Exosomes derived from hypertrophic cardiomyocytes induce inflammation in macrophages via miR-155 mediated MAPK pathway.
Ontology highlight
ABSTRACT:
ORGANISM(S): Rattus norvegicus
PROVIDER: GSE158509 | GEO | 2020/09/25
REPOSITORIES: GEO
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2023-11-01 | GSE246097 | GEO
Project description:MicroRNAs (miRNAs) are endogenous, noncoding, short RNAs directly involved in regulating gene expression at the post-transcriptional level. In spite of immense importance, limited information of P. vulgaris miRNAs and their expression patterns prompted us to identify new miRNAs in P. vulgaris by computational methods. Besides conventional approaches, we have used the simple sequence repeat (SSR) signatures as one of the prediction parameter. Moreover, for all other parameters including normalized Shannon entropy, normalized base pairing index and normalized base-pair distance, instead of taking a fixed cut-off value, we have used 99% probability range derived from the available data. We have identified 208 mature miRNAs in P. vulgaris belonging to 118 families, of which 201 are novel. 97 of the predicted miRNAs in P. vulgaris were validated with the sequencing data obtained from the small RNA sequencing of P. vulgaris. Randomly selected predicted miRNAs were also validated using qRT-PCR. A total of 1305 target sequences were identified for 130 predicted miRNAs. Using 80% sequence identity cut-off, proteins coded by 563 targets were identified. The computational method developed in this study was also validated by predicting 229 miRNAs of A. thaliana and 462 miRNAs of G. max, of which 213 for A. thaliana and 397 for G. max are existing in miRBase 20. There is no universal SSR that is conserved among all precursors of Viridiplantae, but conserved SSR exists within a miRNA family and is used as a signature in our prediction method. Prediction of known miRNAs of A. thaliana and G. max validates the accuracy of our method. Our findings will contribute to the present knowledge of miRNAs and their targets in P. vulgaris. This computational method can be applied to any species of Viridiplantae for the successful prediction of miRNAs and their targets. Small RNA sequencing was done for 10 days old seedlings of Phaseolus vulgaris Cv. Anupam
2015-04-28 | E-GEOD-68305 | biostudies-arrayexpress
Project description:MicroRNAs (miRNAs) are endogenous, noncoding, short RNAs directly involved in regulating gene expression at the post-transcriptional level. In spite of immense importance, limited information of P. vulgaris miRNAs and their expression patterns prompted us to identify new miRNAs in P. vulgaris by computational methods. Besides conventional approaches, we have used the simple sequence repeat (SSR) signatures as one of the prediction parameter. Moreover, for all other parameters including normalized Shannon entropy, normalized base pairing index and normalized base-pair distance, instead of taking a fixed cut-off value, we have used 99% probability range derived from the available data. We have identified 208 mature miRNAs in P. vulgaris belonging to 118 families, of which 201 are novel. 97 of the predicted miRNAs in P. vulgaris were validated with the sequencing data obtained from the small RNA sequencing of P. vulgaris. Randomly selected predicted miRNAs were also validated using qRT-PCR. A total of 1305 target sequences were identified for 130 predicted miRNAs. Using 80% sequence identity cut-off, proteins coded by 563 targets were identified. The computational method developed in this study was also validated by predicting 229 miRNAs of A. thaliana and 462 miRNAs of G. max, of which 213 for A. thaliana and 397 for G. max are existing in miRBase 20. There is no universal SSR that is conserved among all precursors of Viridiplantae, but conserved SSR exists within a miRNA family and is used as a signature in our prediction method. Prediction of known miRNAs of A. thaliana and G. max validates the accuracy of our method. Our findings will contribute to the present knowledge of miRNAs and their targets in P. vulgaris. This computational method can be applied to any species of Viridiplantae for the successful prediction of miRNAs and their targets.
2015-04-28 | GSE68305 | GEO
Project description:Cardiac hypertrophy is an independent risk factor for cardiovascular disease and heart failure. There is increasing evidence that microRNAs (miRNAs) play an important role in the regulation of messenger RNA (mRNA) and the pathogenesis of various cardiovascular diseases. However, the ability to comprehensively study cardiac hypertrophy on a gene regulatory level is impacted by the limited availability of human cardiomyocytes. Human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs) offer the opportunity for disease modeling. We utilized a previously established in vitro model of cardiac hypertrophy to interrogate the regulatory mechanism associated with the cardiac disease process. We performed miRNA sequencing and mRNA expression analysis on endothelin 1 (ET-1) stimulated hiPSC-CMs to describe associated RNA expression profiles. MicroRNA sequencing revealed over 250 known and 34 predicted novel miRNAs to be differentially expressed between ET-1stimulated and unstimulated control hiPSC-CMs. Messenger RNA expression analysis identified 731 probe sets with significant differential expression. Computational target prediction on significant differentially expressed miRNAs and mRNAs identified nearly 2000 target pairs. To characterize miRNA and mRNA expression patterns we utilized iCell Cardiomyocytes derived from human iPSCs (hiPSC-CMs). Based on preliminary dose-response and time-course studies, we stimulated these cells with ET-1 at 10-8M for 18h. We used unstimulated control (control-CM) and ET-1 stimulated (ET1-CM) hiPSCs from 3 separate experiments as triplicate data for this study. For the analysis of miRNA expression changes after ET-1 stimulation, single-end small RNA sequencing was performed using the Ion Torrent Personal Genome Machine (PGMTM) sequencing platform.
2014-10-03 | E-GEOD-60292 | biostudies-arrayexpress
Project description:More and more studies have showed that plasma exosomal miRNAs are biomarkers for disease. The aim of the study were to investigate the miRNA profiling in plasma exosomes of patients with non-segmental vitiligo (NSV) and to find biomarkers in plasma exosomes for patients with NSV. Plasma exosomes and exosomal RNA of 10 NSV patients and 10 health persons were purified by exoRNeasy Serum/Plasma Maxi Kit. The miRNA profiles of the 20 samples were sequenced using HiSeq 2500 (Illumina) and analyzed by Reads Per Million (RPM) values and edgeR algorithm. Some differently expressed miRNAs in plasma exosomes and skin tissues of the two sets were validated by qRT–PCR.Several miRNAs were confirmed by qRT–PCR and showed similar expression patterns between plasma exosomes and skin tissues. Our study depict the miRNAs expression profiles in plasma exosomes of NSV patients and suggest that several miRNAs in plasma exosomes may serve as biomarkers for NSV.
2022-12-09 | GSE141655 | GEO
Project description:More and more studies have showed that plasma exosomal miRNAs are biomarkers for disease. The aim of the study were to investigate the miRNA profiling in plasma exosomes of patients with segmental vitiligo (SV) and to find biomarkers in plasma exosomes for patients with SV. Plasma exosomes and exosomal RNA of 7 SV patients and 8 health persons were purified by exoRNeasy Serum/Plasma Maxi Kit. The miRNA profiles of the 15 samples were sequenced using HiSeq 2500 (Illumina) and analyzed by Reads Per Million (RPM) values and edgeR algorithm. Some differently expressed miRNAs in plasma exosomes and skin tissues of the two sets were validated by qRT–PCR.A total of 85 miRNAs in plasma exosomes showed differential expression between SV patients and health persons, with a |log2（Fold Change）|≥1 and P-value < 0.05. Several miRNAs were confirmed by qRT–PCR and showed similar expression patterns between plasma exosomes and skin tissues. Our study depict the miRNAs expression profiles in plasma exosomes of SV patients and suggest that several miRNAs in plasma exosomes may serve as biomarkers for SV.
2022-03-24 | GSE198956 | GEO
Project description:Schmitz2014 - RNA triplex formation
The model is parameterized using the
parameters for gene CCDC3 from Supplementary Table S1. The two
miRNAs which form the triplex together with CCDC3 are miR-551b and
miR-138.
This model is described in the article:
Cooperative gene regulation
by microRNA pairs and their identification using a
computational workflow.
Schmitz U, Lai X, Winter F,
Wolkenhauer O, Vera J, Gupta SK.
Nucleic Acids Res. 2014 Jul; 42(12):
7539-7552
Abstract:
MicroRNAs (miRNAs) are an integral part of gene regulation
at the post-transcriptional level. Recently, it has been shown
that pairs of miRNAs can repress the translation of a target
mRNA in a cooperative manner, which leads to an enhanced
effectiveness and specificity in target repression. However, it
remains unclear which miRNA pairs can synergize and which genes
are target of cooperative miRNA regulation. In this paper, we
present a computational workflow for the prediction and
analysis of cooperating miRNAs and their mutual target genes,
which we refer to as RNA triplexes. The workflow integrates
methods of miRNA target prediction; triplex structure analysis;
molecular dynamics simulations and mathematical modeling for a
reliable prediction of functional RNA triplexes and target
repression efficiency. In a case study we analyzed the human
genome and identified several thousand targets of cooperative
gene regulation. Our results suggest that miRNA cooperativity
is a frequent mechanism for an enhanced target repression by
pairs of miRNAs facilitating distinctive and fine-tuned target
gene expression patterns. Human RNA triplexes predicted and
characterized in this study are organized in a web resource at
www.sbi.uni-rostock.de/triplexrna/.
This model is hosted on
BioModels Database
and identified by:
BIOMD0000000530.
To cite BioModels Database, please use:
BioModels Database:
An enhanced, curated and annotated resource for published
quantitative kinetic models.
To the extent possible under law, all copyright and related or
neighbouring rights to this encoded model have been dedicated to
the public domain worldwide. Please refer to
CC0
Public Domain Dedication for more information.
2013-10-23 | BIOMD0000000530 | BioModels
Project description:MicroRNAs (miRNAs) are endogenous small RNAs that play important roles in various biological and metabolic processes in plants. Caragana intermedia is an important ecological and economic tree species that is prominent in the desert environment of west and northwest China. To date, no investigation into C. intermedia miRNAs has been reported. In this study, high-throughput sequencing of small RNAs was performed to identify both conserved and novel miRNAs, and also their target mRNA genes in C. intermedia. Based on sequence similarity and hairpin structure prediction, 132 putative conserved miRNAs (12 of which were confirmed to form hairpin precursors) belonging to 31 known miRNA families were identified. Ten novel miRNAs (including the miRNA* sequences of three novel miRNAs) were also discovered. The expression of 12 miRNAs was validated in different tissues, and the 12 miRNAs were further assessed by qRT-PCR after salt treatment. Furthermore, 36 potential target genes of 17 known miRNA families and two potential target genes of one novel miRNA were predicted, and some target genes were also assessed by qRT-PCR after salt treatment. Our study provides a basic catalog of miRNAs and their targets, which will promote further understanding of the important roles of miRNAs in C. intermedia and in other species of the leguminous genus, Caragana. Examination of small RNA expression profiling in three-weeks-old seedings of Caragana intermedia.
2015-12-31 | E-GEOD-44819 | biostudies-arrayexpress
Project description:We found that cardiac fibroblasts produce and secrete exosomes. miRNA profiling and TaqMan qRT-PCR experiments identified miR-21 expression to be higher in cardiac fibroblasts compared to those of miR-21*, whereas in exosomes miR-21* expression was higher compared to miR-21. The purpose of the study was to validate these findings by miRNA sequencing in cardiac fibroblasts and fibroblasts-derived exosomes. Neonatal rat cardiac fibroblasts were cultured in DMEM + 1% exosome-depleted FBS for 48h. Conditioned medium was collected and exosomes were purified by several centrifugation and filtration steps, following ultracentrifugation. Afterwards total RNA from cardiac fibroblasts and exosomes was isolated for miRNA sequencing.
2015-12-19 | E-GEOD-76175 | biostudies-arrayexpress
Project description:MicroRNAs (miRNAs) are endogenous small RNAs that play important roles in various biological and metabolic processes in plants. Caragana intermedia is an important ecological and economic tree species that is prominent in the desert environment of west and northwest China. To date, no investigation into C. intermedia miRNAs has been reported. In this study, high-throughput sequencing of small RNAs was performed to identify both conserved and novel miRNAs, and also their target mRNA genes in C. intermedia. Based on sequence similarity and hairpin structure prediction, 132 putative conserved miRNAs (12 of which were confirmed to form hairpin precursors) belonging to 31 known miRNA families were identified. Ten novel miRNAs (including the miRNA* sequences of three novel miRNAs) were also discovered. The expression of 12 miRNAs was validated in different tissues, and the 12 miRNAs were further assessed by qRT-PCR after salt treatment. Furthermore, 36 potential target genes of 17 known miRNA families and two potential target genes of one novel miRNA were predicted, and some target genes were also assessed by qRT-PCR after salt treatment. Our study provides a basic catalog of miRNAs and their targets, which will promote further understanding of the important roles of miRNAs in C. intermedia and in other species of the leguminous genus, Caragana.
2015-12-31 | GSE44819 | GEO