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You searched for: EV170037 (EV-TRACK ID)

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Experiment number
  • If needed, multiple experiments were identified in a single publication based on differing sample types, isolation protocols and/or vesicle types of interest.
Species
  • Species of origin of the EVs.
Isolation protocol
  • Gives a short, non-chronological overview of the different steps of the isolation protocol.
    • dUC = differential ultracentrifugation
    • DG = density gradient
    • UF = ultrafiltration
    • SEC = size-exclusion chromatography
Experiment number
  • Experiments differ in Sample type
Experiment number
  • Experiments differ in Sample type
Experiment number
  • Experiments differ in Sample type
Details EV-TRACK ID Experiment nr. Species Sample type Isolation protocol First author Year EV-METRIC
EV170037 1/3 Homo sapiens Serum dUC Klump, Jennifer 2018 28%

Study summary

Full title
All authors
Klump J, Phillipp U, Follo M, Eremin A, Lehmann H, Nestel S, von Bubnoff N, Nazarenko I
Journal
Nanomedicine
Abstract
Clinical evidence in oncology argues for the advantages of performing molecular analysis of blood bi (show more...)Clinical evidence in oncology argues for the advantages of performing molecular analysis of blood biomarkers to provide information about systemic changes and tumor heterogeneity. Whereas the diagnostic value of cell-free circulating DNA (fcDNA) has successfully been demonstrated in several studies, DNA enclosed in extracellular vesicles (EV) has only recently been described, and its potential diagnostic value is unclear. We established a protocol for separation of EV and fc fractions and tested for presence of mutant BRAFV600E mediating resistance to Vemurafenib and cKITD816V mediating resistance to Imatinib in blood of patients with melanoma and mastocytosis. Our results show that EV contain significantly higher amounts of total DNA as compared to the fc fraction. However, about ten-fold higher copy numbers of the wild type and mutant BRAF and cKIT were detected in the fcDNA fraction supporting its diagnostic value and pointing to differences in fc and EV DNA content. (hide)
EV-METRIC
28% (80th 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
electron microscopy images
Particle analysis: inclusion of a widefield and close-up electron microscopy image
density gradient
Isolation method: density gradient, at least as validation of results attributed to EVs
EV density
Isolation method: reporting of obtained EV density
ultracentrifugation specifics
Isolation 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
Serum
Focus vesicles
extracellular vesicle
Isolation protocol
Isolation protocol
  • Gives a short, non-chronological overview of the
    different steps of the isolation protocol.
    • dUC = differential ultracentrifugation
    • DG = density gradient
    • UF = ultrafiltration
    • SEC = size-exclusion chromatography
dUC
Adj. k-factor
213.2 (pelleting) / 213.2 (washing)
Protein markers
EV: None
non-EV: None
Proteomics
no
Show all info
Study aim
Biomarker
Sample
Species
Homo sapiens
Sample Type
Serum
Sample Condition
Control condition
Isolation Method
Differential ultracentrifugation
dUC: centrifugation steps
Below or equal to 800 g
Between 800 g and 10,000 g
Between 10,000 g and 50,000 g
Between 100,000 g and 150,000 g
Pelleting: time(min)
90
Pelleting: rotor type
SW 41 Ti
Pelleting: speed (g)
120000
Pelleting: adjusted k-factor
213.2
Wash: time (min)
120
Wash: Rotor Type
SW 41 Ti
Wash: speed (g)
120000
Wash: adjusted k-factor
213.2
Protein Concentration Method
microBCA
Protein Concentration
10-50 dependent whether healthy donors or cancer patients were analyzed
Fluorescent NTA
Characterization: Particle analysis
DLS
Report type
Size range/distribution
Reported size (nm)
different populations of vesicles were detected by DLS and NTA;120-500 nm; and over 1000 nm
NTA
Report type
Size range/distribution
Reported size (nm)
90-300
EV concentration
Yes
Particle yield
3.00E+09 particles/ml start sample
EM
EM-type
Transmission-EM
Image type
Wide-field
Report size (nm)
90-120
Extra information
Publication aimed to determine the content of mutated DNA oncogenes copy inside of the vesicles (post- DNase treatments) and in the free-circulating fractions. For that DNA was isolated from different EV and fc fractions and DNA was analyzed using ddPCR. Conclusion was that the mutated BRAF and c-KIT copies are preferably located in the free-circulating fractions and not in EVs.
EV170037 2/3 Homo sapiens Serum dUC Klump, Jennifer 2018 28%

Study summary

Full title
All authors
Klump J, Phillipp U, Follo M, Eremin A, Lehmann H, Nestel S, von Bubnoff N, Nazarenko I
Journal
Nanomedicine
Abstract
Clinical evidence in oncology argues for the advantages of performing molecular analysis of blood bi (show more...)Clinical evidence in oncology argues for the advantages of performing molecular analysis of blood biomarkers to provide information about systemic changes and tumor heterogeneity. Whereas the diagnostic value of cell-free circulating DNA (fcDNA) has successfully been demonstrated in several studies, DNA enclosed in extracellular vesicles (EV) has only recently been described, and its potential diagnostic value is unclear. We established a protocol for separation of EV and fc fractions and tested for presence of mutant BRAFV600E mediating resistance to Vemurafenib and cKITD816V mediating resistance to Imatinib in blood of patients with melanoma and mastocytosis. Our results show that EV contain significantly higher amounts of total DNA as compared to the fc fraction. However, about ten-fold higher copy numbers of the wild type and mutant BRAF and cKIT were detected in the fcDNA fraction supporting its diagnostic value and pointing to differences in fc and EV DNA content. (hide)
EV-METRIC
28% (80th 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
electron microscopy images
Particle analysis: inclusion of a widefield and close-up electron microscopy image
density gradient
Isolation method: density gradient, at least as validation of results attributed to EVs
EV density
Isolation method: reporting of obtained EV density
ultracentrifugation specifics
Isolation 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
Serum
Focus vesicles
extracellular vesicle
Isolation protocol
Isolation protocol
  • Gives a short, non-chronological overview of the
    different steps of the isolation protocol.
    • dUC = differential ultracentrifugation
    • DG = density gradient
    • UF = ultrafiltration
    • SEC = size-exclusion chromatography
dUC
Adj. k-factor
213.2 (pelleting) / 213.2 (washing)
Protein markers
EV: None
non-EV: None
Proteomics
no
Show all info
Study aim
Biomarker
Sample
Species
Homo sapiens
Sample Type
Serum
Sample Condition
Melanoma
Isolation Method
Differential ultracentrifugation
dUC: centrifugation steps
Below or equal to 800 g
Between 800 g and 10,000 g
Between 10,000 g and 50,000 g
Between 100,000 g and 150,000 g
Pelleting: time(min)
90
Pelleting: rotor type
SW 41 Ti
Pelleting: speed (g)
120000
Pelleting: adjusted k-factor
213.2
Wash: time (min)
120
Wash: Rotor Type
SW 41 Ti
Wash: speed (g)
120000
Wash: adjusted k-factor
213.2
Protein Concentration Method
microBCA
Protein Concentration
10-50 dependent whether healthy donors or cancer patients were analyzed
Fluorescent NTA
Characterization: Particle analysis
DLS
Report type
Size range/distribution
Reported size (nm)
different populations of vesicles were detected by DLS and NTA;120-500 nm; and over 1000 nm
NTA
Report type
Size range/distribution
Reported size (nm)
90-300
EV concentration
Yes
Particle yield
3.00E+09 particles/ml start sample
EM
EM-type
Transmission-EM
Image type
Wide-field
Report size (nm)
90-120
Extra information
Publication aimed to determine the content of mutated DNA oncogenes copy inside of the vesicles (post- DNase treatments) and in the free-circulating fractions. For that DNA was isolated from different EV and fc fractions and DNA was analyzed using ddPCR. Conclusion was that the mutated BRAF and c-KIT copies are preferably located in the free-circulating fractions and not in EVs.
EV170037 3/3 Homo sapiens Serum dUC Klump, Jennifer 2018 28%

Study summary

Full title
All authors
Klump J, Phillipp U, Follo M, Eremin A, Lehmann H, Nestel S, von Bubnoff N, Nazarenko I
Journal
Nanomedicine
Abstract
Clinical evidence in oncology argues for the advantages of performing molecular analysis of blood bi (show more...)Clinical evidence in oncology argues for the advantages of performing molecular analysis of blood biomarkers to provide information about systemic changes and tumor heterogeneity. Whereas the diagnostic value of cell-free circulating DNA (fcDNA) has successfully been demonstrated in several studies, DNA enclosed in extracellular vesicles (EV) has only recently been described, and its potential diagnostic value is unclear. We established a protocol for separation of EV and fc fractions and tested for presence of mutant BRAFV600E mediating resistance to Vemurafenib and cKITD816V mediating resistance to Imatinib in blood of patients with melanoma and mastocytosis. Our results show that EV contain significantly higher amounts of total DNA as compared to the fc fraction. However, about ten-fold higher copy numbers of the wild type and mutant BRAF and cKIT were detected in the fcDNA fraction supporting its diagnostic value and pointing to differences in fc and EV DNA content. (hide)
EV-METRIC
28% (80th 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
electron microscopy images
Particle analysis: inclusion of a widefield and close-up electron microscopy image
density gradient
Isolation method: density gradient, at least as validation of results attributed to EVs
EV density
Isolation method: reporting of obtained EV density
ultracentrifugation specifics
Isolation 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
Serum
Focus vesicles
extracellular vesicle
Isolation protocol
Isolation protocol
  • Gives a short, non-chronological overview of the
    different steps of the isolation protocol.
    • dUC = differential ultracentrifugation
    • DG = density gradient
    • UF = ultrafiltration
    • SEC = size-exclusion chromatography
dUC
Adj. k-factor
213.2 (pelleting) / 213.2 (washing)
Protein markers
EV: None
non-EV: None
Proteomics
no
Show all info
Study aim
Biomarker
Sample
Species
Homo sapiens
Sample Type
Serum
Sample Condition
Mastocytosis
Isolation Method
Differential ultracentrifugation
dUC: centrifugation steps
Below or equal to 800 g
Between 800 g and 10,000 g
Between 10,000 g and 50,000 g
Between 100,000 g and 150,000 g
Pelleting: time(min)
90
Pelleting: rotor type
SW 41 Ti
Pelleting: speed (g)
120000
Pelleting: adjusted k-factor
213.2
Wash: time (min)
120
Wash: Rotor Type
SW 41 Ti
Wash: speed (g)
120000
Wash: adjusted k-factor
213.2
Protein Concentration Method
microBCA
Protein Concentration
10-50 dependent whether healthy donors or cancer patients were analyzed
Fluorescent NTA
Characterization: Particle analysis
DLS
Report type
Size range/distribution
Reported size (nm)
different populations of vesicles were detected by DLS and NTA;120-500 nm; and over 1000 nm
NTA
Report type
Size range/distribution
Reported size (nm)
90-300
EV concentration
Yes
Particle yield
3.00E+09 particles/ml start sample
EM
EM-type
Transmission-EM
Image type
Wide-field
Report size (nm)
90-120
Extra information
Publication aimed to determine the content of mutated DNA oncogenes copy inside of the vesicles (post- DNase treatments) and in the free-circulating fractions. For that DNA was isolated from different EV and fc fractions and DNA was analyzed using ddPCR. Conclusion was that the mutated BRAF and c-KIT copies are preferably located in the free-circulating fractions and not in EVs.
1 - 3 of 3
  • dUC = differential ultracentrifugation
  • DG = density gradient
  • UF = ultrafiltration
  • SEC = size-exclusion chromatography
EV-TRACK ID
EV170037
species
Homo sapiens
sample type
Serum
condition
Control condition
Melanoma
Mastocytosis
isolation protocol
dUC
dUC
dUC
case number
1
2
3
EV-METRIC %
28
28
28