Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

The miRNAs high-throughput sequencing of extracellular vesicles derived from A549 cell lines treated with and without intermittent hypoxia

ABSTRACT: The miRNAs high-throughput sequencing for extracellular vesicles derived from A549 cell lines treated with and without intermittent hypoxia (EV-NA and EV-IH) were carried out. Three samples were processed for each group. The total RNA or purified sRNA fragment of the sample was extracted, and the 3 'and 5' connectors were successively connected to reverse transcription into cDNA, and then PCR amplification was performed. Then the target fragment library was recovered by glue cutting, and the qualified library was sequenced. Clean reads obtained by sequencing were compared with all mature miRNA sequences in miRDeep2 and miRBase. v22 database to obtain the structure, length and other information of miRNA and calculate its expression level.

INSTRUMENT(S): Illumina HiSeq 1500, miRDeep2 and miRBase. v22 database

ORGANISM(S): Homo sapiens

SUBMITTER:

PROVIDER: E-MTAB-11838 | biostudies-arrayexpress |

SECONDARY ACCESSION(S): ERP138611

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Extracellular Vesicles from patients with Antibody-Mediated Rejection induce tubular senescence and endothelial to mesenchymal transition by regulating complement activation through horizontal transfer of miRNAs

Project description:Extracellular vesicles (EV) has been shown to deliver potential microRNA (miRNA) as cargo for specific target cells; effectively, the EV unique nature of the bilayer allows miRNA to be protected from degradation. We used microarray analysis to compare the miRNA profiles of EV isolated from acute antibody-mediated allograft rejection patients (AAMR) and chronic antibody-mediated allograft rejection (CAMR) compared to Tx Controls patients. By microarray miRNA profiling we detected 42 miRNAs downregulated and 34 miRNAs upregulated with FDR < 0.05 and Fold change >2. Principal Component analysis showed that these 76 miRNAs were able to distinguish AMR-derived EV from healthy TX patients. We also investigated whether differences in EV miRNA content could separate AAMR and CAMR patients. We found 9 miRNAs differentially expressed in the two AMR groups (eight downregulated and only one upregulated in AAMR compared to CAMR; effectively, these miRNAs could distinguish AAMR-derived EV from CAMR-derived EV. We then investigated the possible target genes of these miRNAs according to their expression, fold change and the p value; interestingly, several targets were associated to CDKN1A and CDKN2A genes regulation.

2021-09-10 | E-MTAB-10447 | biostudies-arrayexpress

miRNA profiling of Adenosine treated Endothelial Progenitor Cells (EPCs)

Project description:Studies of miRNA profiling in early and late endothelial progenitor cells treated or not by cardioprotective nucleoside adenosine. Early outgrowth endothelial progenitor cells were obtained by adhesion of peripheral blood mononuclear cells of healthy volunteers. Late endothelial progenitor cells were obtained by purification of CD34+ peripheral blood cells and were cultured and amplified in endothelial-specific medium containing growth factors. Both cell types were treated by adenosine (10micromol/L) for 6 hours. Total RNA was extracted using mirVana Kit and quantified by Nanodrop. RNA was labeled and hybridized using Agilent miRNA Complete Labeling and Hyb Kit. 3 to 4 arrays per sample were hybridized and scanned with the Genepix 4000B Scanner (Molecular Devices). Six independent experiments were performed.

2011-03-15 | E-GEOD-27874 | biostudies-arrayexpress

Circulating microRNAs to predict neurological outcome after sudden cardiac arrest

Project description:Studies of miRNA profiling to predict outcome in cardiac arrest patients treated with therapeutic hypothermia (TH) Venous blood was collected in citrated tubes prior discharge. Plasma was harvested by centrifugation and stored at -80Â°C until assayed. Identical volumes of plasma from the 14 patients of a group (cerebral performance category (CPC): 1-2 or CPC: 3-5) were pooled to reach a final volume of 400ÂµL for each group. The two pools were processed conjointly. Total RNA was extracted using miRVana isolation kit (Applied Biosystems), dephosphorylated and labeled using miRNA Complete Labeling and hybridization kit (Agilent). Hybridization was performed on miRNA Human Microarray Release 12.0 slides (Agilent). 4 arrays per pool were hybridized. Scanning was achieved with the Genepix 4000B Scanner (Molecular Devices, Sunnyvale, USA). Raw data were acquired with the Genepix Pro software (Molecular Devices).

2013-01-11 | E-GEOD-34643 | biostudies-arrayexpress

miRNA profiling in the plasma of patients with acute myocardial infarction (AMI)

Project description:Studies of miRNA profiling in the plasma of AMI patients with Left ventricular end diastolic volume (LVEDV) increase or LVEDV decrease between discharge and follow-up Venous blood was collected in citrated tubes prior discharge. Plasma was harvested by centrifugation and stored at -80Â°C until assayed. Identical volumes of plasma from the 30 patients of a group (LVEDV increase or LVEDV decrease) were pooled to reach a final volume of 400ÂµL for each group. The two pools were processed conjointly. Total RNA was extracted using miRVana isolation kit (Applied Biosystems), dephosphorylated and labeled using miRNA Complete Labeling and hybridization kit (Agilent). Hybridization was performed on miRNA Human Microarray Release 12.0 slides (Agilent). 4 arrays per pool were hybridized. Scanning was achieved with the Genepix 4000B Scanner (Molecular Devices, Sunnyvale, USA). Raw data were acquired with the Genepix Pro software (Molecular Devices).

2013-05-14 | E-GEOD-34571 | biostudies-arrayexpress

Extracellular vesicles (EV) secreted by embryonic stem cell-derived cardiovascular progenitor cells (hES-CPg) recapitulate the therapeutic effects of these cells in a model of chronic heart failure (CHF).

Project description:Background: We have found that extracellular vesicles (EV) secreted by embryonic stem cell-derived cardiovascular progenitor cells (hES-CPg) recapitulate the therapeutic effects of these cells in a model of chronic heart failure (CHF). Objectives: Our goal was to test other cellular sources of EV and to explore their mechanism of action.

2017-10-06 | E-MTAB-5164 | biostudies-arrayexpress

miRNA anlysis of extracellular vesicles (EV) secreted by embryonic stem cell-derived cardiovascular progenitor cells (hES-CPg) which recapitulate the therapeutic effects of these cells in a model of chronic heart failure (CHF).

2017-10-06 | E-MTAB-5165 | biostudies-arrayexpress

Crosstalk between the effects of extracellular vesicles (Evs) and TNF on U937 human monocyte cell line

Project description:Under physiological conditions, extracellular vesicles (EVs) are present simultaneously in the extracellular compartment together with cytokines. Thus, we hypothesized that EVs in combination with cytokines induce different responses of monocyte cells compared to EVs or cytokines alone. Human monocyte U937 cells were incubated with EV-containing or EV-free CCRF human T-cell supernatant, with or without the addition of TNF. U937 cells cultured in EV-free supernatant, supernatant containing CCRF t-cell derived EVs, TNF or both. Each treatment option was measured in 3 replicates.

2013-06-19 | E-GEOD-47897 | biostudies-arrayexpress

Human iPSC-derived cardiomyocytes under hypoxia/normoxia, treated with bone marrow or cardiac stromal cell extracellular vesicles

Project description:RNA-seq was performed on cultured human induced pluripotent cell derived cardiomyocytes (iPSC-CMs). There are four groups, with three samples per group: H1,H2,H3. Negative control. Healthy, normoxic iPSC-CMs D1,D2,D3. Positive control. iPSCs cultured under hypoxic (0-1% O2) for 48h with 2% v/v PBS as vehicle control EV1,EV2,EV3. Treatment 1. iPSCs cultured under hypoxic (0-1% O2) for 48h, with cardiac stromal cell derived extracellular vesicles, provided at a dose of 67ng/µl (2% v/v) EV21, EV23, EV24. Treatment 2 iPSCs cultured under hypoxic (0-1% O2) for 48h, with bone marrow mesenchymal stromal cell (BM-MSC) derived extracellular vesicles, provided at a dose of 67ng/µl (2% v/v) All EVs were isolated from cultured human cells using sequential centrifugation methods. Cells were cultured using commercial EV-depleted FBS to avoid contamination of bovine EVs. EVs were validated for CD81, CD9, ALIX positivity, and visualised by cryoEM. Particle to protein ratios were not different between cardiac and bone marrow EV isolates. Therefore EV doses were standardised so that the same dose by protein (67ng/µl) and EV number (~2,000 EVs per iPSC-CM) were added.

2024-10-02 | E-MTAB-13966 | biostudies-arrayexpress

Packaging of DNA:RNA hybrids in extracellular vesicles and their horizontal transfer in cancer

Project description:RNAs isolated from ZR751 (acceptors/responders) and BT474 (non-acceptors/non-responders) cells following education with EV-Hybridlow (EV-DNA from normoxic cancer cells) and EV-Hybridhigh (EV-DNA from IH-derived cancer cells) were sequenced.

2020-12-31 | E-MTAB-7586 | biostudies-arrayexpress

Murine small intestinal crypt cell line IEC-6: control vs. TGF-beta stimulated

Project description:microRNA profiling of rat small intestinal crypt cell IEC-6. Comparing control untreated with cells treated with transforming growth factor-beta (TGF-beta). TGF-beta stimulated cell differentiation, as observed in the stimulation of intestinal epithelial cell markers (alkaline phophotase, villin, aminopeptidase N, etc.). Two condition experiment. Control vs TGF-beta treatment. Biological replicates: 3 control, 3 treated. Independently grown and harvested. One replicate per array

2012-06-18 | E-GEOD-20982 | 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