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5,031 results for “mirnas”
Unveiling the role of miRNAs from MSC-EVs in neuroinflammation and behavioral impairments induced by chronic alcohol consumption
<p><strong>Part of the project: "Unveiling the role of miRNAs from MSC-EVs in neuroinflammation and behavioral impairments induced by chronic alcohol consumption."</strong></p> <p>This dataset contains small RNA sequencing data derived from extracellular vesicles (EVs) isolated from human adipose tissue-derived mesenchymal stem cells (MSC-EVs). The data was generated to study the potential therapeutic effects of repeated intravenous administration of MSC-EVs on neuroinflammation, cognitive dysfunction, and addictive-like behaviors induced by chronic alcohol consumption.</p> <p>Total RNA from MSC-EVs was extracted using the Total Exosome RNA Isolation Kit (Invitrogen). Small RNA libraries were constructed with the Small RNA-Seq Library Prep Kit (Lexogen) and sequenced on the Illumina NextSeq 550 platform with a 1 x 150 bp read length. The raw sequencing data are provided in fastq format.</p> <p> </p> <div> </div>
miRNA target finder training datasets
<p>Datasets needed to run the Galaxy training: miRNA target finder in <em>Arabidopsis thaliana</em></p>
Synergistic label-free fluorescence imaging and miRNA studies reveal dynamic human neuron-glial metabolic interactions following injury
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Interactive Web-based Annotation of Plant MicroRNAs with iwa-miRNA
<p>MicroRNAs (miRNAs) are important regulators of gene expression. The large-scale detection and profiling of miRNAs has accelerated with the development of high-throughput small RNA sequencing (sRNA-Seq) techniques and bioinformatics tools. However, generating high-quality comprehensive miRNA annotations remains challenging, due to the intrinsic complexity of sRNA-Seq data and inherent limitations of existing miRNA predictions. Here, we present iwa-miRNA, a Galaxy-based framework that can facilitate miRNA annotation in plant species by combining computational analysis and manual curation. iwa-miRNA is specifically designed to generate a comprehensive list of miRNA candidates, bridging the gap between already annotated miRNAs provided by public miRNA databases and new predictions from sRNA-Seq datasets. It can also assist users to select promising miRNA candidates in an interactive mode through the automated and manual steps, contributing to the accessibility and reproducibility of genome-wide miRNA annotation. iwa-miRNA is user-friendly and can be easily deployed as a web application for researchers without programming experience. With flexible, interactive, and easy-to-use features, iwa-miRNA is a valuable tool for annotation of miRNAs in plant species with reference genomes. We illustrated the application of iwa-miRNA for miRNA annotation of plant species with varying complexity. The sources codes and web server of iwa-miRNA is freely accessible at: <a href="http://iwa-miRNA.omicstudio.cloud">http://iwa-miRNA.omicstudio.cloud</a>/.</p>
miRNA counts identified by RNA seq in the caudate nucleus of patients neuropathologically diagnosed with late-onset Alzheimer's disease (non-carriers and carriers of intermediate expansions in the HTT gene) and healthy subjects.
<p>These data include the raw miRNA counts identified by RNA-seq in <em>post mortem</em> caudate nucleus samples. Samples with identifier <strong>A</strong> belong to patients with a neuropathological diagnosis of late-onset Alzheimer's disease. Group <strong>B</strong> samples belong to patients with the same neuropathological diagnosis, but carrying CAG expansions in the intermediate range (27-35 CAG) in the <em>HTT</em> gene. Finally, group <strong>C </strong>samples belong to healthy subjects without neuropathological diagnosis. </p> <p> </p>
Datasets of positive and negative miRNA-target interactions from 4 species
<p>The datasets provided accompany the paper "Empowering Prediction of miRNA-mRNA Interactions in Species with Limited Training Data through Transfer Learning." These datasets encompass all positive and negative data relevant to the paper.</p> <p>The datasets were created in a prior paper (https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-021-04164-x) by Gilad Ben-Or.</p> <div> <p> </p> </div>
RNA-sequencing of meningioma cell lines with miRNA constructs
<p>RNA-sequencing of meningioma cell lines with miRNA constructs.</p>
Data for: A novel and ubiquitous miRNA-involved regulatory module ensures precise phosphorylation of RNA polymerase II and proper transcription
<p>Proper transcription orchestrated by RNA polymerase II (RNPII) is crucial for cellular development, which relies on the phosphorylation state of RNPII's carboxyl-terminal domain (CTD). Sporangia, developed from mycelia, are essential for the destructive oomycetes<em> Phytophthora</em>, remarkable transcriptional changes are observed during the morphological transition. However, how these changes are rapidly triggered and their relationship with the versatile RNPII-CTD phosphorylation remain enigmatic. Herein, we found that <em>Phytophthora</em> <em>capsici</em> had undergone an elevation of Ser5-phosphorylation in its uncanonical heptapeptide repeats of RNPII-CTD during sporangia development, which subsequently changed the chromosomal occupation of RNPII and primarily activated transcription of certain genes. A cyclin-dependent kinase,<em> </em>PcCDK7, was highly induced and phosphorylated RNPII-CTD during this morphological transition. Mechanistically, a novel DCL1-dependent microRNA, pcamiR1, was found to be a feedback modulator for the precise phosphorylation of RNPII-CTD by complexing with PcAGO1 and regulating the accumulation of PcCDK7. Moreover, this study revealed that the pcamiR1-CDK7-RNPII regulatory module is evolutionarily conserved and the impairment of the balance between pcamiR1 and <em>PcCDK7 </em>could efficiently reduce the growth and virulence of<em> P. capsici</em>. Collectively, this study uncovers a novel and evolutionarily conserved mechanism of transcription regulation that could facilitate correct development and identifies pcamiR1 as a promising target for disease control.</p>
POTENCIALES CIRCUITOS REGULATORIOS ENTRE miRNAs, MITF Y HIF1α EN LA LÍNEA CELULAR DE MELANOMA B16 BAJO CONDICIONES DE SUPRESIÓN DE CRECIMIENTO CELULAR E HIPOPIGMENTACIÓN INDUCIDOS.
<p>El melanoma es un cáncer de melanocitos, células especializadas en la síntesis de melanina, que muestra variación en la expresión de moléculas como RNAs mensajeros (mRNAs), factores de transcripción y microRNAs (miRNAs), entre otras. Los miRNAs son RNAs pequeños no codificantes entre los 18-22 nt, asociados con la regulación de cerca del 30% de los genes que codifican para proteínas, incluidos factores de transcripción, tanto en condiciones fisiológicas, como fisiopatológicas. A su vez, los factores de transcripción regulan la expresión de cientos de genes, incluidos los miRNAs; sin embargo, a la fecha, la asociación funcional entre estos tres actores moleculares y el fenotipo tumoral no es del todo clara. El objetivo de la presente investigación fue evaluar la expresión de miRNAs y de los mRNAs de los factores de transcripción Mitf y Hif1α en la línea celular de melanoma B16F1 expuesta a la 5-bromo-2´-deoxiuridina (5-Br-2’-dU), y plantear potenciales circuitos regulatorios asociados al fenotipo de hipopigmentación y disminución de la proliferación celular. Para ello, células B16F1 fueron expuestas a 5-Br-2’-dU 2.5 µg.mL-1 durante 72 horas, en medio DMEM (Dulbecco Modified Eagle Medium) a 37°C y 5% de CO2. Mediante small RNAseq se determinó la expresión diferencial de miRNAs maduros, mientras que la predicción de sus blancos moleculares, Mitf y Hif1α se realizó por TargetScanMouse versión 7.2. La expresión fue confirmada para los miRNAs miR-211-5p, miR-138-5p, miR-129-5p, miR-470-5p y miR-470-3p por RT-qPCR stem loop con un N= 3 y establecida para Mitf y Hif1α por RT-qPCR con un N=4; en todos los casos, el nivel de significación (*) fue determinado mediante una prueba t-Student a dos colas con corrección del Welch y las diferencias fueron consideradas como estadísticamente significativas para un valor p <0.05, ns: no significativo. Usando DEseq2, se analizaron los conteos obtenidos por small RNAseq y se determinó la expresión diferencial de 33 miRNAs por exposición a 5-Br-2’-dU, 11 sobre-expresados y 21 sub-expresados. Se confirmó por RT-qPCR el nivel de expresión de cinco miRNAs, dos de ellos a la baja (miR-211-5p (2.2X) y 138-5p (2.8X) y tres al alta (miR-129-5p (1.5X), miR-470-5p (22.7X) y miR-470-3p (124X)). El nivel de expresión de los mRNAs Mitf y Hif1α, se encontró para ambos a la baja (3.48X y, 4.58X, respectivamente). El análisis bioinformático por TargetScanMouse facilitó la construcción de potenciales circuitos regulatorios entre los miRNAs diferencialmente expresados y los factores Mitf y Hif1α para el fenotipo de hipopigmentación y disminución de la proliferación celular inducidos por la 5-Br-2’-dU. Los resultados obtenidos, plantean nuevos escenarios en el estudio del melanoma y mejoran nuestra comprensión de las potenciales asociaciones funcionales entre conjuntos de miRNAs, factores de transcripción como MITF y HIF1α y algunos genes que participan en el control de la pigmentación y la proliferación celular; sin embargo, se requiere establecer mediante ensayos de gen reportero de la luciferasa y otros ensayos funcionales, donde se usen estrategias como miRNAs miméticos y antimiRs, si para los circuitos regulatorios planteados, existe asociación funcional.</p>
miRNA profiling of human nasopharyngeal carcinoma cell lines HONE1 and CNE2 after X-ray therapy
<p>The package contains two file:</p> <p>Supplementary Table 1. Kruskal Wallis test for cell viability rate</p> <p>Supplementary Table 2. Kruskal Wallis test for apoptosis rate</p> <p>The HONE1 and CNE2 cells were irradiated with X-rays at doses of 4 Gy, 8 Gy, 16 Gy and 20 Gy for 24 h. The cell viability rate and apoptosis rate were compared.</p>
Raw Data for the article: miRNA expression analysis in the human heart: Undifferentiated progenitors vs. bioptic tissues-Implications for proliferation and ageing
<p>In developed countries, cardiovascular diseases are currently the first cause of death. Cardiospheres (CSs) and cardiosphere-derived cells (CDCs) have been found to have the ability to regenerate the myocardium after myocardial infarction (MI). In recent years, much effort has been made to gain insight into the human heart repair mechanisms, in which miRNAs have been shown to play an important role. In this regard, to elucidate the involvement of miRNAs, we evaluated the miRNA expression profile across human heart biopsy, CSs and CDCs using microarray and next-generation sequencing (NGS) technologies. We identified several miRNAs more represented in the progenitors, where some of them can be responsible for the proliferation or the maintenance of an undifferentiated state, while others have been found to be downregulated in the undifferentiated progenitors compared with the biopsies. Moreover, we also found a correlation between downregulated miRNAs in CSs/CDCs and patient age (eg miR-490) and an inverse correlation among miRNAs upregulated in CSs/CDCs (eg miR-31).</p>
Brain-Derived Neurotrophic Factor and extracellular vesicle-derived miRNAs in an Italian cohort of individuals with obesity: a key to explain the link between depression and atherothrombosis.
<p>This record contains raw data related to the article “Brain-Derived Neurotrophic Factor and Extracellular Vesicle-Derived miRNAs in an Italian Cohort of Individuals With Obesity: A Key to Explain the Link Between Depression and Atherothrombosis” </p> <p><em><strong>Abstract: </strong></em></p> <p><strong>Background</strong>: Obesity and depression are intertwined diseases often associated with an increased risk of cardiovascular (CV) complications. Brain-Derived Neurotrophic Factor (BDNF), altered in the brain both of subjects with depression and obesity, provides a potential link between depression and thrombosis. Since the relationship among peripheral BDNF, depression and obesity is not well-defined, the aim of the present report has been to address this issue taking advantage of the contribution played by extracellular vesicle (EV)-derived miRNAs. <strong>Research Process</strong>: Associations among circulating BDNF, depression and EVderived miRNAs related to atherothrombosis have been evaluated in a large Italian cohort of obese individuals (n = 743), characterized by the Beck Depression Inventory (BDI-II) score.<br> <strong>Results</strong>: BDI-II was negatively associated with BDNF levels without a significant impact of the rs6265 BDNF polymorphism; this association was modified by raised levels of IFN-g. BDNF levels were linked to an increase of 80 EV-derived miRNAs and a decrease of 59 miRNAs related to atherosclerosis and thrombosis. Network analysis identified at least 18 genes targeted by these miRNAs, 7 of which involved in depression and CV<br> risk. The observation of a possible link among BDNF, depression, and miRNAs related to atherothrombosis and depression in obesity is novel and may lead to a wider use of BDNF as a CV risk biomarker in this specific subject group.</p>
miRNA in Gastric Cancer
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Fig. 32 in Taxonomic re-evaluation of Andrena cyanomicans PÉREZ, 1895, A. fratella WARNCKE, 1968, A. maderensis WARNCKE, 1969, A. mirna WARNCKE, 1969, A. notata WARNCKE, 1968, and A. portosanctana WARNCKE, 1969 (Hymenoptera, Anthophila)
Fig. 32: Morphometric analyses (males) of pterostigma length (PSL) and wing length (WL).
Sequence feature comparison between xenomiRs and mobile miRNA, and xenomiRs and circulating miRNA
<p>Sequence feature comparison between xenomiRs and mobile miRNA, and xenomiRs and circulating miRNA. Bold indicates the mean of that feature in xenomiR is larger.</p>
Pathways enriched in downstream target genes of miRNAs associated with NT-proBNP and OPN
<p>The full set of 30 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways that were significantly enriched (FDR-adjusted p<0.01) in the predicted mRNA targets of either the OPN- or NT-proBNP-associated miRNAs; 21 of these pathways were significantly enriched in both sets of targets.</p> <p>KEGG: Kyoto Encyclopedia of Genes and Genomes; miRNAs: microRNAs; NT-proBNP: N-terminal pro <a href="http://www.mayomedicallaboratories.com/test-catalog/Clinical+and+Interpretive/83873">B-type natriuretic peptide</a>; OPN: osteopontin</p>
The miRBase release 22 reference files: stem-loop sequences (hairpins) and mature miRNA sequences
<pre>The miRBase Sequence Database -- Release 22 ------------------------------------------- The miRBase database provides a searchable online repository for published microRNA sequences and associated annotation. miRBase also provides a gene naming and nomenclature function in the miRBase Registry. Release 22 of the database contains 38589 entries representing hairpin precursor miRNAs, expressing 48885 mature miRNA products, in 271 species. The data are freely available to all through the web interface at http://www.mirbase.org/ and in flatfile form from ftp://mirbase.org/pub/mirbase/. </pre>
Dataset related to the article "Extraction-Free Absolute Quantification of Circulating miRNAs by Chip-Based Digital PCR"
<p>This record contains raw data related to the article "Extraction-Free Absolute Quantification of Circulating miRNAs by Chip-Based Digital PCR"</p> <p>Circulating microRNAs (miRNA) have been proposed as specific biomarkers for several diseases. Quantitative Real-Time PCR (RT-qPCR) is the gold standard technique currently used to evaluate miRNAs expression from different sources. In the last few years, digital PCR (dPCR) emerged as a complementary and accurate detection method. When dealing with gene expression, the first and most delicate step is nucleic-acid isolation. However, all currently available protocols for RNA extraction suffer from the variable loss of RNA species due to the chemicals and number of steps involved, from sample lysis to nucleic acid elution. Here, we evaluated a new process for the detection of circulating miRNAs, consisting of sample lysis followed by direct evaluation by dPCR in plasma from healthy donors and in the cardiovascular setting. Our results showed that dPCR is able to detect, with high accuracy, low-copy-number as well as highly expressed miRNAs in human plasma samples without the need for RNA extraction. Moreover, we assessed a known myocardial infarction-related miR-133a in acute myocardial infarct patients vs. healthy subjects. In conclusion, our results show the suitability of the extraction-free quantification of circulating miRNAs as disease markers by direct dPCR.</p>
Dataset related to article "Archival skin biopsy specimens as a tool for miRNA-based diagnosis: Technical and post-analytical considerations".
<p>microRNA raw data</p>
The EGFR signaling modulates in mesenchymal stem cells the expression of miRNAs involved in the interaction with breast cancer cells
<p>We previously demonstrated that the epidermal growth factor receptor (EGFR) modulates in mesenchymal stem cells (MSCs) the expression of a number of genes coding for secreted proteins that promote breast cancer progression. However, the role of the EGFR in modulating in MSCs the expression of miRNAs potentially involved in the progression of breast cancer remains largely unexplored. Following small RNA-sequencing, we identified 36 miRNAs differentially expressed between MSCs untreated or treated with the EGFR ligand transforming growth factor α (TGFα), with a fold change (FC) <0.56 or FC ≥1.90 (CI, 95%). KEGG analysis revealed a significant enrichment in signaling pathways involved in cancer development and progression. EGFR activation in MSCs downregulated the expression of different miRNAs, including miR-23c. EGFR signaling also reduced the secretion of miR-23c in conditioned medium from MSCs. Functional assays demonstrated that miR-23c acts as tumor suppressor in basal/claudin-low MDA-MB-231 and MDA-MB-468 cells, through the repression of IL-6R. MiR-23c downregulation promoted cell proliferation, migration and invasion of these breast cancer cell lines. Collectively, our data suggested that the EGFR signaling regulates in MSCs the expression of miRNAs that might be involved in breast cancer progression, providing novel information on the mechanisms that regulate the MSC-tumor cell cross-talk.We previously demonstrated that the epidermal growth factor receptor (EGFR) modulates in mesenchymal stem cells (MSCs) the expression of a number of genes coding for secreted proteins that promote breast cancer progression. However, the role of the EGFR in modulating in MSCs the expression of miRNAs potentially involved in the progression of breast cancer remains largely unexplored. Following small RNA-sequencing, we identified 36 miRNAs differentially expressed between MSCs untreated or treated with the EGFR ligand transforming growth factor α (TGFα), with a fold change (FC) <0.56 or FC ≥1.90 (CI, 95%). KEGG analysis revealed a significant enrichment in signaling pathways involved in cancer development and progression. EGFR activation in MSCs downregulated the expression of different miRNAs, including miR-23c. EGFR signaling also reduced the secretion of miR-23c in conditioned medium from MSCs. Functional assays demonstrated that miR-23c acts as tumor suppressor in basal/claudin-low MDA-MB-231 and MDA-MB-468 cells, through the repression of IL-6R. MiR-23c downregulation promoted cell proliferation, migration and invasion of these breast cancer cell lines. Collectively, our data suggested that the EGFR signaling regulates in MSCs the expression of miRNAs that might be involved in breast cancer progression, providing novel information on the mechanisms that regulate the MSC-tumor cell cross-talk.</p>
ScienceDex guides
Understand access before you commit
These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.