D-EVs miRNA
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ABSTRACT:
PROVIDER: PRJNA1243749 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:miRNA expression data from HPC-EVs
| PRJNA1030338 | ENA
Project description:The goal of this study is to identify unique miRNA profiles of EVs from MCF7 and MCF10A cells that distinguish their cellular origin. 654 human mature miRNAs were analyzed in NanoString assays to identify miRNA with high abundance in MCF7 EVs and the greatest fold change for MCF7 EVs relative to MCF10A EVs.
2015-02-21 | E-GEOD-66165 | biostudies-arrayexpress
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:To investigated dysregulated miRNAs in human MDS patients, we performed miRNA-sequencing (miRNA-seq) of serum EVs from 38 MDS patients and 8 healthy subjects. The miRNA profile in EVs from MDS patients was distinctly clustered from that in healthy individuals. In addition, the miRNAs significantly upregulated in the MDS group target pathways linked to cell survival, proliferation, and MSC differentiation, indicating that they have remarkably similar properties to miRNAs in murine EVs from MDS cells. These results suggest that miRNAs play an essential role in the MSC impairment observed in MDS.
2023-01-01 | GSE199980 | GEO
Project description:Purpose: The goal of this study was to determine the microRNA (miRNA) content of extracellular vesicles (EVs) derived from murine mesenchymal stem cells (mMSC), and evaluate reproducibility among distinct EV productions. We also aimed at assessing the effect of freeze-drying on EV miRNA content, by performing sequencing on freeze-dried EVs and calculating statistical difference between unmodified and freeze-dried EVs. Methods: mMSC-derived EVs were obtained from mMSC in culture in reduced serum medium Opti-MEM by differential centrifugation, with a final step at 100,000 g for 110 min at 4°C. EV pellets (freeze-dried (n=3) or not (n=2)) were resuspended in Qiazol lysis buffer and RNA was extracted following RNeasy Micro kit. cDNA libraries for sequencing were prepared using the TruSeq Small RNA Sample Preparation Kit. Amplified cDNA constructs were purified on 6 % PAGE gel and DNA molecules corresponding to 15–50 nucleotide transcripts were excised, eluted from gel, and concentrated. Image analyses and base calling were performed using the HiSeq Control Software and Real-Time Analysis component (Illumina). Before statistical analysis, genes with less than 15 reads (cumulating all the analysed samples) were filtered out. Differentially expressed miRNA were identified using three Bioconductor packages: edgeR, DESeq and DESeq2. Results: Considering miRNAs detected with at least 5 counts (in terms of normalised counts), 339 miRNAs were identified and miRNA content was highly conserved among the two batches tested, with 237 miRNAs out of the 339 present in both batches (70%). Statistical analysis did not evidence statistical difference between unmodified EVs (n=2) and freeze-dried EVs (n=3) (DESeq2, p<0.05). No statistical difference was found using other Bioconductor packages DESeq and edgeR. These results indicated conservation of miRNA content following freeze-drying. Conclusion: mMSC-EV miRNA content was comparable between the two EV productions analysed, indicating reproducibility. Some of the miRNAs identified were consistent with previously published results on MSC-derived EVs. Freeze-drying conserved miRNA content.
2019-12-09 | GSE140479 | GEO
Project description:The goal of this project was to analyze the EVs cargoes. EVs were isolated from dental pulp mesenchymal stem cells.
2021-09-22 | GSE179940 | GEO
Project description:To identify the mechanism by which miRNAs in EVs derived from MDS cells suppressed the osteolineage differentiation of MSCs and disrupted normal hematopoiesis, we comprehensively explored the miRNAs encapsulated in EVs by miRNA-array. Consistent with the heterogeneous nature of MDS, the hypoplastic Abcg2-MDS/AML model and the hyperplastic NHD13Tg model share few elevated miRNAs. However, it is noteworthy that the pathways targeted by each upregulated miRNA are mutually shared, such as the pathways associated with MSC differentiation and survival, including axon guidance and MAPK signaling. These results suggest that miRNAs play an essential role in the MSC impairment observed in MDS.
2022-10-01 | GSE199997 | GEO
Project description:Vascular calcification often occurs with osteoporosis, a contradictory association called “calcification paradox”. We find that extracellular vesicles (EVs) released from aged bone matrix (AB-EVs) during bone resorption favor adipogenesis rather than osteogenesis of BMSCs and augment calcification of vascular smooth muscle cells (VSMCs). Intravenous or intramedullary injection of AB-EVs promotes bone-fat imbalance and exacerbates Vitamin D3 (VD3)-induced vascular calcification in young or old mice. To explore the involvement of miRNAs in the AB-EVs-induced promotion of adipocyte formation and vascular calcification, the Agilent miRNA array was conducted to compare the miRNA expression profiles in AB-EVs and YB-EVs from mouse bone specimens. Our study uncovers the role of AB-EVs as a messenger for calcification paradox by transferring functional miRNAs.
2022-02-15 | E-MTAB-11417 | biostudies-arrayexpress