Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Isolation of Extracellular Vesicles from human plasma samples: The importance of controls

ABSTRACT: EV isolation from the plasma using differential Ultracentrifugation method

INSTRUMENT(S):

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Blood Plasma

SUBMITTER: Migmar Tsamchoe

LAB HEAD: peter metrakos

PROVIDER: PXD037903 | Pride | 2026-05-07

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	Migmar_EV07-20_Aug_2020.mzid.gz_EV07_04_08_2020__F013506_.MGF	Mzid
	Migmar_EV07-20_Aug_2020.mzid.gz_EV08_04_08_2020__F013507_.MGF	Mzid
	Migmar_EV07-20_Aug_2020.mzid.gz_EV09_04_08_2020__F013508_.MGF	Mzid
	Migmar_EV07-20_Aug_2020.mzid.gz_EV10_04_08_2020__F013509_.MGF	Mzid
	Migmar_EV07-20_Aug_2020.mzid.gz_EV11_04_08_2020__F013510_.MGF	Mzid

Items per page:

1 - 5 of 19

Publications

Isolation of extracellular vesicles from human plasma samples: The importance of controls.

Tsamchoe Migmar M Petrillo Stephanie S Lazaris Anthoula A Metrakos Peter P

Biotechnology journal 20230409 6

<h4>Background</h4>Extracellular vesicles (EV) are enriched with proteins and RNA cargo, promoting cell-to-cell communication. Biofluid derived EV cargo is used for discovering disease specific markers for diagnosis and disease monitoring.<h4>Rational</h4>Blood is a complex fluid with an abundance of protiens and thus isolation of EVs is challenging. Therefore, methods for EV isolation, including commercial kits use thromboplastin D (TP-D) for pretreatment of plasma to increase EV purity and yie ...[more]

PMID: 36988156

Similar Datasets

Localized synthesis of molecular chaperones sustains neuronal proteostasis

Project description:Proteostasis at neuronal projections supports the molecular basis behind long-term information storage and movement control. It is maintained through regulated protein synthesis and degradation and chaperone-assisted protein folding. Using high-resolution fluorescent microscopy, we discovered that neurons localize a subset of chaperone mRNAs to their dendrites and increase this asymmetric localization following proteotoxic stress. The most abundant chaperone mRNA in dendrites encodes for the constitutive heat shock protein 70, HSPA8. Most Hspa8 mRNAs travel in dendrites as single molecules. In the dendrites, Hspa8 mRNAs are locally translated by mono and polyribosomes, and proteotoxic stress further enhances the percentage of mRNAs engaged in translation and their efficiency. We discovered that Fused in Sarcoma (FUS) and heterogenous nuclear ribonucleoprotein A2/B1 (HNRNPA2B1) participate in stress-mediated localization of Hspa8 mRNA in dendrites of mouse and human motor neurons, respectively. As such, FUS knocked down neurons accumulate misfolded proteins in dendrites upon stress exposure. Together, these results reveal a novel mechanism allowing neurons to uphold proteostasis at dendrites and spines upon stress.

2024-11-13 | PXD046036 | Pride

Heterozygous variants in MGP lead to endoplasmic reticulum stress causing spondyloepiphyseal dysplasia

Project description:Matrix Gla protein (MGP) is a vitamin K-dependent post-translationally modified protein, highly expressed in vascular and cartilaginous tissues. It is a potent inhibitor of extracellular matrix mineralization. Biallelic loss of function variants in the MGP gene cause Keutel syndrome, an autosomal recessive disorder characterized by widespread calcification of various cartilaginous tissues and skeletal and vascular anomalies. In this study, we report four individuals from two unrelated families with two heterozygous variants in MGP, both altering the Cysteine 19 residue to phenylalanine or tyrosine. These individuals presented with a spondyloepiphyseal skeletal dysplasia characterized by short stature with a short trunk, diffuse platyspondyly, midface retrusion, progressive epiphyseal anomalies and brachytelephalangism. We investigated the cellular and molecular effects of one of the heterozygous deleterious variants (C19F) using both cell and genetically modified mouse models. Heterozygous ‘knock-in’ mice expressing C19F MGP recapitulated most of the skeletal anomalies observed in the affected individuals. We demonstrated that the main underlying mechanism leading to the observed skeletal dysplasia is endoplasmic reticulum stress-induced apoptosis of the growth plate chondrocytes. Our findings support that heterozygous variants in MGP altering Cys19 residue cause autosomal dominant spondyloepiphyseal dysplasia, a condition distinct from Keutel syndrome both clinically and molecularly.

2024-01-26 | PXD043374 | Pride

Untargeted proteomics of Enterocloster asparagiformis, E. citroniae, E. pacaense treated with DMSO or urolithin M6

Project description:Urolithins are a class of bioactive metabolites derived from the metabolism of dietary ellagitannins by the human gut microbiota. In the gut, urolithins are dehydroxylated regioselectively based on microbiota composition and activity. A single 9-hydroxy urolithin dehydroxylase (ucd) operon in gut resident Enterocloster species has been described to date; however, most enzymes in the urolithin metabolic pathway remain uncharacterized. Here, we investigate urolithin cross-feeding between members of the gut microbiota and discover a novel urolithin dehydroxylase in a subset of Enterocloster species. We show that urolithin intermediates, released by gut resident Gordonibacter species during ellagic acid metabolism, are dehydroxylated at both the 9- and 10-positions by E. asparagiformis, E. citroniae, and E. pacaense, but not E. bolteae. Using untargeted proteomics, we uncover a 10-hydroxy urolithin dehydroxylase operon, termed uxd, responsible for these species-specific differences in urolithin metabolism. By inducing uxd expression with diverse urolithins, we show that 9-hydroxy urolithins are required for uxd transcription and 10-position dehydroxylation. Collectively, this study reveals some of the genes, proteins, and substrate features underlying differences in urolithin metabolism by the human gut microbiota.

2025-11-12 | PXD066865 | Pride

Protein profile of purified plasma and aqueous humor-derived extracellular vesicles from patients with ocular toxoplasmosis

Project description:To characterize extracellular vesicles proteins cargo from the aqueous humor and plasma of patients with ocular toxoplasmosis. Methods: Aqueous humor (AH) and plasma were collected from 6 patients with active ocular toxoplasmosis (OT) and 6 cataract patients (CAT). Extracellular vesicles (EVs) were isolated, and western blotting and mass spectrometry were performed for protein analysis. Results: All plasma samples from OT and CAT patients were positive for tetraspanins CD63 and TSG101 markers. However, only the AH from OT patients were positive for CD63. A total of 67 new proteins not previously reported in EVs were found in the AH and plasma from OT and CAT groups. Among these, 10 and 7 proteins were found only in the samples from CAT and OT groups, respectively. In general, these proteins were involved in immune system activation, retina homeostasis, factors related to infections and retina-associated disease. Conclusion: The distinct protein signatures between OT and CAT patients may be helpful in the differential diagnosis of OT. However, more studies are needed to better understand the role of these proteins in the pathogenesis of OT.

2025-11-10 | PXD046167 | Pride

CD44 regulates epigenetic plasticity by mediating iron endocytosis - part 2

Project description:The biological process termed Epithelial-to-Mesenchymal Transition (EMT) plays a central role in cancer cell invasion, metastasis, self-renewal and resistance to therapy(1,2). Here, using western blot technique, we show that H3K9me2 decreases when MDA-MB-468 breast cancer cells undergo EMT upon EGF. We validate this decrease by performing high-resolution MS/MS spectrum. Interestingly, we find that H3K9me2 is associated with mesenchymal genes regulation. 1. Nieto, M. A., Huang, R. Y., Jackson, R. A. & Thiery, J. P. EMT: 2016. Cell 166, 21–45 (2016). 2. Puisieux, A. & Brabletz, T. & Caramel, J. Oncogenic roles of EMT-inducing transcription factors. Nat. Cell Biol. 16, 488–494 (2014).

2010-10-09 | PXD012862 | Pride

Antibodies to protozoan variable surface antigens induce antigenic variation

Project description:The genomes of most protozoa encode families of variant surface antigens, whose mutually exclusive changes in expression allow parasitic microorganisms to evade the host immune response1. It is widely assumed that antigenic variation in protozoan parasites is accomplished by the spontaneous appearance within the population of cells expressing antigenic variants that escape antibody-mediated cytotoxicity1,2. Here we show, both in vitro and in animal infections, that antibodies to Variant-specific Surface Proteins (VSPs) of the intestinal parasite Giardia lamblia are not cytotoxic; instead, anti-VSP antibodies induce VSP clustering into microdomains, triggering a massive release of microvesicles carrying the original VSP and switching in expression to different VSPs by a calcium-dependent process. Surface microvesiculization and antigenic switching are also stimulated when Trypanosoma brucei and Tetrahymena thermophila are confronted to antibodies directed to their GPI-anchored variable surface glycoproteins. This novel mechanism of antigen clearance throughout its release into microvesicles coupled to the stochastic induction of new phenotypic variants not only changes the current paradigm of spontaneous antigenic switching but also provides a new framework for understanding the course of infections as a host/parasite adaptive process.

2023-05-10 | PXD031141 | Pride

TP53 sequence of human glioblastoma stem cells sorted for p53-Ser15 induction and NS1 virus protein expression upon parvovirus MVMp infection

Project description:We have analyzed whether mutations in the TP53 gene and post-translational phosphorylation in the Ser-15 residue of the p53 protein (Pp53) may confer permissiveness to the prototype strain of the parvovirus Minute Virus of MIce ( MVMp) infection in human glioblastoma stem cells (GSCs) isolated from brain tumours. Infected (MVMp samples) and control uninfected (mock samples) GSCs from four patients (GS5, GS7, GS8, GS9) were sorted for the Pp53 modification (which is required for virus genome replication) and the NS1 protein (a major marker of virus cytotoxic gene expression). Cells sorted through restrictive gates for the NS1+/Pp53+ and NS1+/Pp53- phenotypes were proceeded for mRNA purification, the TP53 gene was amplified with specific primers and subjected to NGS analysis.

2021-07-13 | E-MTAB-9359 | biostudies-arrayexpress

Genotyping of Arabidopsis ecotypes

Project description:Large-scale screening studies carried out to date to elucidate the causal mechanism of an allelic imbalance are generally limited to descriptions of allele-specific differences in expression detected in vivo and to linking them to differences in cis- and trans-regulatory changes. Although such gene surveys for regulatory variation leave the underlying mechanisms unexplored, they are a first step in identifying the specific nucleotide changes that govern gene expression differences. We describe a quantitative genetics approach to distinguish between cis- and trans-regulatory changes at a genome-wide scale and, hence, to detect cis-regulatory variation. For this purpose, we took advantage of diallel designs that are often used in plant breeding programs in which the goal is the estimation of general combining abilities (GCAs) of specific inbred lines and the identification of high yielding hybrid combinations of parents based on their specific combining abilities (SCAs). We show that in a context of gene expression, empirical estimates of GCA and SCA are valid parameters to distinguish between cis- and trans-regulatory changes and, hence, to detect cis-regulatory variation. By using this approach, we identified a considerable number of genes that showed evidence of cis-regulated allele-specific expression in a total of 10 diploid Arabidopsis hybrids. The method can also be used to explore naturally occurring cis-regulatory variation among inbred lines for laboratory animals, such as mouse and rat. This experiment covers data from 10 pairs of reciprocal hybrid samples, referred to as Hx.y where x=1...10 and y=1,2; The related data from 20 Recombinant Inline Line samples is submitted as experiment : - VIB Plant Systems Biology "RIL")

2006-12-02 | E-TABM-67 | biostudies-arrayexpress

Generation of chromatin maps for ASH1 and FSH applying ChIP-seq

Project description:see Super Series Summary Cross-linked chromatin derived from Drosophila S2-DRSC cells was immunoprecipitated using antibodies targeting ASH1 and FSH. Precipitated chromatin was sequenced applying Illumina sequencing.

2013-02-06 | E-GEOD-36404 | biostudies-arrayexpress

Human T-cells EVs LC-MSMS - Extracellular Vesicle Subtypes Released From Activated or Apoptotic T-Lymphocytes Carry a Specific and Stimulus-Dependent Protein Cargo

Project description:As it is likely that different stimuli promote the release of distinct EV populations, we analyzed EVs from human lymphocytes considering the respective release stimuli (activation vs. apoptosis induction). Morphology and size were analyzed by electron microscopy and nanoparticle tracking analysis. The protein content of these vesicles was analyzed by bidimensional gel electrophoresis followed by mass spec and western blot.

2018-03-15 | PXD009074 | Pride

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data