Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Dichotomic size-exclusion chromatography（SEC）

ABSTRACT: directDIA proteomics raw data of plasma extracellular vesicles isolated by SEC and UC

ORGANISM(S): Homo Sapiens

SUBMITTER: Tong Wang

PROVIDER: PXD026034 | iProX | Mon May 17 00:00:00 BST 2021

REPOSITORIES: iProX

ACCESS DATA

Json Xml

Publications

Establishment of a simplified dichotomic size-exclusion chromatography for isolating extracellular vesicles toward clinical applications.

Guo Jiahui J Wu Caihong C Lin Xinyi X Zhou Jian J Zhang Jiayi J Zheng Wenting W Wang Tong T Cui Yizhi Y

Journal of extracellular vesicles 20210901 11

Size-exclusion chromatography (SEC) is a widely adopted method for the isolation of extracellular vesicles (EVs) from complex samples. SEC can efficiently remove high-abundant proteins, while often requires multiple fractionation operation using diversified column settings. In this study, we aim to establish a simplified SEC method to acquire high quality EVs. In comparison of all three cross-linked Sepharose resins with the sample types of FBS and human serum (HS), CL-6B and CL-4B showed superi ...[more]

PMID: 34514732

Similar Datasets

Comparison of three methods for isolating human plasma EVs by LC-MSMS

Project description:The lack of standardized protocols for isolating extracellular vesicles (EVs), particularly from biobank-stored plasma, poses a substantial limitation for the study of biomarkers. Combining current isolation methods could enhance the specificity and purity of EVs isolation for their further use in diagnosis and personalized medicine. In this study, plasma samples from healthy individuals were subjected to extracellular vesicle isolation using ultracentrifugation (UC), size exclusion chromatography (SEC), and a combined approach of SEC and UC (SEC+UC). Characterization of the isolated EVs with NTA and TEM indicated that all isolation methods successfully isolated EVs, being not altered due to the long-term storage. Also, the western blot analysis confirmed the presence of exosome markers in all isolates but showed a higher expression of albumin in EVs-UC, suggesting potential plasma protein contamination. Proteomic analysis of samples from different isolation methods identified 542 proteins, with SEC+UC yielding the most complex proteome at 364 proteins. GO analysis of cellular component revealed differences in terms related to EVs and plasma, where SEC+UC proteins had the highest proportion of exosomal proteins. As a result of further study of the unique proteins detected in each isolation method, it was revealed that the SEC+UC method detected 181 unique proteins, demonstrating its superiority in the detection of low plasma concentration proteins. These findings support the robustness of the SEC+UC approach for EV isolation and proteomic studies due to its high efficiency and purity in isolating EVs. This study emphasizes the efficacy of the SEC+UC approach in obtaining highly pure and diverse EV populations suitable for comprehensive proteomic analysis with application to the discovery of biomarkers from biobank-stored plasma.

2024-07-03 | PXD049342 | Pride

Profiling mouse exosomal RNA to understand antibiotics treatment consequences

Project description:We isolated circulating extracellular vesicles (EVs) from plasma collected from adolescent mus musculus. RNA sequencing revealed that mouse plasma EVs contain RNA aligned to the microbiome.

2025-07-24 | GSE302894 | GEO

The proteome of circulating extracellular vesicles and their functional effect on platelets vary with the isolation method

Project description:Extracellular vesicles (EVs) play a crucial role in cell-to-cell communication and serve as a source of biomarkers in several pathologies. In this study, we aimed to characterize plasma-derived EVs isolated by ultracentrifugation (UC) or size exclusion chromatography (SEC) to define the best method for proteomic and functional studies. EVs characterization included nanoparticle tracking analysis (NTA), transmission electron microscopy (TEM), detection of biomarkers by western blotting, and quantitative proteomic analysis. SEC-EVs samples had higher particle and protein concentration, particle-to-protein ratio, and smaller size compared to UC-EVs. A total of 171 proteins were identified through Sequential Window Acquisition of All Theoretical Mass Spectra (SWATH-MS) analysis, with 11 increased in SEC-EVs and 5 in UC-EVs. The proteins increased in UC-EVs are complement proteins and immunoglobulins, while the proteins increased in SEC-EVs are apolipoproteins and proteins present in the extracellular space. Functional studies with EVs from activated platelets confirmed that EVs isolated by SEC exacerbate platelet aggregation, whereas there was no effect induced by UC-EVs. The latter suggests that EVs obtained by SEC seem more suitable for platelet-related functional studies compared to those obtained by UC. The results presented pave the way for future clinical orientated studies involving plasma-derived EVs.

2025-02-14 | PXD056613 | Pride

Optimization of ultracentrifugation-based method to enhance the purity and proteomic profiling depth of plasma-derived extracellular vesicles and particles

Project description:Circulating extracellular vesicles and particles (EVPs) are being investigated as potential biomarkers for early cancer detection, prognosis, and disease monitoring. However, the suboptimal purity of EVPs isolated from peripheral blood plasma has posed a challenge of in-depth analysis of the EVP proteome. Here, we compared the effectiveness of different methods for isolating EVPs from healthy donor plasma, including ultracentrifugation (UC)-based protocols, phosphatidylserine-Tim4 interaction-based affinity capture (referred to as "PS"), and several commercial kits. Modified UC methods with an additional UC washing or size exclusion chromatography step substantially improved EVP purity and enabled the detection of additional proteins via proteomic mass spectrometry, including many plasma membrane and cytoplasmic proteins involved in vesicular regulation pathways. This improved performance was reproduced in cancer patient plasma specimens, resulting in the identification of a greater number of differentially expressed EVP proteins, thus expanding the range of potential biomarker candidates. However, PS and other commercial kits did not outperform UC-based methods in improving plasma EVP purity. PS yielded abundant contaminating proteins and a biased enrichment for specific EVP subsets, thus unsuitable for proteomic profiling of plasma EVPs. Therefore, we have optimized UC-based protocols for circulating EVP isolation, which enable further in-depth proteomic analysis for biomarker discovery.

2024-08-10 | PXD052726 | Pride

Profiles of exRNA in CSF and Plasma from Subarachnoid Hemorrhage Patients

Project description:<p>Brain injury resulting from hemorrhagic stroke is clinically challenging to manage and results in high rates of morbidity and mortality. The pathophysiology of brain damage resulting from aneurysmal subarachnoid hemorrhage (aSAH) is largely unknown, and methods to treat and monitor patients are variable with no meaningful correlations to patient outcome. Prediction of patient risk for serious neurological complications is currently a significant clinical obstacle. An extracellular RNA (exRNA) biomarker to predict onset and severity of brain damage would improve patient outcomes. We sequenced plasma and CSF samples from adult patients with SAH. Samples were collected from post bleed day 1 to day 7. Total exRNA was isolated from each sample. In addition, we prepared a subset of 140 CSF samples, isolating the RNA contained within extracellular vesicles and vesicle-depleted biofluid.</p>

| phs001759 | dbGaP

Project description:seminal plasma-derived extracellular vesicles isolated from cryopreserved bull semen

| PRJNA1101695 | ENA

Whole transcriptome analysis of endothelial cells (HUVECs) after treatment with plasma-sEVs from polytrauma patients

Project description:To assess inflammation associated gene expression in endothelial cells mediated by small extracellular vesicles (sEVs), HUVECs were treated for 8hrs with plasma-Evs isolated from polytrauma patients 4 and 24hrs after trauma and healthy probands.

2021-04-17 | GSE172210 | GEO

Small RNA Landscape of Platelet Dust: Platelet-Derived Extracellular Vesicles from Patients with Non-Small-Cell Lung Cancer

Project description:Abstract: Background: Platelet-derived Extracellular Vesicles, or “Platelet Dust” (PD), are reported as the most-abundant extracellular vesicles in plasma. However, the PD molecular content, especially the small RNA profile, is still poorly characterized. This study aims to characterize PD and other extracellular vesicles (EVs) in patients with non- small-cell lung cancer (NSCLC), focusing on their small RNA signatures and diagnostic potential. Methods: The EVs were isolated directly from the plasma of healthy donors and patients with NSCLC using the surface markers CD9, CD63, CD81 (overall EVs), and CD61 (PD). Small RNA sequencing was then performed to comprehensively profile the miRNAs. Results: Our analysis revealed distinct small RNA profiles in the EVs and the PD from the patients with NSCLC. The EVs (CD9-, CD63-, and CD81-positive) showed the enrichment of four miRNAs and the depletion of ten miRNAs, while the PD (CD61- positive) exhibited a more complex profile, with nineteen miRNAs enriched and nine miRNAs depleted in the patients with NSCLC compared to those of the healthy controls. Conclusions: This exploratory study enhances our understanding of miRNA composition within different plasma vesicle populations, shedding light on the biology of plasma vesicles and their contents. Furthermore, utilizing an extracellular vesicle isolation method with potential clinical applicability offers the prospect of improved cancer characterization and detection by selecting the most informative subpopulation of plasma vesicles.

2025-05-07 | GSE244416 | GEO

Differential expression of extracellular vesicles-derived long RNA sequencing of plasma from patients after myocardial infarction with or without cardiac remodeling and healthy individuals

Project description:The goals of this study are to compare extracellular vesicles-derived circRNAs-lncRNAs-mRNA(RNA-seq) from the plasma of myocardial infarction patients with cardiac remodeling (C), without cardiac remodeling (NC), and normal healthy people (N). Human plasma was separated by centrifugation at 3,000 rpm for 10 min at room temperature (25°C) within 2 h after blood collection and then centrifuged at 13,000 rpm for 10 min at 4°C to remove debris. Isolated plasma samples were stored at -80°C until use. Extracellular vesicles RNA were isolated by affinity-based binding to spin columns using an exoRNeasy Serum/Plasma kit (Qiagen, Hilden, Germany). RNA libraries were prepared for sequencing using SMARTer Stranded Total RNA-Seq Kit - Pico Input Mammalian. RNA-seq was performed by the Illumina NovaSeq 6000 on a 150-bp paired-end run.

2023-02-08 | GSE194388 | GEO

Human plasma extracellular vesicles

Project description:Human Plasma Extracellular Vesicles Parkinsons Disease

| PRJNA1234656 | ENA