Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Small RNA sequencing facilitates analysis of exosomal RNA transcriptomes

ABSTRACT: Smal RNA is a type of single-stranded small-molecule RNA with a size of about 18-40 bases, mainly including microRNA, piRNA, snoRNA, snRNA, tRNA and so on. Small RNAs have important regulatory functions in cells and have the potential to be used as disease diagnostic markers or drug targets. We report the results of all small RNAs in exosomes from HTNV infected/uninfected HUVECs by high-throughput sequencing technology. We find that the transcriptomes of Exo-NC group (exosomes from HTNV uninfected cells) and Exo-HV group (exosomes from HTNV infected cells) expressed distinctly different expression patterns of miRNA.

ORGANISM(S): Homo sapiens

PROVIDER: GSE147257 | GEO | 2023/03/19

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

miRNA sequencing

Project description:We established a BCG-infected THP-1 cell model in vitro, obtained the total RNA of cell culture supernatant exosomes and total RNA of the infected group and the uninfected group, and performed miRNA sequencing analysis to find exosomes related to tuberculosis infection The body-derived miRNA is verified by cell lines and primary cells, and the diagnostic value of small sample clinical samples and preliminary functional research and exploration are explored for candidate molecules.

2022-11-28 | GSE148900 | GEO

RNA-seq of HTNV-infected murine bone marrow-derived macrophages (mBMDM) from 0 to 36 hours

Project description:The murine bone marrow-derived macrophages (mBMDMs) were infected with Hantaan viruses (HTNV) with an MOI of 1, or mock-infected with Co60-inactivated HTNV. The mBMDM RNAs were extracted for RNA sequencing (RNA-seq) at 0 (mock-infected), 12, 24, and 36 hours post-infection (hpi). Each group contained three repeats (mBMDM from three different C57/6L mice). The data of 0 hpi group (labeled as A) were shown as A1, A2 and A3.The data of 12 hpi group (labeled as B) were shown as B1, B2 and B3. The data of 24 hpi group (labeled as C) were shown as C1, C2 and C3. The data of 36 hpi group (labeled as D) were shown as D1, D2 and D3.

2022-02-05 | E-MTAB-11353 | biostudies-arrayexpress

Evaluating Differential Tropism, Pathogenesis, and Antiviral Agents of Hemorrhagic Fever Renal Syndrome and Cardiopulmonary Syndrome Causative Hantaviruses: Andes virus (ANDV), Sin Nombre virus (SNV), and Hantaan virus (HTNV)

Project description:We report RNAseq analysis of control, calu3, astrocytes and cardiomyocytes cells under uninfected (mock) and Andes virus (ANDV), Sin Nombre virus (SNV), Hantaan virus (HTNV) infected and drug (synthetic 6AZA and Favipiravir, herbal Silymarin and Urolithin B) treated conditions

2024-05-16 | GSE232641 | GEO

Anti-tumor Effect and Action Mechanism of Exosomes Derived from Toxoplasma gondii-Infected Dendritic Cells in Mice Colorectal Cancer

Project description:Toxoplasma gondii is an obligate intracellular protozoan with anti-tumor activity against a variety of cancers. However, the therapeutic effect of T. gondii on colorectal cancer is unclear, and using direct Toxoplasma infection in immunotherapy involves safety concerns. This study investigated the anti-tumor effect and mechanism of exosomes derived from dendritic cells (DC) infected with T. gondii (Me49-DC-Exo). We used the density gradient centrifugation to isolate exosomes from uninfected DCs (DC-Exo) and T. gondii Me49-infected DCs (Me49-DC-Exo). The isolated exosomes were identified by transmission electron microscopy, nanoparticle tracking analysis, and western blotting. Me49-DC-Exo significantly inhibited tumor growth and reduced the proportion of M2 macrophages in the blood of tumor-bearing mice. In vitro, Me49-DC-Exo suppressed macrophage (RAW264.7) polarization to M2 phenotype. miRNA sequencing revealed that multiple miRNAs in Me49-DC-Exo were differentially expressed compared with DC-Exo. miR-182-5p, miR-155-5p, miR-125b-2-3p, and miR-155-3p were up-regulated, while miR-9-5p was significantly down-regulated. Transfecting mimics or inhibitors of these differential miRNAs into RAW264.7 cells showed that miR-155-5p promoted M1 macrophage polarization while inhibiting M2 macrophage polarization. Bioinformatics prediction and dual-luciferase reporter assay confirmed the suppressor of cytokine signaling 1 (SOCS1) as a direct target of miR-155-5p. Silencing SOCS1 gene expression in RAW264.7 cells increased CD86 + CD206 - M1 macrophage proportion and inducible nitric oxide synthase and tumor necrosis factor-α mRNA levels. However, arginase1 and transglutaminase 2 expression levels decreased. These results suggest that the exosomes inhibit macrophage polarization to M2 phenotype and regulate SOCS1 expression by delivering functional miR-155-5p. These findings provide new ideas for colorectal cancer immunotherapy.

2022-02-24 | GSE197114 | GEO

Comprehensive analyses of function and molecular interaction of differential expressed non-coding RNAs and mRNA in Hantaan virus infection

Project description:Hantaan virus (HTNV), the prevalent prototype of the hantavirus in Asia, causes hemorrhagic fever with renal syndrome (HFRS) with high mortality in human being. However, the pathogenesis of HTNV infection remains elusive. Accumulating evidences indicate that non-coding RNAs (ncRNAs), including long non-coding RNA (lncRNA), circular RNA (circRNA) and microRNA (miRNA) play crucial roles in the progression of virus infection. Here, we identified differential lncRNA/miRNA/circRNA and mRNA expression profiles of HTNV-infected human umbilical vein endothelial cells (HUVECs) compared with mock-infected HUVECs by whole transcriptome sequencing. Subsequently, comprehensive bioinformatics analyses established miRNA-mRNA co-expression, protein-protein interaction and competing endogenous RNA (ceRNA) networks in miRNA-lncRNA-circRNA-mRNA regulatory axis. The trans or cis regulatory roles of identified RNAs on HTNV infection were ascertained by RNA interference and key ceRNA relationships were verified by dual-luciferase reporter experiments. Moreover, gene ontology (GO) enrichment analysis showed that dysregulated RNAs were mostly related to antiviral innate immune response. In conclusion, our findings firstly revealed that circRNAs and ceRNA network were involved in regulating HTNV infection, and also confirmed several key lncRNAs and miRNAs which had vital effects on HTNV infection. The identification and characterization of RNAs provide the new insights on ceRNA networks in HTNV-host interactions, which lays the foundation for future research of the potential roles of ncRNAs in the pathogenesis of HFRS.

2020-04-06 | GSE133319 | GEO

Comprehensive analyses of function and molecular interaction of differential expressed non-coding RNAs and mRNA in Hantaan virus infection

2020-04-06 | GSE133634 | GEO

Comprehensive analyses of function and molecular interaction of differentially expressed non-coding RNAs and mRNA in Hantaan virus infection

2020-04-06 | GSE133751 | GEO

Expression analysis for detection of mycobacterial transcripts present in exosomes derived from M.tb infected macrophages

Project description:Mycobacterial transcripts were identified in exosomes released from M.tb infected RAW264.7 macrophages that were not present in uninfected exosomes suggesting export of mycobacterial RNA via exosomes Mycobacterial RNA was used as positive control and RNA from exosomes released from uninfected macrophages was used as negative control

2014-09-15 | GSE54444 | GEO

Umbilical Cord Blood-derived Exosomes from Very Preterm Infants with Bronchopulmonary Dysplasia Impaired Endothelial Angiogenesis: Roles of Exosomal MicroRNAs

Project description:Premature infants have a high risk of bronchopulmonary dysplasia (BPD), which is characterized by abnormal development of alveoli and pulmonary vessels. Exosomes and exosomal miRNAs (EXO-miRNAs) from bronchoalveolar lavage fluid are involved in the development of BPD and might serve as predictive biomarkers for BPD. However, the roles of exosomes and EXO-miRNAs from umbilical cord blood of BPD infants in regulating angiogenesis are yet to be elucidated. In this study, we showed that umbilical cord blood-derived exosomes from BPD infants impaired angiogenesis in vitro. Next generation sequencing of EXO-miRNAs from preterm infants without (NBPD group) or with BPD (BPD group) uncovered a total of 418 differentially expressed (DE) EXO-miRNAs. These DE EXO-miRNAs were primarily enriched in cellular function-associated pathways including the PI3K/Akt and angiogenesis- related signaling pathways. Among those EXO-miRNAs which are associated with PI3K/Akt and angiogenesis-related signaling pathways, BPD reduced expression of hsa-miR-103a-3p and hsa-miR-185-5p exhibiting most significant reduction (14.3% and 23.1% of NBPD group, respectively); BPD increased hsa-miR-200a-3p expression by 2.64 folds of NBPD group. Furthermore, overexpression of hsa-miR-103a-3p and hsa-miR-185-5p in normal human umbilical vein endothelial cells (HUVECs) significantly enhanced endothelial cell proliferation, tube formation and cell migration, whereas overexpressing hsa-miR-200a-3p inhibited these cellular responses. This study demonstrates that exosomes derived from umbilical cord blood of BPD infants impair angiogenesis, possibly via DE EXO-miRNAs, which might contribute to the development of BPD.

2021-02-16 | GSE166762 | GEO

A customizable purification assay designed for small-RNA biomarker identification and functional evaluation of circulating exosomes: Exosome Capture by AnTibody of CHoice and Enzymatic Release (exo-CATCHER)

Project description:Circulating nucleic acids, encapsulated within exosomes, can provide a remote cellular snapshot of biomarkers associated with disease, however selective exosome isolation is critical. Current laboratory-based purification techniques rely on the physical properties of exosomes for selection, rather than their inherited cellular characteristics. Therefore, we established a highly selective purification assay, termed exosome Capture by AnTibody of CHoice and Enzymatic Release (exo-CATCHER), designed for high-throughput analysis of low-abundance small-RNA cargos by next-generation sequencing. We demonstrated its sensitivity by specifically isolating and sequencing small-RNA from mouse exosomes spiked into human plasma. Furthermore, we used Western blotting, nanoparticle tracking, and transmission electron microscopy to validate, quantify, and demonstrate capture and release of intact exosomes. As proof of principle, we utilized exo-CATCHER to purify serum exosomes from mildly and severely ill Covid-19 patients, identified, and validated hsa-miR-146a and hsa-miR-126-3p to be significantly downregulated in a small sample set of severely ill patients. We used exo-CATCHER to purify intact exosomes from high IgG titer convalescent sera and confirmed unexpected neutralizing properties, against SARS-CoV-2 in vitro, identified using ultracentrifuged exosomes, not observable with exosomes from sera with IgG titers below quantification level. Exo-CATCHER represents a versatile molecular assay for highly specific purification of circulating exosomes.

2021-05-13 | GSE158948 | GEO

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