Search > Results

You searched for: EV190045 (EV-TRACK ID)

Showing 1 - 4 of 4

Experiment number
  • If needed, multiple experiments were identified in a single publication based on differing sample types, separation protocols and/or vesicle types of interest.
Species
  • Species of origin of the EVs.
Separation protocol
  • Gives a short, non-chronological overview of the different steps of the separation protocol.
    • dUC = differential ultracentrifugation
    • DG = density gradient
    • UF = ultrafiltration
    • SEC = size-exclusion chromatography
Experiment number
  • Experiments differ in EV subtype
Experiment number
  • Experiments differ in EV subtype
Experiment number
  • Experiments differ in EV subtype
Experiment number
  • Experiments differ in EV subtype
Details EV-TRACK ID Experiment nr. Species Sample type separation protocol First author Year EV-METRIC
EV190045 1/4 Homo sapiens Cell culture supernatant FC
DG
dUC
Lázaro-Ibáñez E 2019 100%

Study summary

Full title
All authors
Lázaro-Ibáñez E, Lässer C, Shelke GV, Crescitelli R, Jang SC, Cvjetkovic A, García-Rodríguez A, Lötvall J.
Journal
J Extracell Vesicles
Abstract
Extracellular vesicles have the capacity to transfer lipids, proteins, and nucleic acids between cel (show more...)Extracellular vesicles have the capacity to transfer lipids, proteins, and nucleic acids between cells, thereby influencing the recipient cell's phenotype. While the role of RNAs in EVs has been extensively studied, the function of DNA remains elusive. Here, we distinguished novel heterogeneous subpopulations of small extracellular vesicles (sEVs) based on their DNA content and topology. Low- and high-density sEV subsets from a human mast cell line (HMC-1) and an erythroleukemic cell line (TF-1) were separated using high-resolution iodixanol density gradients to discriminate the nature of the DNA cargo of the sEVs. Paired comparisons of the sEV-associated DNA and RNA molecules showed that RNA was more abundant than DNA and that most of the DNA was present in the high-density fractions, demonstrating that sEV subpopulations have different DNA content. DNA was predominately localised on the outside or surface of sEVs, with only a small portion being protected from enzymatic degradation. Whole-genome sequencing identified DNA fragments spanning all chromosomes and mitochondrial DNA when sEVs were analysed in bulk. Our work contributes to the understanding of how DNA is associated with sEVs and thus provides direction for distinguishing subtypes of EVs based on their DNA cargo and topology. (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
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 ultracentrifugation
    • DG = density gradient
    • UF = ultrafiltration
    • SEC = size-exclusion chromatography
FC + DG + dUC
Protein markers
EV: TSG101/ CD63/ CD81/ Alix/ Flotillin1/ BrdU/ beta-actin/ CD9
non-EV: Calnexin
Proteomics
yes
EV density (g/ml)
1.111-1.133
Show all info
Study aim
Identification of content (omics approaches)
Sample
Species
Homo sapiens
Sample Type
Cell culture supernatant
Sample Condition
Control condition
EV-producing cells
HMC-1
EV-harvesting Medium
EV-depleted medium
Preparation of EDS
>=18h at >= 100,000g
Cell viability
Yes
Cell viability (%)
Yes
Separation 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)
150
Pelleting: rotor type
Type 45 Ti
Pelleting: speed (g)
118500
Density gradient
Density medium
Iodixanol
Type
Discontinuous
Number of initial discontinuous layers
9
Lowest density fraction
20%
Highest density fraction
45%
Total gradient volume, incl. sample (mL)
12
Sample volume (mL)
1
Orientation
Bottom-up
Rotor type
SW 41 Ti
Speed (g)
180000
Duration (min)
960
Fraction volume (mL)
1
Fraction processing
Centrifugation
Pelleting: volume per fraction
94
Pelleting: duration (min)
210
Pelleting: rotor type
Type 45 Ti
Pelleting: speed (g)
118500
Characterization: Protein analysis
Protein Concentration Method
Fluorometric assay (e.g. Qubit, NanoOrange,...)
Western Blot
Detected EV-associated proteins
Flotillin1/ CD9/ CD63/ TSG101/ Alix/ CD81
Not detected EV-associated proteins
beta-actin
Not detected contaminants
Calnexin
ELISA
Detected EV-associated proteins
BrdU/ CD9
Flow cytometry specific beads
Detected EV-associated proteins
CD63
Proteomics database
Yes:
Characterization: Particle analysis
NTA
Report type
Size range/distribution
Reported size (nm)
50-300
EV concentration
Yes
EM
EM-type
Transmission-EM
Image type
Close-up, Wide-field
EV190045 2/4 Homo sapiens Cell culture supernatant FC
DG
dUC
Lázaro-Ibáñez E 2019 100%

Study summary

Full title
All authors
Lázaro-Ibáñez E, Lässer C, Shelke GV, Crescitelli R, Jang SC, Cvjetkovic A, García-Rodríguez A, Lötvall J.
Journal
J Extracell Vesicles
Abstract
Extracellular vesicles have the capacity to transfer lipids, proteins, and nucleic acids between cel (show more...)Extracellular vesicles have the capacity to transfer lipids, proteins, and nucleic acids between cells, thereby influencing the recipient cell's phenotype. While the role of RNAs in EVs has been extensively studied, the function of DNA remains elusive. Here, we distinguished novel heterogeneous subpopulations of small extracellular vesicles (sEVs) based on their DNA content and topology. Low- and high-density sEV subsets from a human mast cell line (HMC-1) and an erythroleukemic cell line (TF-1) were separated using high-resolution iodixanol density gradients to discriminate the nature of the DNA cargo of the sEVs. Paired comparisons of the sEV-associated DNA and RNA molecules showed that RNA was more abundant than DNA and that most of the DNA was present in the high-density fractions, demonstrating that sEV subpopulations have different DNA content. DNA was predominately localised on the outside or surface of sEVs, with only a small portion being protected from enzymatic degradation. Whole-genome sequencing identified DNA fragments spanning all chromosomes and mitochondrial DNA when sEVs were analysed in bulk. Our work contributes to the understanding of how DNA is associated with sEVs and thus provides direction for distinguishing subtypes of EVs based on their DNA cargo and topology. (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
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 ultracentrifugation
    • DG = density gradient
    • UF = ultrafiltration
    • SEC = size-exclusion chromatography
FC + DG + dUC
Protein markers
EV: TSG101/ Histone H3/ CD63/ CD81/ Alix/ Flotillin1/ Histone H2A/ beta-actin/ CD9
non-EV: Calnexin
Proteomics
yes
EV density (g/ml)
1.144-1.176
Show all info
Study aim
Identification of content (omics approaches)
Sample
Species
Homo sapiens
Sample Type
Cell culture supernatant
Sample Condition
Control condition
EV-producing cells
HMC-1
EV-harvesting Medium
EV-depleted medium
Preparation of EDS
>=18h at >= 100,000g
Cell viability
Yes
Cell viability (%)
Yes
Separation 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)
150
Pelleting: rotor type
Type 45 Ti
Pelleting: speed (g)
118500
Density gradient
Density medium
Iodixanol
Type
Discontinuous
Number of initial discontinuous layers
9
Lowest density fraction
20%
Highest density fraction
45%
Total gradient volume, incl. sample (mL)
12
Sample volume (mL)
1
Orientation
Bottom-up
Rotor type
SW 41 Ti
Speed (g)
180000
Duration (min)
960
Fraction volume (mL)
4
Fraction processing
Centrifugation
Pelleting: volume per fraction
94
Pelleting: duration (min)
210
Pelleting: rotor type
Type 45 Ti
Pelleting: speed (g)
118500
Characterization: Protein analysis
Protein Concentration Method
Fluorometric assay (e.g. Qubit, NanoOrange,...)
Western Blot
Detected EV-associated proteins
Flotillin1/ Alix/ CD9/ CD63/ beta-actin/ TSG101/ CD81/ Histone H2A/ Histone H3
Detected contaminants
Calnexin
ELISA
Detected EV-associated proteins
CD9
Flow cytometry specific beads
Detected EV-associated proteins
CD63
Proteomics database
Yes:
Characterization: Particle analysis
NTA
Report type
Size range/distribution
Reported size (nm)
100-300
EV concentration
Yes
EM
EM-type
Transmission-EM
Image type
Close-up, Wide-field
EV190045 3/4 Homo sapiens Cell culture supernatant FC
DG
dUC
Lázaro-Ibáñez E 2019 100%

Study summary

Full title
All authors
Lázaro-Ibáñez E, Lässer C, Shelke GV, Crescitelli R, Jang SC, Cvjetkovic A, García-Rodríguez A, Lötvall J.
Journal
J Extracell Vesicles
Abstract
Extracellular vesicles have the capacity to transfer lipids, proteins, and nucleic acids between cel (show more...)Extracellular vesicles have the capacity to transfer lipids, proteins, and nucleic acids between cells, thereby influencing the recipient cell's phenotype. While the role of RNAs in EVs has been extensively studied, the function of DNA remains elusive. Here, we distinguished novel heterogeneous subpopulations of small extracellular vesicles (sEVs) based on their DNA content and topology. Low- and high-density sEV subsets from a human mast cell line (HMC-1) and an erythroleukemic cell line (TF-1) were separated using high-resolution iodixanol density gradients to discriminate the nature of the DNA cargo of the sEVs. Paired comparisons of the sEV-associated DNA and RNA molecules showed that RNA was more abundant than DNA and that most of the DNA was present in the high-density fractions, demonstrating that sEV subpopulations have different DNA content. DNA was predominately localised on the outside or surface of sEVs, with only a small portion being protected from enzymatic degradation. Whole-genome sequencing identified DNA fragments spanning all chromosomes and mitochondrial DNA when sEVs were analysed in bulk. Our work contributes to the understanding of how DNA is associated with sEVs and thus provides direction for distinguishing subtypes of EVs based on their DNA cargo and topology. (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
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 ultracentrifugation
    • DG = density gradient
    • UF = ultrafiltration
    • SEC = size-exclusion chromatography
FC + DG + dUC
Protein markers
EV: TSG101/ CD63/ CD81/ Alix/ Flotillin1/ CD9
non-EV: Calnexin
Proteomics
no
EV density (g/ml)
1.103-1.137
Show all info
Study aim
Identification of content (omics approaches)
Sample
Species
Homo sapiens
Sample Type
Cell culture supernatant
Sample Condition
Control condition
EV-producing cells
TF-1
EV-harvesting Medium
EV-depleted medium
Preparation of EDS
>=18h at >= 100,000g
Cell viability
Yes
Cell viability (%)
Yes
Separation 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)
150
Pelleting: rotor type
Type 45 Ti
Pelleting: speed (g)
118500
Density gradient
Density medium
Iodixanol
Type
Discontinuous
Number of initial discontinuous layers
9
Lowest density fraction
20%
Highest density fraction
45%
Total gradient volume, incl. sample (mL)
12
Sample volume (mL)
1
Orientation
Bottom-up
Rotor type
SW 41 Ti
Speed (g)
180000
Duration (min)
960
Fraction volume (mL)
1
Fraction processing
Centrifugation
Pelleting: volume per fraction
94
Pelleting: duration (min)
210
Pelleting: rotor type
Type 45 Ti
Pelleting: speed (g)
118500
Characterization: Protein analysis
Protein Concentration Method
Fluorometric assay (e.g. Qubit, NanoOrange,...)
Western Blot
Detected EV-associated proteins
Flotillin1/ Alix/ CD63/ TSG101/ CD81
Not detected EV-associated proteins
CD9
Not detected contaminants
Calnexin
Flow cytometry specific beads
Detected EV-associated proteins
CD63
Characterization: Particle analysis
NTA
Report type
Size range/distribution
Reported size (nm)
50-300
EV concentration
Yes
EM
EM-type
Transmission-EM
Image type
Close-up, Wide-field
EV190045 4/4 Homo sapiens Cell culture supernatant FC
DG
dUC
Lázaro-Ibáñez E 2019 100%

Study summary

Full title
All authors
Lázaro-Ibáñez E, Lässer C, Shelke GV, Crescitelli R, Jang SC, Cvjetkovic A, García-Rodríguez A, Lötvall J.
Journal
J Extracell Vesicles
Abstract
Extracellular vesicles have the capacity to transfer lipids, proteins, and nucleic acids between cel (show more...)Extracellular vesicles have the capacity to transfer lipids, proteins, and nucleic acids between cells, thereby influencing the recipient cell's phenotype. While the role of RNAs in EVs has been extensively studied, the function of DNA remains elusive. Here, we distinguished novel heterogeneous subpopulations of small extracellular vesicles (sEVs) based on their DNA content and topology. Low- and high-density sEV subsets from a human mast cell line (HMC-1) and an erythroleukemic cell line (TF-1) were separated using high-resolution iodixanol density gradients to discriminate the nature of the DNA cargo of the sEVs. Paired comparisons of the sEV-associated DNA and RNA molecules showed that RNA was more abundant than DNA and that most of the DNA was present in the high-density fractions, demonstrating that sEV subpopulations have different DNA content. DNA was predominately localised on the outside or surface of sEVs, with only a small portion being protected from enzymatic degradation. Whole-genome sequencing identified DNA fragments spanning all chromosomes and mitochondrial DNA when sEVs were analysed in bulk. Our work contributes to the understanding of how DNA is associated with sEVs and thus provides direction for distinguishing subtypes of EVs based on their DNA cargo and topology. (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
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 ultracentrifugation
    • DG = density gradient
    • UF = ultrafiltration
    • SEC = size-exclusion chromatography
FC + DG + dUC
Protein markers
EV: TSG101/ Histone H3/ CD63/ CD81/ Alix/ Flotillin1/ Histone H3/ Histone H2A/ beta-actin/ CD9
non-EV: Calnexin
Proteomics
no
EV density (g/ml)
1.148-1.192
Show all info
Study aim
Identification of content (omics approaches)
Sample
Species
Homo sapiens
Sample Type
Cell culture supernatant
Sample Condition
Control condition
EV-producing cells
TF-1
EV-harvesting Medium
EV-depleted medium
Preparation of EDS
>=18h at >= 100,000g
Cell viability
Yes
Cell viability (%)
Yes
Separation 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)
150
Pelleting: rotor type
Type 45 Ti
Pelleting: speed (g)
118500
Density gradient
Density medium
Iodixanol
Type
Discontinuous
Number of initial discontinuous layers
9
Lowest density fraction
20%
Highest density fraction
45%
Total gradient volume, incl. sample (mL)
12
Sample volume (mL)
1
Orientation
Bottom-up
Rotor type
SW 41 Ti
Speed (g)
180000
Duration (min)
960
Fraction volume (mL)
1
Fraction processing
Centrifugation
Pelleting: volume per fraction
94
Pelleting: duration (min)
210
Pelleting: rotor type
Type 45 Ti
Pelleting: speed (g)
1185000
Characterization: Protein analysis
Protein Concentration Method
Fluorometric assay (e.g. Qubit, NanoOrange,...)
Western Blot
Detected EV-associated proteins
Flotillin1/ beta-actin/ CD9/ CD63/ TSG101/ CD81/ Histone H2A/ Histone H3
Not detected EV-associated proteins
Alix
Not detected contaminants
Calnexin
Flow cytometry specific beads
Detected EV-associated proteins
CD63
Characterization: Particle analysis
NTA
Report type
Size range/distribution
Reported size (nm)
100-300
EV concentration
Yes
EM
EM-type
Transmission-EM
Image type
Close-up, Wide-field
1 - 4 of 4
  • CM = Commercial method
  • dUC = differential ultracentrifugation
  • DG = density gradient
  • UF = ultrafiltration
  • SEC = size-exclusion chromatography
EV-TRACK ID
EV190045
species
Homo sapiens
sample type
Cell culture
cell type
HMC-1
HMC-1
TF-1
TF-1
condition
Control condition
Control condition
Control condition
Control condition
separation protocol
FC
DG
dUC
FC
DG
dUC
FC
DG
dUC
FC
DG
dUC
Exp. nr.
1
2
3
4
EV-METRIC %
100
100
100
100