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opencc-by-4.0Jan 2021View details →

Summary statistics data for "Genetic variation and microRNA targeting of A-to-I RNA editing fine tune human tissue transcriptomes"

edQTL and ASED summary statistics data for the manuscript titled "Genetic variation and microRNA targeting of A-to-I RNA editing fine tune human tissue transcriptomes"

opencc-zeroDec 2015View details →

Data from: MicroRNA stability in FFPE tissue samples: dependence on GC content

MicroRNAs (miRNAs) are small non-coding RNAs responsible for fine-tuning of gene expression at post-transcriptional level. The alterations in miRNA expression levels profoundly affect human health and often lead to the development of severe diseases. Currently, high throughput analyses, such as microarray and deep sequencing, are performed in order to identify miRNA biomarkers, using archival patient tissue samples. MiRNAs are more robust than longer RNAs, and resistant to extreme temperatures, pH, and formalin-fixed paraffin-embedding (FFPE) process. Here, we have compared the stability of miRNAs in FFPE cardiac tissues using next-generation sequencing. The mode read length in FFPE samples was 11 nucleotides (nt), while that in the matched frozen samples was 22 nt. Although the read counts were increased 1.7-fold in FFPE samples, compared with those in the frozen samples, the average miRNA mapping rate decreased from 32.0% to 9.4%. These results indicate that, in addition to the fragmentation of longer RNAs, miRNAs are to some extent degraded in FFPE tissues as well. The expression profiles of total miRNAs in two groups were highly correlated (0.88

opencc-zeroDec 2012View details →

Data from: Impact of microRNA expression in human atrial tissue in patients with atrial fibrillation undergoing cardiac surgery

Background: Although microRNA (miRNA) regulates initiation and/or progression of atrial fibrillation (AF) in canine AF models, the underlying mechanism in humans remains unclear. We speculated that certain miRNAs in atrial tissue are related to AF, and evaluated the relationship of miRNA expression in human atrial tissue in cardiac surgery patients. Methods: Right atrial tissues from 29 patients undergoing cardiovascular surgery were divided into 3 groups [A: chronic AF or unsuccessful maze, n=6; B: successful maze, n=10; C: sinus rhythm (SR) n=13]. miRNA expression was determined using high density microarrays and with Reverse transcriptase-polymerase chain reaction (RT-PCR). Fibrosis was examined using Masson trichrome staining. Results: miRNA microarray analysis showed elevated miRNA-21, miRNA-23b, miRNA-199b, and miRNA-208b in AF as compared to SR groups. RT-PCR showed elevated miRNA-21 (1.9-fold) and miRNA-208b (4.2-fold) in AF as compared to the SR groups. miRNA-21 expression increased from Group C to A (A: 2.1-fold, B: 1.8-fold, C: 1.0-fold). Fibrosis increased from C to A (A: 43.0±12.9%, B: 21.3±6.1%, C: 11.9±3.1%). Percent fibrosis and miRNA-21 expression were correlated (r=0.508, p<0.05). The plasma levels of miRNA-21 in AF patients was significantly decreased as compared to the healthy volunteers (p<0.05). Conclusion: The expression of miRNA-21 in human atrial tissue was found to be related to atrial fibrosis and might affect AF occurrence, indicating its usefulness as a biomarker for cardiac surgery management.

opencc-by-4.0Dec 2022View details →

Evolution of microRNAs in Amoebozoa and implications for the origin of multicellularity

<h2>Evolution of microRNAs in Amoebozoa and implications for the origin of multicellularity</h2> Repository accompanying "Evolution of microRNAs in Amoebozoa and implications for the origin of multicellularity" manuscript   <h3>microRNA curation</h3> Potential miRNA clusters, generated using Shortstack (https://github.com/MikeAxtell/ShortStack), are analyzed with miRNA_curation.py. An example run of the miRNA curation can be performed by running the 'example_run/explore_all.sh' and 'example_run/refine_all.sh' scripts in order. A sample of the sRNA sequences from D. discoideum is included in the 'example/example_sizeselected_data' folder. A sample of miRNA candidates are included in 'example_run/pot-miRNAs_merged.fa' to facilitate the example run. Prerequisites: Python 3, Biopython, RNAlib, matplotlib, numpy   <h3>microRNA analysis</h3> Following miRNA curation, high confidence miRNAs are identified and further analysed in amoeba_miRNAevo.Rmd. The data for the analysis is located in  'data_in' and are mostly derived from the miRNA_curation.py script and other scripts located in the 'helper_scripts' folder. The plots generated in the analysis is located in the 'plots' folder. Tables and other data generated from the analysis are located in the 'data_out' folder. In order to perform the miRNA conservation search, refer to the 'helper_scripts/miRNA_conservation_search/' folder. Prerequisites: R, Blast, bash   <h3>Access genomes/annotations</h3> For Dictyostelium firmibasis, the genome was de-novo sequenced and assembled and is located in 'data_in/novel_assembly'. Assembly was done using Flye v2.9.1 in nano-hq mode, and two rounds of long-read polishing were done using Medaka v1.7.2. The filtered reads used for assembly can be accessed from NCBI BioProject PRJNA972620. The Acanthamoeba castellanii genome and annotation were accessed at https://www.doi.org/10.5281/zenodo.680005. The other genomes and annotations for this study were accessed from NCBI and can be downloaded using the 'get_references.sh' script located in the helper_scripts folder.

opencc-zeroNov 2021View details →

Expression profile of microRNAs in different stages of wound healing in mice

Wound healing response is characterized by progression from clot formation to an inflammatory phase, a repair phase, and finally remodeling. MicroRNAs (miRNAs) are 20-24 nucleotide noncoding RNAs that can affect protein expression at the posttranscriptional level by modulating the stability and translation of corresponding messenger RNAs (mRNAs). The roles that miRNAs play in various physiological and pathological processes have received increasingly widespread attention. However, the differentially expressed miRNAs involved in different stages of wound healing and their roles remain to be further explored. In this study, we established wound model on the shaved dorsum using a punch biopsy tool in C57BL/6J mice. Biopsies were harvested on postoperative days 0, 1, 3, and 7. Then, we identified the differentially expressed miRNAs in different stages of wound healing through Illumina sequencing and miRDeep2 analysis. This study help to find out the expression profile of microRNAs during normal wound healing in mice.

opencc-zeroJun 2022View details →

Tables of microRNA and gene expression of an echolocating bat

MicroRNAs (miRNAs) are important post-transcriptional regulators of gene expression and play key roles in many biological processes, such as development and response to multiple stresses. However, little is known about their roles in generating novel phenotypes and phenotypic variation during the course of animal evolution. Here, we, for the first time, characterized the miRNAs of the cochlea in an echolocating bat (Rhinolophus affinis). We sampled eight individuals from two R. affinis subspecies with significant echolocation call frequency differences. We identified 365 miRNAs and 121 of them were novel. By searching sequences of these miRNAs precursors in multiple high-quality mammal genomes, no specific miRNAs were found to be shared by all echolocating mammals. Together with the matched mRNA-seq data, we identified 1,766 differentially expressed genes (DEGs) between the two subspecies and 555 of them were negatively regulated by differentially expressed miRNAs (DEMs). We found that almost half of known hearing genes in the list of all DEGs were regulated negatively by DEMs, suggesting an important role of miRNAs in call frequency variation of the two subspecies. These targeted DEGs included several important hearing genes (e.g. Piezo1, Piezo2 and CDH23) that have been shown to be important in ultrasonic hearing of echolocating mammals.

opencc-by-4.0Jun 2022View details →

MicroRNA-574-5p targeting HOXC6 expression inhibits the hepatocyte lipid uptake to alleviate NAFLD

In recent times, the non-alcoholic fatty liver disease (NAFLD) is increasing worldwide. Increasing evidence supports the role of miRNAs in the pathogenesis of NAFLD. The miR-574-5p has been shown to be involved in lipid metabolism. However, studies on the correlation between miR-574-5p and NAFLD are lacking. Hence, in this study, we wanted to investigate whether miR-574-5p is associated with the pathogenesis of NAFLD. Through various in vivo and in vitro experiments, we found that miR-574-5p can inhibit lipid accumulation and lipid formation by targeting the HOXC6 3' UTR. We believe that our study makes a significant contribution to the literature because this study is the first to show that miR-574-5p is downregulated in liver tissue in a mouse NAFLD model. Further, understanding the miRNAs and their targets that regulate NAFLD may help us better understand the disease and lead to the design of a potential therapeutic against NAFLD in the future.In recent times, the non-alcoholic fatty liver disease (NAFLD) is increasing worldwide. Increasing evidence supports the role of miRNAs in the pathogenesis of NAFLD. The miR-574-5p has been shown to be involved in lipid metabolism. However, studies on the correlation between miR-574-5p and NAFLD are lacking. Hence, in this study, we wanted to investigate whether miR-574-5p is associated with the pathogenesis of NAFLD. Through various in vivo and in vitro experiments, we found that miR-574-5p can inhibit lipid accumulation and lipid formation by targeting the HOXC6 3' UTR. We believe that our study makes a significant contribution to the literature because this study is the first to show that miR-574-5p is downregulated in liver tissue in a mouse NAFLD model. Further, understanding the miRNAs and their targets that regulate NAFLD may help us better understand the disease and lead to the design of a potential therapeutic against NAFLD in the future.

opencc-by-4.0Apr 2018View details →

A Web-resource for Nutrient Use Efficiency related Genes, QTLs, and microRNA in important cereals and model plants

Cereals are key contributors to global food security. Genes involved in the uptake (transport), assimilation and utilization of macro- and micronutrients are responsible for the presence of these nutrients in grain and straw. Although many genomic databases for cereals are available, there is currently no cohesive web resource of manually curated nutrient use efficiency (NtUE)-related genes and quantitative trait loci (QTLs). In this study, we present a <a href="http://bioclues.org/NtUE/index.php">web- resource</a> containing information on NtUE-related genes/QTLs and the corresponding available microRNAs for some of these genes in four major cereal crops (wheat (Triticum aestivum), rice (Oryza sativa), maize (Zea mays), barley (Hordeum vulgare)), two alien species related to wheat (Triticum urartu and Aegilops tauschii), and two model species (Brachypodium distachyon and Arabidopsis thaliana). Gene annotations integrated in the current web resource were manually curated from the existing databases and the available literature. The primary goal of developing this web resource is to provide descriptions of the NtUE-related genes and their functional annotation. MicroRNAs targeting some of the NtUE related genes and the QTLs for NtUE-related traits are also included. The genomic information embedded in the web resource should help users to search for the desired information.

opencc-by-4.0May 2024View details →

Figures for the publication ''The role of small extracellular vesicles and microRNA as their cargo in the spinal cord injury pathophysiology and therapy''

Open the record for dataset details and reuse information.

opencc-by-4.0Aug 2021View details →

Example micrographs of RNA polymerase II localization to the zebrafish microRNA miR-430 cluster

Contains the raw images and MatLab scripts to show localization of recruited (Ser5P) and elongating (Ser2P) RNA polymerase II to the zebrafish microRNA miR-430 cluster. Embryos were fixed in the oblong stage of development, labeled by immunofluorescence, and images were recorded with an instant-SIM microscope. To produce example images, first run the extraction script, then the example images script. You need to add the bfmatlab importer function from OME for data import before running the extraction script. Otherwise, extracted data are also provided with this repository,

opencc-by-4.0Sep 2021View details →

dataset related to article "Dysregulation of Muscle-Specific MicroRNAs as Common Pathogenic Feature Associated with Muscle Atrophy in ALS, SMA and SBMA: Evidence from Animal Models and Human Patients"

CINZIA CAGNOLI 0000-0001-6863-6687, MICHELA TAIANA 0000-0001-8257-8831, MONICA NIZZARDO 0000-0001-5447-0882, STEFANIA CORTI 0000-0001-5425-969X, VIVIANA PENSATO 0000-0001-9798-2669, ANNA VENERANDO <a href="https://orcid.org/0000-0002-7489-1833">0000-0002-7489-1833</a>, CINZIA GELLERA <a href="https://orcid.org/0000-0002-3582-665X">0000-0002-3582-665X</a>, SILVIA FENU 0000-0002-5233-6580, DAVIDE PAREYSON 0000-0001-6854-765X, RICCARDO MASSON 0000-0002-9311-452X, LORENZO MAGGI 0000-0002-0932-5173, ELEONORA DALLA BELLA 0000-0001-6267-9651, GIUSEPPE LAURIA 0000-0001-9773-020X, RENATO MANTEGAZZA 0000-0002-9810-5737, PIA BERNASCONI 0000-0003-0869-2104, ANGELO POLETTI 0000-0002-8883-0468, SILVIA BONANNO 0000-0002-8823-6821, STEFANIA MARCUZZO 0000-0001-6893-6372.

Optimal Pediatric Heart Transplant Immunosuppression With MicroRNAs

ClinicalTrials.gov study NCT06532890. IPD Sharing: NO. Countries: 1. Publications: 2.

restrictedIPD-UNDECIDEDFeb 2026View details →

Microarray Analysis of microRNA Expression in Basal Cell Carcinoma

ClinicalTrials.gov study NCT01498250. IPD Sharing: Not stated. Countries: 1. Publications: 1.

Effect of Vitamin E Supplementation in Methylation and microRNAs Profile

ClinicalTrials.gov study NCT02922491. IPD Sharing: NO. Countries: 1. Publications: 1.

Correlation of Atrial Fibrillation Recurrence After Bipolar Radiofrequency Ablation With microRNA Expression

ClinicalTrials.gov study NCT04134793. IPD Sharing: NO. Countries: 1. Publications: 9.

Predictive Value of microRNA in Thyroid Cytologies of Undetermined Type

ClinicalTrials.gov study NCT04285476. IPD Sharing: NO. Countries: 1. Publications: 16.