Similar Datasets
Project description:To identify the best method for isolating supermeres and their small RNA cargo from colorectal cancer cells
2024-07-31 | GSE272487 | GEO
Project description:Extracellular vesicles, including exosomes, and exomere nanoparticles, are under intense investigation for cargo that may serve as clinical biomarkers or therapeutic targets. Here, we report discovery of a new extracellular nanoparticle, termed supermeres. We performed LC/MS-MS proteomics analyses on gradient-purified sEVs, NVs, exomeres and supermeres. The proteomic profile of supermeres is clearly distinct from that of sEVs, NVs and exomeres. This study identifies a new functional nanoparticle replete with potential circulating biomarkers and therapeutic targets that can be exploited for clinical benefit in a host of diseases.
2021-12-01 | PXD027258 | Pride
Project description:To identify small RNAs coming out of glioblastoma cells in supermeres and other carriers
2024-07-31 | GSE272370 | GEO
Project description:Extracellular vesicles, including exosomes, and exomere nanoparticles, are under intense investigation for cargo that may serve as clinical biomarkers or therapeutic targets. Here, we report discovery of a new extracellular nanoparticle, termed supermeres. We performed LC/MS-MS proteomics analyses on gradient-purified sEVs, NVs, exomeres and supermeres. The proteomic profile of supermeres is clearly distinct from that of sEVs, NVs and exomeres This study identifies a new functional nanoparticle replete with potential circulating biomarkers and therapeutic targets that can be exploited for clinical benefit in a host of diseases.
2021-11-02 | PXD025213 | Pride
Project description:RNA-Seq of cellular and extracellular samples from DiFi cells. The distribution of extracellular RNA among cells, sEV pellet, exomeres and supermeres is distinct.
2021-10-12 | GSE168416 | GEO
Project description:Background & aims: MicroRNAs (miRNAs) encapsulated in EVs are potential diagnostic and prognostic biomarkers. However, discrepancies on miRNA patterns and their validation are still frequent due to differences in sample origin, EVs isolation, miRNA extraction and sequencing methods. Selecting appropriate EVs isolation methods is therefore a critical step for miRNA-based biomarker discovery. The aim of the present study is to find the most suitable EVs isolation method for miRNAs sequencing adequate for clinical application. Material & Methods EVs were isolated by Size Exclusion Chromatography (SEC), iodixanol gradients (GRAD) and the combination of both (SEC+GRAD), using the same plasma sample, in triplicate isolation assays. Isolated EVs were characterized and RNA was extracted. Three different protocols for miRNA library preparation were compared (NEBNext, NEXTFlex and SMARTer smRNA-seq) and miRNAs encapsulated on EVs were sequenced using NextSeq 500 system (Illumina). Finally, the yield, abundance and diversity of miRNAs using the three different EVs isolation protocols were analyzed and compared between them. Results The majority of lipoproteins, total cholesterol and plasma proteins were removed from the EVs-containing fractions by using SEC, GRAD, and SEC+GRAD. SEC method recovered a larger amount of EVs followed by GRAD and SEC+GRAD, while GRAD and SEC+GRAD yielded the purest vesicles. NEBNext was the library preparation kit that showed the highest reproducibility among replicas, higher number of reads corresponding to miRNAs and more different miRNAs, followed by NEXTFlex and SMARTer smRNA-seq. GRAD method showed the highest reproducibility among replicas, a higher number of reads corresponding to miRNAs and more different miRNAs, followed by SEC and SEC+GRAD methods. Conclusions These results render the GRAD method to isolate EVs as one of the most appropriate to detect miRNAs from Evs.
2023-04-26 | GSE223838 | GEO
Project description:Urinary extracellular vesicles (uEVs) are a promising source for biomarker discovery, including miRNAs. The optimal isolation method of uEVs for miRNA profiling in patients with proteinuria is unknown. Six different methods were compared for the isolation of microvesicles and these were compared to raw urine (method A). 2 methods failed and further analysis was performed with the following methods: ExoRNeasy (method C), modified protocol for ExoRNeasy (method E) and ultracentrifugation (method F). Different miRNAs are enriched by method C and F. No differences were observed between method C and E.
2020-08-01 | GSE102627 | GEO
Project description:We show that the combination of spatially restricted uracil phosphoribosyltransferase (UPRT) expression with 4-thiouracil (4TU) delivery can be used to label and purify cell type specific RNA from intact complex tissues. This method is useful for isolating RNA from cell types that are difficult to isolate by dissection or dissociation methods and should work in any organism where UPRT can be spatially expressed, including mammals and other vertebrates.
2009-04-24 | GSE15445 | GEO
Project description:Here, we report a novel and inexpensive method of rapidly isolating EVs from small volumes of human blood plasma by PRotein Organic Solvent PRecipitation (PROSPR). PROSPR encompasses a rapid three-step protocol to remove soluble proteins from plasma via precipitation in cold acetone, leaving the lipid-encapsulated EVs behind in suspension. This generates higher purity EVs that can then be obtained from filtration or classical ultracentrifugation methods.
2015-10-05 | PXD002668 | Pride
Project description:Cancer stem cells (CSCs) are pluripotent cells that have been implicated in tumor proliferation, metastatic dissemination, and recurrence of various cancers. The prognosis of colorectal cancer, which often presents late due to absence of early symptoms, depends on the stage at presentation. In the present study we have isolated and characterized cancer stem cells from colorectal cancer tissues and normal stem cells from normal colon tissues. Only sporadic colorectal cancer cases were considered where the patient had not received any neo-adjuvant therapy to avoid any bias introduced in the cellular transcriptome by external agents. Normal colon tissues were taken from adjacent region of resected specimen as well as non-cancerous operative colon cases. For our study, we have used cancer and normal stem cell markers defined in established literature. For isolating cancer stem cells by FACS, CD44 and CD166 tagged to phycoerythrin (PE) and Alexa Fluor 647 respectively, were used. For isolating normal colon stem cells, CD29, tagged to PE, and Lgr5, tagged to Alexa Fluor 647 were used. Only dual marker-positive cells were isolated to get an enriched population. Tumor sphere assay was done on representative samples to validate the stemness of isolated cells. RNA was isolated from the isolated cell populations and microarray was done to study the whole genome transcriptomic changes.
2023-11-01 | GSE160988 | GEO