discontinuous layers 4 Lowest density fraction 5% Highest density fraction 40% Total gradient volume, incl. sample (mL) 15.5 Sample volume (mL) 1 Orientation Top-down Speed (g) 100000 Duration (min) 1080 Fraction volume (mL) 1 Fraction processing Centrifugation Pelleting: volume per fraction 16 Pelleting: speed (g) 100000 Filtration steps Between 0.22 and 0.45 _m Ultra filtration Cut-off size (kDa) 10 kDa Membrane type Regenerated cellulose Size-exclusion chromatography Resin type Characterization: Protein analysis None Protein Concentration Method Fluorometric assay Protein Yield (µg) per microliter Characterization: RNA analysis RNA analysis Type (RT)(q)PCR Proteinase treatment No RNAse treatment No Characterization: Lipid analysis No Characterization: Particle analysis EM EM-type Transmission-EM Image type Close-up, Wide-field Report size (nm) 120-250

	EV220300	5/18	Homo sapiens	BEAS2B	UF (d)(U)C Filtration DG	Pinheiro C	2024	43%
Study summary Full title Identification and validation of extracellular vesicle reference genes for the normalization of RT-qPCR data. All authors Pinheiro C, Guilbert N, Lippens L, Roux Q, Boiy R, Fischer S, Van Dorpe S, De Craene B, Berx G, Boterberg T, Sys G, Denys H, Miinalainen I, Mestdagh P, Vandesompele J, De Wever O, Hendrix A Journal J Extracell Vesicles Abstract Extracellular vesicles (EVs) contain a plethora of biomolecules, including nucleic acids, with diver (show more...)Extracellular vesicles (EVs) contain a plethora of biomolecules, including nucleic acids, with diverse diagnostic and therapeutic application potential. Although reverse transcription-quantitative PCR (RT-qPCR) is the most widely applied laboratory technique to evaluate gene expression, its applicability in EV research is challenged by the lack of universal and stably present reference genes (RGs). In this study, we identify, validate and establish SNRPG, OST4, TOMM7 and NOP10 as RGs for the normalization of EV-associated genes by RT-qPCR. We show the stable presence of SNRPG, OST4, TOMM7 and NOP10 in multiple cell lines and their secreted EVs (n = 12) under different (patho)physiological conditions as well as in human-derived biofluids (n = 3). Enzymatic treatments confirm the presence of SNRPG, OST4, TOMM7 and NOP10 inside EVs. In addition, the four EV-associated RGs are stably detected in a size-range of EV subpopulations. RefFinder analysis reveals that SNRPG, OST4, TOMM7 and NOP10 are more stable compared to RGs established specifically for cultured cells or tissues such as HMBS, YWHAZ, SDHA and GAPDH. In summary, we present four universal and stably present EV-associated RGs to enable normalization and thus steer the implementation of RT-qPCR for the analysis of EV-associated RNA cargo for research or clinical applications. (hide) EV-METRIC 43% (81st 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 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 Ultrafiltration (Differential) (ultra)centrifugation Filtration Density gradient Protein markers EV: None non-EV: None Proteomics no EV density (g/ml) 1.09-1.11 Show all info Study aim Validation of standards Sample Species Homo sapiens Sample Type Cell culture supernatant EV-producing cells BEAS2B EV-harvesting Medium EV-depleted medium Preparation of EDS >=18h at >= 100,000g Cell viability (%) 91 Cell count 3.17e8 Separation Method (Differential) (ultra)centrifugation dUC: centrifugation steps Below or equal to 800 g Between 100,000 g and 150,000 g Pelleting performed Yes Pelleting: rotor type SW32.1 Ti Pelleting: speed (g) 100000 Density gradient Type Discontinuous Number of initial discontinuous layers 4 Lowest density fraction 5% Highest density fraction 40% Total gradient volume, incl. sample (mL) 15.5 Sample volume (mL) 1 Orientation Top-down Speed (g) 100000 Duration (min) 1080 Fraction volume (mL) 1 Fraction processing Centrifugation Pelleting: volume per fraction 16 Pelleting: speed (g) 100000 Filtration steps Between 0.22 and 0.45 _m Ultra filtration Cut-off size (kDa) 10 kDa Membrane type Regenerated cellulose Size-exclusion chromatography Resin type Characterization: Protein analysis None Protein Concentration Method Not determined Protein Yield (µg) particles per milliliter of starting sample: 9.88E10 Characterization: RNA analysis RNA analysis Type (RT)(q)PCR Proteinase treatment No RNAse treatment No Characterization: Lipid analysis No Characterization: Particle analysis None

	EV220300	6/18	Homo sapiens	HCT116	UF (d)(U)C Filtration DG	Pinheiro C	2024	43%
Study summary Full title Identification and validation of extracellular vesicle reference genes for the normalization of RT-qPCR data. All authors Pinheiro C, Guilbert N, Lippens L, Roux Q, Boiy R, Fischer S, Van Dorpe S, De Craene B, Berx G, Boterberg T, Sys G, Denys H, Miinalainen I, Mestdagh P, Vandesompele J, De Wever O, Hendrix A Journal J Extracell Vesicles Abstract Extracellular vesicles (EVs) contain a plethora of biomolecules, including nucleic acids, with diver (show more...)Extracellular vesicles (EVs) contain a plethora of biomolecules, including nucleic acids, with diverse diagnostic and therapeutic application potential. Although reverse transcription-quantitative PCR (RT-qPCR) is the most widely applied laboratory technique to evaluate gene expression, its applicability in EV research is challenged by the lack of universal and stably present reference genes (RGs). In this study, we identify, validate and establish SNRPG, OST4, TOMM7 and NOP10 as RGs for the normalization of EV-associated genes by RT-qPCR. We show the stable presence of SNRPG, OST4, TOMM7 and NOP10 in multiple cell lines and their secreted EVs (n = 12) under different (patho)physiological conditions as well as in human-derived biofluids (n = 3). Enzymatic treatments confirm the presence of SNRPG, OST4, TOMM7 and NOP10 inside EVs. In addition, the four EV-associated RGs are stably detected in a size-range of EV subpopulations. RefFinder analysis reveals that SNRPG, OST4, TOMM7 and NOP10 are more stable compared to RGs established specifically for cultured cells or tissues such as HMBS, YWHAZ, SDHA and GAPDH. In summary, we present four universal and stably present EV-associated RGs to enable normalization and thus steer the implementation of RT-qPCR for the analysis of EV-associated RNA cargo for research or clinical applications. (hide) EV-METRIC 43% (81st 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 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 Ultrafiltration (Differential) (ultra)centrifugation Filtration Density gradient Protein markers EV: None non-EV: None Proteomics no EV density (g/ml) 1.09-1.11 Show all info Study aim Validation of standards Sample Species Homo sapiens Sample Type Cell culture supernatant EV-producing cells HCT116 EV-harvesting Medium EV-depleted medium Preparation of EDS >=18h at >= 100,000g Cell viability (%) 93 Cell count 6.19e8 Separation Method (Differential) (ultra)centrifugation dUC: centrifugation steps Below or equal to 800 g Between 100,000 g and 150,000 g Pelleting performed Yes Pelleting: rotor type SW32.1 Ti Pelleting: speed (g) 100000 Density gradient Type Discontinuous Number of initial discontinuous layers 4 Lowest density fraction 5% Highest density fraction 40% Total gradient volume, incl. sample (mL) 15.5 Sample volume (mL) 1 Orientation Top-down Speed (g) 100000 Duration (min) 1080 Fraction volume (mL) 1 Fraction processing Centrifugation Pelleting: volume per fraction 16 Pelleting: speed (g) 100000 Filtration steps Between 0.22 and 0.45 _m Ultra filtration Cut-off size (kDa) 10 kDa Membrane type Regenerated cellulose Size-exclusion chromatography Resin type Characterization: Protein analysis None Protein Concentration Method Not determined Protein Yield (µg) particles per milliliter of starting sample: 9.88E10 Characterization: RNA analysis RNA analysis Type (RT)(q)PCR Proteinase treatment No RNAse treatment No Characterization: Lipid analysis No Characterization: Particle analysis None

	EV220300	9/18	Homo sapiens	LNCaP	UF (d)(U)C Filtration DG	Pinheiro C	2024	43%
Study summary Full title Identification and validation of extracellular vesicle reference genes for the normalization of RT-qPCR data. All authors Pinheiro C, Guilbert N, Lippens L, Roux Q, Boiy R, Fischer S, Van Dorpe S, De Craene B, Berx G, Boterberg T, Sys G, Denys H, Miinalainen I, Mestdagh P, Vandesompele J, De Wever O, Hendrix A Journal J Extracell Vesicles Abstract Extracellular vesicles (EVs) contain a plethora of biomolecules, including nucleic acids, with diver (show more...)Extracellular vesicles (EVs) contain a plethora of biomolecules, including nucleic acids, with diverse diagnostic and therapeutic application potential. Although reverse transcription-quantitative PCR (RT-qPCR) is the most widely applied laboratory technique to evaluate gene expression, its applicability in EV research is challenged by the lack of universal and stably present reference genes (RGs). In this study, we identify, validate and establish SNRPG, OST4, TOMM7 and NOP10 as RGs for the normalization of EV-associated genes by RT-qPCR. We show the stable presence of SNRPG, OST4, TOMM7 and NOP10 in multiple cell lines and their secreted EVs (n = 12) under different (patho)physiological conditions as well as in human-derived biofluids (n = 3). Enzymatic treatments confirm the presence of SNRPG, OST4, TOMM7 and NOP10 inside EVs. In addition, the four EV-associated RGs are stably detected in a size-range of EV subpopulations. RefFinder analysis reveals that SNRPG, OST4, TOMM7 and NOP10 are more stable compared to RGs established specifically for cultured cells or tissues such as HMBS, YWHAZ, SDHA and GAPDH. In summary, we present four universal and stably present EV-associated RGs to enable normalization and thus steer the implementation of RT-qPCR for the analysis of EV-associated RNA cargo for research or clinical applications. (hide) EV-METRIC 43% (81st 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 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 Ultrafiltration (Differential) (ultra)centrifugation Filtration Density gradient Protein markers EV: None non-EV: None Proteomics no EV density (g/ml) 1.09-1.11 Show all info Study aim Validation of standards Sample Species Homo sapiens Sample Type Cell culture supernatant EV-producing cells LNCaP EV-harvesting Medium EV-depleted medium Preparation of EDS >=18h at >= 100,000g Separation Method (Differential) (ultra)centrifugation dUC: centrifugation steps Below or equal to 800 g Between 100,000 g and 150,000 g Pelleting performed Yes Pelleting: rotor type SW32.1 Ti Pelleting: speed (g) 100000 Density gradient Type Discontinuous Number of initial discontinuous layers 4 Lowest density fraction 5% Highest density fraction 40% Total gradient volume, incl. sample (mL) 15.5 Sample volume (mL) 1 Orientation Top-down Speed (g) 100000 Duration (min) 1080 Fraction volume (mL) 1 Fraction processing Centrifugation Pelleting: volume per fraction 16 Pelleting: speed (g) 100000 Filtration steps Between 0.22 and 0.45 _m Ultra filtration Cut-off size (kDa) 10 kDa Membrane type Regenerated cellulose Size-exclusion chromatography Resin type Characterization: Protein analysis None Protein Concentration Method Not determined Protein Yield (µg) particles per milliliter of starting sample: 9.19E10-3.08E11 Characterization: RNA analysis RNA analysis Type (RT)(q)PCR Proteinase treatment No RNAse treatment No Characterization: Lipid analysis No Characterization: Particle analysis NTA Report type Mean Reported size (nm) 152-177.6 EV concentration Yes Particle yield particles per milliliter of starting sample: 9.19E10-3.08E11

	EV220300	10/18	Homo sapiens	OVCAR3	UF (d)(U)C Filtration DG	Pinheiro C	2024	43%
Study summary Full title Identification and validation of extracellular vesicle reference genes for the normalization of RT-qPCR data. All authors Pinheiro C, Guilbert N, Lippens L, Roux Q, Boiy R, Fischer S, Van Dorpe S, De Craene B, Berx G, Boterberg T, Sys G, Denys H, Miinalainen I, Mestdagh P, Vandesompele J, De Wever O, Hendrix A Journal J Extracell Vesicles Abstract Extracellular vesicles (EVs) contain a plethora of biomolecules, including nucleic acids, with diver (show more...)Extracellular vesicles (EVs) contain a plethora of biomolecules, including nucleic acids, with diverse diagnostic and therapeutic application potential. Although reverse transcription-quantitative PCR (RT-qPCR) is the most widely applied laboratory technique to evaluate gene expression, its applicability in EV research is challenged by the lack of universal and stably present reference genes (RGs). In this study, we identify, validate and establish SNRPG, OST4, TOMM7 and NOP10 as RGs for the normalization of EV-associated genes by RT-qPCR. We show the stable presence of SNRPG, OST4, TOMM7 and NOP10 in multiple cell lines and their secreted EVs (n = 12) under different (patho)physiological conditions as well as in human-derived biofluids (n = 3). Enzymatic treatments confirm the presence of SNRPG, OST4, TOMM7 and NOP10 inside EVs. In addition, the four EV-associated RGs are stably detected in a size-range of EV subpopulations. RefFinder analysis reveals that SNRPG, OST4, TOMM7 and NOP10 are more stable compared to RGs established specifically for cultured cells or tissues such as HMBS, YWHAZ, SDHA and GAPDH. In summary, we present four universal and stably present EV-associated RGs to enable normalization and thus steer the implementation of RT-qPCR for the analysis of EV-associated RNA cargo for research or clinical applications. (hide) EV-METRIC 43% (81st 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 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 Ultrafiltration (Differential) (ultra)centrifugation Filtration Density gradient Protein markers EV: None non-EV: None Proteomics no EV density (g/ml) 1.09-1.11 Show all info Study aim Validation of standards Sample Species Homo sapiens Sample Type Cell culture supernatant EV-producing cells OVCAR3 EV-harvesting Medium EV-depleted medium Preparation of EDS >=18h at >= 100,000g Separation Method (Differential) (ultra)centrifugation dUC: centrifugation steps Below or equal to 800 g Between 100,000 g and 150,000 g Pelleting performed Yes Pelleting: rotor type SW32.1 Ti Pelleting: speed (g) 100000 Density gradient Type Discontinuous Number of initial discontinuous layers 4 Lowest density fraction 5% Highest density fraction 40% Total gradient volume, incl. sample (mL) 15.5 Sample volume (mL) 1 Orientation Top-down Speed (g) 100000 Duration (min) 1080 Fraction volume (mL) 1 Fraction processing Centrifugation Pelleting: volume per fraction 16 Pelleting: speed (g) 100000 Filtration steps Between 0.22 and 0.45 _m Ultra filtration Cut-off size (kDa) 10 kDa Membrane type Regenerated cellulose Size-exclusion chromatography Resin type Characterization: Protein analysis None Protein Concentration Method Not determined Protein Yield (µg) particles per milliliter of starting sample: 9.19E10-3.08E11 Characterization: RNA analysis RNA analysis Type (RT)(q)PCR Proteinase treatment No RNAse treatment No Characterization: Lipid analysis No Characterization: Particle analysis None

	EV220300	11/18	Homo sapiens	SKOV3	UF (d)(U)C Filtration DG	Pinheiro C	2024	43%
Study summary Full title Identification and validation of extracellular vesicle reference genes for the normalization of RT-qPCR data. All authors Pinheiro C, Guilbert N, Lippens L, Roux Q, Boiy R, Fischer S, Van Dorpe S, De Craene B, Berx G, Boterberg T, Sys G, Denys H, Miinalainen I, Mestdagh P, Vandesompele J, De Wever O, Hendrix A Journal J Extracell Vesicles Abstract Extracellular vesicles (EVs) contain a plethora of biomolecules, including nucleic acids, with diver (show more...)Extracellular vesicles (EVs) contain a plethora of biomolecules, including nucleic acids, with diverse diagnostic and therapeutic application potential. Although reverse transcription-quantitative PCR (RT-qPCR) is the most widely applied laboratory technique to evaluate gene expression, its applicability in EV research is challenged by the lack of universal and stably present reference genes (RGs). In this study, we identify, validate and establish SNRPG, OST4, TOMM7 and NOP10 as RGs for the normalization of EV-associated genes by RT-qPCR. We show the stable presence of SNRPG, OST4, TOMM7 and NOP10 in multiple cell lines and their secreted EVs (n = 12) under different (patho)physiological conditions as well as in human-derived biofluids (n = 3). Enzymatic treatments confirm the presence of SNRPG, OST4, TOMM7 and NOP10 inside EVs. In addition, the four EV-associated RGs are stably detected in a size-range of EV subpopulations. RefFinder analysis reveals that SNRPG, OST4, TOMM7 and NOP10 are more stable compared to RGs established specifically for cultured cells or tissues such as HMBS, YWHAZ, SDHA and GAPDH. In summary, we present four universal and stably present EV-associated RGs to enable normalization and thus steer the implementation of RT-qPCR for the analysis of EV-associated RNA cargo for research or clinical applications. (hide) EV-METRIC 43% (81st 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 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 Ultrafiltration (Differential) (ultra)centrifugation Filtration Density gradient Protein markers EV: None non-EV: None Proteomics no EV density (g/ml) 1.09-1.11 Show all info Study aim Validation of standards Sample Species Homo sapiens Sample Type Cell culture supernatant EV-producing cells SKOV3 EV-harvesting Medium EV-depleted medium Preparation of EDS >=18h at >= 100,000g Cell viability (%) 94 Cell count 2.33e8 Separation Method (Differential) (ultra)centrifugation dUC: centrifugation steps Below or equal to 800 g Between 100,000 g and 150,000 g Pelleting performed Yes Pelleting: rotor type SW32.1 Ti Pelleting: speed (g) 100000 Density gradient Type Discontinuous Number of initial discontinuous layers 4 Lowest density fraction 5% Highest density fraction 40% Total gradient volume, incl. sample (mL) 15.5 Sample volume (mL) 1 Orientation Top-down Speed (g) 100000 Duration (min) 1080 Fraction volume (mL) 1 Fraction processing Centrifugation Pelleting: volume per fraction 16 Pelleting: speed (g) 100000 Filtration steps Between 0.22 and 0.45 _m Ultra filtration Cut-off size (kDa) 10 kDa Membrane type Regenerated cellulose Size-exclusion chromatography Resin type Characterization: Protein analysis None Protein Concentration Method Not determined Protein Yield (µg) particles per milliliter of starting sample: 4.79E10-1.55E11 Characterization: RNA analysis RNA analysis Type (RT)(q)PCR Proteinase treatment No RNAse treatment No Characterization: Lipid analysis No Characterization: Particle analysis NTA Report type Mean Reported size (nm) 143.1-156.9 EV concentration Yes Particle yield particles per milliliter of starting sample: 4.79E10-1.55E11

	EV220300	1/18	Homo sapiens	MCF7	UF (d)(U)C Filtration DG SEC (non-commercial)	Pinheiro C	2024	38%
Study summary Full title Identification and validation of extracellular vesicle reference genes for the normalization of RT-qPCR data. All authors Pinheiro C, Guilbert N, Lippens L, Roux Q, Boiy R, Fischer S, Van Dorpe S, De Craene B, Berx G, Boterberg T, Sys G, Denys H, Miinalainen I, Mestdagh P, Vandesompele J, De Wever O, Hendrix A Journal J Extracell Vesicles Abstract Extracellular vesicles (EVs) contain a plethora of biomolecules, including nucleic acids, with diver (show more...)Extracellular vesicles (EVs) contain a plethora of biomolecules, including nucleic acids, with diverse diagnostic and therapeutic application potential. Although reverse transcription-quantitative PCR (RT-qPCR) is the most widely applied laboratory technique to evaluate gene expression, its applicability in EV research is challenged by the lack of universal and stably present reference genes (RGs). In this study, we identify, validate and establish SNRPG, OST4, TOMM7 and NOP10 as RGs for the normalization of EV-associated genes by RT-qPCR. We show the stable presence of SNRPG, OST4, TOMM7 and NOP10 in multiple cell lines and their secreted EVs (n = 12) under different (patho)physiological conditions as well as in human-derived biofluids (n = 3). Enzymatic treatments confirm the presence of SNRPG, OST4, TOMM7 and NOP10 inside EVs. In addition, the four EV-associated RGs are stably detected in a size-range of EV subpopulations. RefFinder analysis reveals that SNRPG, OST4, TOMM7 and NOP10 are more stable compared to RGs established specifically for cultured cells or tissues such as HMBS, YWHAZ, SDHA and GAPDH. In summary, we present four universal and stably present EV-associated RGs to enable normalization and thus steer the implementation of RT-qPCR for the analysis of EV-associated RNA cargo for research or clinical applications. (hide) EV-METRIC 38% (79th 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 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 Ultrafiltration (Differential) (ultra)centrifugation Filtration Density gradient Size-exclusion chromatography (non-commercial) Protein markers EV: CD9/ Syntenin non-EV: None Proteomics no EV density (g/ml) 1.09-1.11 Show all info Study aim Validation of standards Sample Species Homo sapiens Sample Type Cell culture supernatant EV-producing cells MCF7 EV-harvesting Medium EV-depleted medium Preparation of EDS >=18h at >= 100,000g Cell viability (%) 96 Cell count 4.43e8 Separation Method (Differential) (ultra)centrifugation dUC: centrifugation steps Below or equal to 800 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) 15.5 Sample volume (mL) 1 Orientation Top-down Speed (g) 100000 Duration (min) 1080 Fraction volume (mL) 1 Fraction processing Centrifugation Pelleting: volume per fraction 16 Pelleting: speed (g) 100000 Filtration steps Between 0.22 and 0.45 _m Ultra filtration Cut-off size (kDa) 10 kDa Membrane type Regenerated cellulose Size-exclusion chromatography Resin type EV-subtype Distinction between multiple subtypes Size Used subtypes 50-90 Characterization: Protein analysis Protein Concentration Method Not determined Protein Yield (µg) particles per milliliter of starting sample: 3.39E10-5.54E10 Western Blot Detected EV-associated proteins CD9/ Syntenin Characterization: RNA analysis RNA analysis Type (RT)(q)PCR Proteinase treatment No RNAse treatment No Characterization: Lipid analysis No Characterization: Particle analysis NTA Report type Mean Reported size (nm) 132.5-146.1 EV concentration Yes Particle yield particles per milliliter of starting sample: 3.39E10-5.54E10 EM EM-type Transmission-EM Image type Wide-field

	EV220300	2/18	Homo sapiens	MCF7	UF (d)(U)C Filtration DG SEC (non-commercial)	Pinheiro C	2024	38%
Study summary Full title Identification and validation of extracellular vesicle reference genes for the normalization of RT-qPCR data. All authors Pinheiro C, Guilbert N, Lippens L, Roux Q, Boiy R, Fischer S, Van Dorpe S, De Craene B, Berx G, Boterberg T, Sys G, Denys H, Miinalainen I, Mestdagh P, Vandesompele J, De Wever O, Hendrix A Journal J Extracell Vesicles Abstract Extracellular vesicles (EVs) contain a plethora of biomolecules, including nucleic acids, with diver (show more...)Extracellular vesicles (EVs) contain a plethora of biomolecules, including nucleic acids, with diverse diagnostic and therapeutic application potential. Although reverse transcription-quantitative PCR (RT-qPCR) is the most widely applied laboratory technique to evaluate gene expression, its applicability in EV research is challenged by the lack of universal and stably present reference genes (RGs). In this study, we identify, validate and establish SNRPG, OST4, TOMM7 and NOP10 as RGs for the normalization of EV-associated genes by RT-qPCR. We show the stable presence of SNRPG, OST4, TOMM7 and NOP10 in multiple cell lines and their secreted EVs (n = 12) under different (patho)physiological conditions as well as in human-derived biofluids (n = 3). Enzymatic treatments confirm the presence of SNRPG, OST4, TOMM7 and NOP10 inside EVs. In addition, the four EV-associated RGs are stably detected in a size-range of EV subpopulations. RefFinder analysis reveals that SNRPG, OST4, TOMM7 and NOP10 are more stable compared to RGs established specifically for cultured cells or tissues such as HMBS, YWHAZ, SDHA and GAPDH. In summary, we present four universal and stably present EV-associated RGs to enable normalization and thus steer the implementation of RT-qPCR for the analysis of EV-associated RNA cargo for research or clinical applications. (hide) EV-METRIC 38% (79th 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 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 Ultrafiltration (Differential) (ultra)centrifugation Filtration Density gradient Size-exclusion chromatography (non-commercial) Protein markers EV: CD9/ Syntenin non-EV: None Proteomics no EV density (g/ml) 1.09-1.11 Show all info Study aim Validation of standards Sample Species Homo sapiens Sample Type Cell culture supernatant EV-producing cells MCF7 EV-harvesting Medium EV-depleted medium Preparation of EDS >=18h at >= 100,000g Cell viability (%) 96 Cell count 4.43e8 Separation Method (Differential) (ultra)centrifugation dUC: centrifugation steps Below or equal to 800 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) 15.5 Sample volume (mL) 1 Orientation Top-down Speed (g) 100000 Duration (min) 1080 Fraction volume (mL) 1 Fraction processing Centrifugation Pelleting: volume per fraction 16 Pelleting: speed (g) 100000 Filtration steps Between 0.22 and 0.45 _m Ultra filtration Cut-off size (kDa) 10 kDa Membrane type Regenerated cellulose Size-exclusion chromatography Resin type EV-subtype Distinction between multiple subtypes Size Used subtypes 90-120 Characterization: Protein analysis Protein Concentration Method Not determined Protein Yield (µg) particles per milliliter of starting sample: 1.68E10-2.95E10 Western Blot Detected EV-associated proteins CD9/ Syntenin Characterization: RNA analysis RNA analysis Type (RT)(q)PCR Proteinase treatment No RNAse treatment No Characterization: Lipid analysis No Characterization: Particle analysis NTA Report type Mean Reported size (nm) 149.4-181.4 EV concentration Yes Particle yield particles per milliliter of starting sample: 1.68E10-2.95E10 EM EM-type Transmission-EM Image type Wide-field

	EV220300	17/18	Homo sapiens	urine	UF (d)(U)C Filtration DG SEC (non-commercial)	Pinheiro C	2024	33%
Study summary Full title Identification and validation of extracellular vesicle reference genes for the normalization of RT-qPCR data. All authors Pinheiro C, Guilbert N, Lippens L, Roux Q, Boiy R, Fischer S, Van Dorpe S, De Craene B, Berx G, Boterberg T, Sys G, Denys H, Miinalainen I, Mestdagh P, Vandesompele J, De Wever O, Hendrix A Journal J Extracell Vesicles Abstract Extracellular vesicles (EVs) contain a plethora of biomolecules, including nucleic acids, with diver (show more...)Extracellular vesicles (EVs) contain a plethora of biomolecules, including nucleic acids, with diverse diagnostic and therapeutic application potential. Although reverse transcription-quantitative PCR (RT-qPCR) is the most widely applied laboratory technique to evaluate gene expression, its applicability in EV research is challenged by the lack of universal and stably present reference genes (RGs). In this study, we identify, validate and establish SNRPG, OST4, TOMM7 and NOP10 as RGs for the normalization of EV-associated genes by RT-qPCR. We show the stable presence of SNRPG, OST4, TOMM7 and NOP10 in multiple cell lines and their secreted EVs (n = 12) under different (patho)physiological conditions as well as in human-derived biofluids (n = 3). Enzymatic treatments confirm the presence of SNRPG, OST4, TOMM7 and NOP10 inside EVs. In addition, the four EV-associated RGs are stably detected in a size-range of EV subpopulations. RefFinder analysis reveals that SNRPG, OST4, TOMM7 and NOP10 are more stable compared to RGs established specifically for cultured cells or tissues such as HMBS, YWHAZ, SDHA and GAPDH. In summary, we present four universal and stably present EV-associated RGs to enable normalization and thus steer the implementation of RT-qPCR for the analysis of EV-associated RNA cargo for research or clinical applications. (hide) EV-METRIC 33% (65th 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 urine 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 Ultrafiltration (Differential) (ultra)centrifugation Filtration Density gradient Size-exclusion chromatography (non-commercial) Protein markers EV: None non-EV: None Proteomics no EV density (g/ml) 1.09-1.11 Show all info Study aim Validation of standards Sample Species Homo sapiens Sample Type urine Separation Method (Differential) (ultra)centrifugation dUC: centrifugation steps Below or equal to 800 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) 15.5 Sample volume (mL) 0.5 Orientation Bottom-up Speed (g) 100000 Duration (min) 1080 Fraction volume (mL) 1 Fraction processing Centrifugation Pelleting: volume per fraction 16 Pelleting: speed (g) 100000 Ultra filtration Cut-off size (kDa) 10 kDa Membrane type Regenerated cellulose Size-exclusion chromatography Total column volume (mL) 10 Sample volume/column (mL) 2 Resin type Sepharose CL-2B Characterization: Protein analysis None Protein Concentration Method Not determined Protein Yield (µg) particles per milliliter of starting sample: 121E11-2.44E11 Characterization: RNA analysis RNA analysis Type (RT)(q)PCR Proteinase treatment No RNAse treatment No Characterization: Lipid analysis No Characterization: Particle analysis NTA Report type Mean Reported size (nm) 142.5-164.2 EV concentration Yes Particle yield particles per milliliter of starting sample: 121E11-2.44E11

	EV220300	18/18	Homo sapiens	tumor interstitial fluid	UF (d)(U)C Filtration DG SEC (non-commercial)	Pinheiro C	2024	33%
Study summary Full title Identification and validation of extracellular vesicle reference genes for the normalization of RT-qPCR data. All authors Pinheiro C, Guilbert N, Lippens L, Roux Q, Boiy R, Fischer S, Van Dorpe S, De Craene B, Berx G, Boterberg T, Sys G, Denys H, Miinalainen I, Mestdagh P, Vandesompele J, De Wever O, Hendrix A Journal J Extracell Vesicles Abstract Extracellular vesicles (EVs) contain a plethora of biomolecules, including nucleic acids, with diver (show more...)Extracellular vesicles (EVs) contain a plethora of biomolecules, including nucleic acids, with diverse diagnostic and therapeutic application potential. Although reverse transcription-quantitative PCR (RT-qPCR) is the most widely applied laboratory technique to evaluate gene expression, its applicability in EV research is challenged by the lack of universal and stably present reference genes (RGs). In this study, we identify, validate and establish SNRPG, OST4, TOMM7 and NOP10 as RGs for the normalization of EV-associated genes by RT-qPCR. We show the stable presence of SNRPG, OST4, TOMM7 and NOP10 in multiple cell lines and their secreted EVs (n = 12) under different (patho)physiological conditions as well as in human-derived biofluids (n = 3). Enzymatic treatments confirm the presence of SNRPG, OST4, TOMM7 and NOP10 inside EVs. In addition, the four EV-associated RGs are stably detected in a size-range of EV subpopulations. RefFinder analysis reveals that SNRPG, OST4, TOMM7 and NOP10 are more stable compared to RGs established specifically for cultured cells or tissues such as HMBS, YWHAZ, SDHA and GAPDH. In summary, we present four universal and stably present EV-associated RGs to enable normalization and thus steer the implementation of RT-qPCR for the analysis of EV-associated RNA cargo for research or clinical applications. (hide) EV-METRIC 33% (50th 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 tumor interstitial fluid 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 Ultrafiltration (Differential) (ultra)centrifugation Filtration Density gradient Size-exclusion chromatography (non-commercial) Protein markers EV: None non-EV: None Proteomics no EV density (g/ml) 1.09-1.11 Show all info Study aim Validation of standards Sample Species Homo sapiens Sample Type tumor interstitial fluid EV-harvesting Medium >=18h at >= 100,000g Separation Method (Differential) (ultra)centrifugation dUC: centrifugation steps Below or equal to 800 g Between 800 g and 10,000 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) 15.5 Sample volume (mL) 1 Orientation Top-down Speed (g) 100000 Duration (min) 1080 Fraction volume (mL) 1 Fraction processing Centrifugation Pelleting: volume per fraction 16 Pelleting: speed (g) 100000 Size-exclusion chromatography Total column volume (mL) 10 Sample volume/column (mL) 2 Resin type Sepharose CL-2B Characterization: Protein analysis None Protein Concentration Method Not determined Characterization: RNA analysis RNA analysis Type (RT)(q)PCR Proteinase treatment No RNAse treatment No Characterization: Lipid analysis No Characterization: Particle analysis NTA Report type Mean Reported size (nm) 221.6-225.3 EV concentration Yes Particle yield particles per milliliter of starting sample: 2.23E11-2.84E11

	EV220300	15/18	Homo sapiens	Blood plasma	(d)(U)C SEC (non-commercial) UF	Pinheiro C	2024	0%
Study summary Full title Identification and validation of extracellular vesicle reference genes for the normalization of RT-qPCR data. All authors Pinheiro C, Guilbert N, Lippens L, Roux Q, Boiy R, Fischer S, Van Dorpe S, De Craene B, Berx G, Boterberg T, Sys G, Denys H, Miinalainen I, Mestdagh P, Vandesompele J, De Wever O, Hendrix A Journal J Extracell Vesicles Abstract Extracellular vesicles (EVs) contain a plethora of biomolecules, including nucleic acids, with diver (show more...)Extracellular vesicles (EVs) contain a plethora of biomolecules, including nucleic acids, with diverse diagnostic and therapeutic application potential. Although reverse transcription-quantitative PCR (RT-qPCR) is the most widely applied laboratory technique to evaluate gene expression, its applicability in EV research is challenged by the lack of universal and stably present reference genes (RGs). In this study, we identify, validate and establish SNRPG, OST4, TOMM7 and NOP10 as RGs for the normalization of EV-associated genes by RT-qPCR. We show the stable presence of SNRPG, OST4, TOMM7 and NOP10 in multiple cell lines and their secreted EVs (n = 12) under different (patho)physiological conditions as well as in human-derived biofluids (n = 3). Enzymatic treatments confirm the presence of SNRPG, OST4, TOMM7 and NOP10 inside EVs. In addition, the four EV-associated RGs are stably detected in a size-range of EV subpopulations. RefFinder analysis reveals that SNRPG, OST4, TOMM7 and NOP10 are more stable compared to RGs established specifically for cultured cells or tissues such as HMBS, YWHAZ, SDHA and GAPDH. In summary, we present four universal and stably present EV-associated RGs to enable normalization and thus steer the implementation of RT-qPCR for the analysis of EV-associated RNA cargo for research or clinical applications. (hide) EV-METRIC 0% (median: 22% 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 Blood plasma 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 (Differential) (ultra)centrifugation Size-exclusion chromatography (non-commercial) Ultrafiltration Protein markers EV: None non-EV: None Proteomics no Show all info Study aim Validation of standards Sample Species Homo sapiens Sample Type Blood plasma Separation Method (Differential) (ultra)centrifugation dUC: centrifugation steps Between 800 g and 10,000 g Pelleting performed No Ultra filtration Cut-off size (kDa) 10 kDa Membrane type Regenerated cellulose Size-exclusion chromatography Total column volume (mL) 10 Sample volume/column (mL) 2 Resin type Sepharose CL-2B Characterization: Protein analysis None Protein Concentration Method Not determined Protein Yield (µg) per microliter Characterization: RNA analysis RNA analysis Type (RT)(q)PCR Proteinase treatment No RNAse treatment No Characterization: Lipid analysis No Characterization: Particle analysis None

	EV220300	16/18	Homo sapiens	Blood plasma	(d)(U)C SEC (non-commercial) UF	Pinheiro C	2024	0%
Study summary Full title Identification and validation of extracellular vesicle reference genes for the normalization of RT-qPCR data. All authors Pinheiro C, Guilbert N, Lippens L, Roux Q, Boiy R, Fischer S, Van Dorpe S, De Craene B, Berx G, Boterberg T, Sys G, Denys H, Miinalainen I, Mestdagh P, Vandesompele J, De Wever O, Hendrix A Journal J Extracell Vesicles Abstract Extracellular vesicles (EVs) contain a plethora of biomolecules, including nucleic acids, with diver (show more...)Extracellular vesicles (EVs) contain a plethora of biomolecules, including nucleic acids, with diverse diagnostic and therapeutic application potential. Although reverse transcription-quantitative PCR (RT-qPCR) is the most widely applied laboratory technique to evaluate gene expression, its applicability in EV research is challenged by the lack of universal and stably present reference genes (RGs). In this study, we identify, validate and establish SNRPG, OST4, TOMM7 and NOP10 as RGs for the normalization of EV-associated genes by RT-qPCR. We show the stable presence of SNRPG, OST4, TOMM7 and NOP10 in multiple cell lines and their secreted EVs (n = 12) under different (patho)physiological conditions as well as in human-derived biofluids (n = 3). Enzymatic treatments confirm the presence of SNRPG, OST4, TOMM7 and NOP10 inside EVs. In addition, the four EV-associated RGs are stably detected in a size-range of EV subpopulations. RefFinder analysis reveals that SNRPG, OST4, TOMM7 and NOP10 are more stable compared to RGs established specifically for cultured cells or tissues such as HMBS, YWHAZ, SDHA and GAPDH. In summary, we present four universal and stably present EV-associated RGs to enable normalization and thus steer the implementation of RT-qPCR for the analysis of EV-associated RNA cargo for research or clinical applications. (hide) EV-METRIC 0% (median: 22% 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 Blood plasma Sample origin ovarian cancer patients 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 (Differential) (ultra)centrifugation Size-exclusion chromatography (non-commercial) Ultrafiltration Protein markers EV: None non-EV: None Proteomics no Show all info Study aim Validation of standards Sample Species Homo sapiens Sample Type Blood plasma Separation Method (Differential) (ultra)centrifugation dUC: centrifugation steps Between 800 g and 10,000 g Pelleting performed No Ultra filtration Cut-off size (kDa) 10 kDa Membrane type Regenerated cellulose Size-exclusion chromatography Total column volume (mL) 10 Sample volume/column (mL) 2 Resin type Sepharose CL-2B Characterization: Protein analysis None Protein Concentration Method Not determined Protein Yield (µg) per microliter Characterization: RNA analysis RNA analysis Type (RT)(q)PCR Proteinase treatment No RNAse treatment No Characterization: Lipid analysis No Characterization: Particle analysis None

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EV-TRACK ID	EV220300
species	Homo sapiens
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	urine	tumor interstitial fluid	Blood plasma	Blood plasma
cell type	MCF7	A549	CT5.3hTeRT	CT5.3hTeRT	PANC1	T47D	U87MG	BEAS2B	HCT116	LNCaP	OVCAR3	SKOV3	MCF7	MCF7	NA	NA	NA	NA
medium	EV-depleted medium	EV-depleted medium	EV-depleted medium	EV-depleted medium	EV-depleted medium	EV-depleted medium	EV-depleted medium	EV-depleted medium	EV-depleted medium	EV-depleted medium	EV-depleted medium	EV-depleted medium	EV-depleted medium	EV-depleted medium	NA	>=18h at >= 100 000g	NA	NA
condition	Control condition	Control condition	Control condition	10Gy single dose	Control condition	Control condition	Control condition	Control condition	Control condition	Control condition	Control condition	Control condition	Control condition	Control condition	Control condition	Control condition	Control condition	ovarian cancer patients
separation protocol	Ultrafiltration/ dUC/ Filtration/ Density gradient/ Size-exclusion chromatography (non-commercial)	Ultrafiltration/ dUC/ Filtration/ Density gradient	Ultrafiltration/ dUC/ Filtration/ Density gradient/ Size-exclusion chromatography (non-commercial)	Ultrafiltration/ dUC/ Filtration/ Density gradient/ Size-exclusion chromatography (non-commercial)	Ultrafiltration/ dUC/ Filtration/ Density gradient	Ultrafiltration/ dUC/ Filtration/ Density gradient	Ultrafiltration/ dUC/ Filtration/ Density gradient	Ultrafiltration/ dUC/ Filtration/ Density gradient	Ultrafiltration/ dUC/ Filtration/ Density gradient	Ultrafiltration/ dUC/ Filtration/ Density gradient	Ultrafiltration/ dUC/ Filtration/ Density gradient	Ultrafiltration/ dUC/ Filtration/ Density gradient	Ultrafiltration/ dUC/ Filtration/ Density gradient/ Size-exclusion chromatography (non-commercial)	Ultrafiltration/ dUC/ Filtration/ Density gradient/ Size-exclusion chromatography (non-commercial)	Ultrafiltration/ dUC/ Filtration/ Density gradient/ Size-exclusion chromatography (non-commercial)	Ultrafiltration/ dUC/ Filtration/ Density gradient/ Size-exclusion chromatography (non-commercial)	dUC/ Size-exclusion chromatography (non-commercial)/ Ultrafiltration	dUC/ Size-exclusion chromatography (non-commercial)/ Ultrafiltration
EV subtype	120-250	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	50-90	90-120	NA	NA	NA	NA
Exp. nr.	3	4	7	8	12	13	14	5	6	9	10	11	1	2	17	18	15	16
EV-METRIC %	100	89	63	63	57	57	57	43	43	43	43	43	38	38	33	33	0	0

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