Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Proteomics of Small Extracellular Vesicles from Melanoma DCC-Derived Cell Lines

ABSTRACT: Small extracellular vesicles (sEVs) were isolated from the culture supernatant of melanoma DCC-derived cell lines (MelDCC) after 48 hours of serum-free culture. sEVs were obtained through differential ultracentrifugation, specifically as the 100K pellet, following the protocol described in detail by Théry et al. (https://doi.org/10.1002/0471143030.cb0322s30). Proteomic analysis of the isolated sEVs was performed using mass spectrometry to characterize their protein content.

INSTRUMENT(S):

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Permanent Cell Line Cell, Cell Culture

SUBMITTER: Peter Oefner

LAB HEAD: Peter J. Oefner

PROVIDER: PXD059510 | Pride | 2025-02-24

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	DDA-Exosomen_hLib.mgf	Mgf
	DDA-Exosomen_hLib_ProteinSummary.txt	Txt
	DDAP18-2018Exos1.wiff	Wiff
	DDAP18-2018Exos1.wiff.scan	Wiff
	DDAP18-2018Exos2.wiff	Wiff

Items per page:

1 - 5 of 19

Similar Datasets

Bottom-up proteomics of FFPE tissue section from DLBCL patients

Project description:FFPE tissue sections of lymphoma patients were analyzed. All patients were enrolled in prospective multicenter DSHNHL clinical trials. The study included DLBCL samples from 357 patients.

2025-09-06 | PXD058736 | Pride

Acute and chronic liver injury change the small RNA cargoes carried by serum small extracellular vesicles in mice

Project description:Compared to whole serum miRNAs, miRNAs in serum small extracellular vesicles (sEVs) are well protected form RNA enzymes, thus provide a consistent source of miRNA for disease biomarker detection. Serum sEVs and their miRNA cargos released by injured liver cells could be promising biomarkers for diagnosis of liver diseases. We were very interested to find out the effects of liver injury on serum extracellular vesicles as well as the small RNA components they transported, if there is any difference between acute and chronic injury. Study in this regard will help us to identify new serum biomarkers for liver injury, and to find out if there are specific markers for acute or chronic liver injury. To identify potential biomarker for liver injury based on serum sEVs miRNAs, we established the carbon tetrachloride (CCL4) induced acute and chronic liver injury mice model, and examined the dynamic changes of small RNA components, especially miRNAs, in serum sEVs.

2021-08-07 | E-MTAB-9462 | biostudies-arrayexpress

Deregulation of miRNAs in Infant Outflow Tract Myocardium of Non-syndromic Tetralogy of Fallot

Project description:Tetralogy of Fallot (TOF) is one of the most common heart defects in children and the underlying mechanisms remain elusive. miRNAs are a recently discovered class of regulators of gene expression and are becoming increasingly recognized as important regulators of heart development and function. The objective of the present study was to identify miRNAs that are abnormally expressed in clinical infant outflow tract myocardium tissues of TOFs. Microarray was used to analyze miRNA expression profiles in infant outflow tract myocardium tissues of TOFs and paired normal ones.

2012-08-14 | E-GEOD-40128 | biostudies-arrayexpress

RNA-Seq for primary rat Kupffer cells and monocytes treated with hepatic stellate cell-derived small extracellular vesicles

Project description:Aim: To find out the effects of small extracellular vesicles (sEVs) from short-term activated and long-term activated hepatic stellate cells (HSCs) on Kupffer cells (KCs) and bone marrow-derived monocytes (MOs). Methods: For the isolation of HSC-derived sEVs, culture media (CMs) from Day 0 to Day 3 and Day 7 to Day 14 were collected. The sEVs from Day 0 to Day 3 HSC CMs were referred to as short-term activated HSC-sEVs (3dHSC-sEVs), and those from Day 7 to Day 14 HSC CMs were referred to as long-term activated HSC-sEVs (14dHSC-sEVs). Purified primary rat KCs and MOs were cocultured with 3dHSC- or 14dHSC-sEVs for 48 h. HSC-sEVs cocultured KCs or MOs were lysed in TRIzol (Life Technologies) for RNA sample preparation at the indicated time points.

2024-08-29 | E-MTAB-12754 | biostudies-arrayexpress

Small RNA-Seq for primary rat hepatic stellate cells and hepatic stellate cell-derived small extracellular vesicles

Project description:Aims: To obtain small non-coding RNA expression profiles of short-term activated and long-term activated hepatic stellate cells (HSCs). To obtain small non-coding RNA expression profiles of small extracellular vesicles (sEVs) from short-term activated and long-term activated HSCs. Methods: Primary rat HSCs were isolated and cultured in vitro. To isolate HSC-derived sEVs, culture media (CMs) from Day 0 to Day 3 and Day 7 to Day 14 were collected. The sEVs from Day 0 to Day 3 HSC CMs were referred to as short-term activated HSC-sEVs (3dHSC-sEVs), and those from Day 7 to Day 14 HSC CMs were referred to as long-term activated HSC-sEVs (14dHSC-sEVs). Day 3 HSCs, Day 14 HSCs, and HSC-sEVs were collected and lysed in TRIzol (Life Technologies) for RNA sample preparation at the indicated time points.

2024-08-29 | E-MTAB-12764 | biostudies-arrayexpress

Proteomic approach for molecular classification of colorectal cancer

Project description:The main objective of this study was to identify potential protein expression signatures by the SWATH technique of proteomic analysis, to aid in the classification of molecular subtypes of colorectal cancer.

2019-10-04 | PXD007810 | Pride

Docosahexaenoic and Arachidonic Free Fatty Acids Exert Different Antitumor Activities on Colorectal Cancer Cells

Project description:Two PUFA, docosahexaenoic (DHA, 22: 6n3) and arachidonic acids (ARA, 20: 4n6), as well as their derivatives such as eicosanoids, regulate different activities, which include changes in receptor signaling, the composition of rafts, cell metabolism, and membrane structures. These also modify the function of transcription factors and their target genes, a key step essential for the function of FA-activated signaling. This work is focused to determine the antitumor actions of these compounds linked to the regulation of gene transcription on HT-29 colorectal cancer. For this, we performed antiproliferative antitumour assay, LDH breakage test, caspase-3 production, and proteome changes were assessed by SWATH-MS quantitative proteomics followed by pathway analysis in order to find out which molecular mechanisms were being affected. In all cases tested, DHA exercised antitumor actions to a higher extent than ARA, acting mainly by means of down-regulating most of the proteasome system particles, while ARA presented a heavy effect on all the six DNA replication helicase particles but did not affect proteasome. The results indicated that both DHA and ARA stopped colorectal cancer growth and proliferation, thus they represent the ideal candidates as chemopreventive agents.

2022-01-28 | PXD008653 | Pride

SWATH-MS based quantitative proteomics analysis reveals that curcumin alters the metabolic enzyme profile of CML cells by affecting the activity of miR-22/IPO7/HIF-1α axis.

Project description:Chronic myelogenous leukemia (CML) is a myeloproliferative disorder caused by expression of the chimeric BCR-ABL tyrosine kinase oncogene, resulting from the t(9;22) chromosomal translocation. Imatinib (gleevec, STI-571) is a selective inhibitor of Bcr-Abl activity highly effective in the treatment of CML. However, even though almost all CML patients respond to treatment with imatinib or third generation inhibitors. These drugs are not curative and need to be taken indefinitely or until patients become resistant. Therefore, to get a definitive eradication of leukemic cells, it is necessary to find novel therapeutic combinations, for achieving greater efficacy and fewer side effects. Nutraceuticals play an increasingly important role in the treatment of cancer. Curcumin is an Indian spice with several therapeutic properties: anti-oxidant, analgesic, anti-inflammatory, antiseptic and anti-cancer. In cancer disease, it acts by blocking cell transformation, proliferation, and invasion and by inducing cell apoptosis. In the present study, byapplying a quantitative proteomic SWATH-MS strategy we evaluated the effect of curcumin onK562 cells. Our findings revealed that the most relevant effect induced by curcumin was a consistent decrease of several proteins involved in glucose metabolism, most of which were HIF-1α targets, concomitant with the up-regulation of functional and structural mitochondrial proteins. The mechanism by which curcumin affects metabolic enzyme profile was associated with the reduction of HIF-1α activity, due to the miR-22-mediated down-regulation of importin 7 (IPO7) expression. Finally, the ability of curcumin to enhance in vitro the efficiency of imatinib was reported. In summary, our data indicates that the miR-22/IPO7/HIF-1α axis may be considered as a novel molecular target of curcumin adding new insights for better defining therapeutic activity and anticancer properties of this natural compound.

2018-07-30 | PXD007771 | Pride

The proteome of large or small extracellular vesicles in pig seminal plasma differs and defines sources and biological functions. Spectral Library

Project description:Seminal plasma contains many and morphologically heterogeneous extracellular vesicles (sEVs) which, released by cells of the testis, epididymis and accessory sex glands, are involved in male and female reproductive processes. The goal of this study was to describe the proteome of porcine sEVs isolated by a size exclusion chromatography (SEC)-based procedure and size-classed as small (S-EVs) or large (L-EVs). The sEV-subsets were characterized for their total protein concentration, morphology, size distribution, EV-specific protein markers and purity. A total of 988 proteins were identified by LC-MS/MS and 737 of them were quantified by SWATH in S-EVs, L-EVs and EVs-free samples. The differential expression analysis revealed 197 differentially abundant proteins between both EV-subsets, and 37 and 199 between S-EVs and L-EVs vs EVs-free samples, respectively. The gene ontology (GO) enrichment analysis of differentially abundant proteins suggested, by the type of protein detected, that S-EVs would be released mainly through an apocrine blebbing pathway and be involved in modulating the immune environment of the female reproductive tract as well as during sperm-oocyte interaction. In contrast, the protein types detected might imply L-EVs are released by fusion of multivesicular bodies with the plasma membrane and would be involved in sperm physiological processes, such as capacitation and avoidance of oxidative stress. In conclusion, this study provides a procedure capable of isolating of subsets of EVs from pig seminal plasma with a high degree of purity and shows differences in the proteomic profile between EV-subsets, suggesting different sources and biological functions.

2023-02-15 | PXD039833 | Pride

Unbiased miRNA screening analysis on myo-sEVs derived from Nor or HG/HL

Project description:The current study aims were to determine the differential expression of Myo-sEVs derived from normal or HG/HL.Mouse primary myocardial cells were isolated and cultured in normal and HG/HL culture medium. Myo-sEVs were separated by ultracentrifugation.Differential myo-sEVs-miRNA expression obtained through Unbiased miRNA array analysis.

2024-02-07 | E-MTAB-13736 | biostudies-arrayexpress

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