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466
datasets available to search
ShareScore release 0.9.0
Dataset results
466 results for “Noncoding RNA”
Data from: Major group-B enterovirus populations deleted in the noncoding 5' region of genomic RNA modulate activation of the type I interferon pathway in cardiomyocytes and induce myocarditis
<p>Major 5'-terminally deleted (5'TD) RNA forms of group-B coxsackievirus (CVB-5'TD) has been associated with myocarditis in both mice and humans. Although it is known that interferon-β (IFN-β) signaling is critical for an efficient innate immune response against CVB-induced myocarditis, the link between CVB-5'TD RNA forms and type I IFN signaling in cardiomyocytes remains to be explored. In a mouse model of CVB3/28-induced myocarditis, major early-emerging forms of CVB-5'TD RNA have been characterized as replicative viral populations that impair IFN-β production in the heart. Synthetic CVB3/28 RNA forms mimicking each of these major 5'TD virus populations were transfected in mice and have been shown to modulate innate immune responses in the heart and to induce myocarditis in mice. Remarkably, transfection of synthetic viral RNA with deletions in the secondary structures of the 5'-terminal CVB3 RNA domain I, modifying stem-loops "b", "c" or "d", were found to impair IFN-β production in human cardiomyocytes. In addition, the activation of innate immune response by Poly(I:C), was found to restore IFN-β production and to reduce the burden of CVB-5'TD RNA-forms in cardiac tissues, thereby reducing the mortality rate of infected mice. Overall, our results indicate that major early-emerging CVB3 populations deleted in the domain I of genomic RNA, in the 5' noncoding region, modulate the activation of the type I IFN pathway in cardiomyocytes and induce myocarditis in mice. These findings shed new light on the role of replicative CVB-5'TD RNA forms as key pathophysiological factors in CVB-induced human myocarditis.</p>
CeNGEN Integrated mRNA data and bulk noncoding RNA lookup table
<p>This CeNGEN web tool provides a user interface to datasets described in Barrett et al(1): <a href="http://bulk.cengen.org:3838/Bulk_Integrated_viz/">http://bulk.cengen.org:3838/Bulk_Integrated_viz/</a>. It can also be run as an Rshiny app locally using the attached files.</p> <p>Raw data are being processed at GEO, and this resource will be updated with the accession number when available.</p> <p>(1)Integrating bulk and single cell RNA-seq refines transcriptomic profiles of specific C. elegans neurons. Alec Barrett, Erdem Varol, Alexis Weinreb, Seth R. Taylor, Rebecca McWhirter, CyrilCros, Manasa Basavaraju, Abigail Poff, John A. Tipps, Maryam Majeed, Berta Vidal, Chen Wang, Eviatar Yemini, Emily A. Bayer, HaoSheng Sun, Oliver Hobert, David M.Miller III, Marc Hammarlund. bioRxiv 2022.04.05.487209; doi: https://doi.org/10.1101/2022.04.05.487209</p> <p> </p>
Flnc: Machine Learning Improves the Identification of Novel Long Noncoding RNAs from Stand-Alone RNA-Seq Data
<p>Flnc is software that can accurately identify full-length long noncoding RNAs (lncRNAs) from human RNA-seq data. lncRNAs are linear transcripts of more than 200 nucleotides that do not encode proteins. The most common approach for identifying lncRNAs from RNA-seq data which examines the coding abilities of assembled transcripts will result in a very high false-positive rate (30%-75%) of lncRNA identification. The falsely discovered lncRNAs lack transcriptional start sites and most of them are RNA fragments or result from transcriptional noise. Unlike the false-positive lncRNAs, true lncRNAs are full-length lncRNA transcripts that include transcriptional start sites (TSSs). To exclude these false lncRNAs, H3K4me3 chromatin immunoprecipitation sequencing (ChIP-seq) data had been used to examine transcriptional start sites of putative lncRNAs, which are transcripts without coding abilities. However, because of cost, time, and the limited availability of sample materials for generating H3K4me3 ChIP-seq data, most samples (especially clinical biospecimens) may have available RNA-seq data but lack matched H3K4me3 ChIP-seq data. This Flnc method solves the problem of lacking transcriptional initiation profiles when identifying lncRNAs.</p> <p>Flnc integrates seven machine-learning algorithms built with four genomic features. Flnc achieves state-of-the-art prediction power with a AUROC score over 0.92. Flnc significantly improves the prediction accuracy from less than 50% using the common approach to over 85% on five independent datasets without requiring matched H3K4me3 ChIP-seq data. In addition to the stranded polyA-selected RNA-seq data, Flnc can also be applied to identify lncRNAs from stranded RNA-seq data of ribosomal RNA depleted samples or unstranded RNA-seq data of polyA-selected samples.</p>
Data from: PITAR, a DNA damage-inducible Cancer/Testis long noncoding RNA, inactivates p53 by binding and stabilizing TRIM28 mRNA
Open the record for dataset details and reuse information.
Data from: Major group-B enterovirus populations deleted in the noncoding 5' region of genomic RNA modulate activation of the type I interferon pathway in cardiomyocytes and induce myocarditis
Open the record for dataset details and reuse information.
Test data for running snakePipes : noncoding-RNA-seq workflow
<p><strong>Test files for running snakePipes workflows</strong></p> <p><strong>snakePipes</strong> are pipelines built using snakemake and python for the analysis of epigenomic datasets. Please refer to <a href="https://snakepipes.readthedocs.io/en/latest/">this link</a> for further information on snakePipes.</p> <p>This folder contains test files that can be used to run the noncoding-RNA-seq workflow under snakePipes. To test the workflow, follow the following steps : </p> <ul> <li>Download or prepare genome fasta, indices and annotations for mouse (<strong>GRCm38</strong>) genome. Repeat Masker file is required for this workflow.</li> <li>Download and install snakePipes via `conda create -n snakePipes -c mpi-ie -c bioconda -c conda-forge snakePipes`</li> <li>Update <a href="https://snakepipes.readthedocs.io/en/latest/content/running_snakePipes.html#genome-configuration-file">Genome configuration file</a> with path to indices and annotations.</li> <li>Move to this repository and run the example <strong>command.sh</strong></li> </ul>
Association of SNPs in Long Intergenic Noncoding RNA 00511 (LINC00511) With Breast Cancer Among the Egyptian Population
ClinicalTrials.gov study NCT06357689. IPD Sharing: UNDECIDED. Countries: 1. Publications: 17.
Assessment Of Long Noncoding RNA CCAT1 In Colorectal Cancer Patients
ClinicalTrials.gov study NCT04269746. IPD Sharing: Not stated. Countries: 0. Publications: 1.
A transcribed ultra-conserved noncoding RNA, uc.285+, promotes colorectal cancer proliferation via directly binding mRNA
GEO Series GSE167326. Homo sapiens. 2 samples. Type: Non-coding RNA profiling by array.
Transcriptomic analysis of neuroblastoma cells in response to stable over-expression of Ets-1 promoter-associated noncoding RNA (pancEts-1)
GEO Series GSE104950. Homo sapiens. 2 samples. Type: Expression profiling by high throughput sequencing.
A long noncoding RNA regulates sister chromatid cohesion
GEO Series GSE81602. Homo sapiens. 15 samples. Type: Expression profiling by array; Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing.
Angiogenic patterning by STEEL, an endothelial-enriched long noncoding RNA
GEO Series GSE108321. Homo sapiens. 32 samples. Type: Expression profiling by array; Non-coding RNA profiling by array.
Oncogenic HPV E7 promotes the expression of a long noncoding RNA lnc-FANCI-2 via YY1 and miR-29a
GEO Series GSE150227. Homo sapiens. 18 samples. Type: Non-coding RNA profiling by high throughput sequencing.
The Long Noncoding RNA Lncenc1 Regulates Glycolysis in Naive Mouse ES Cells II
GEO Series GSE116462. Mus musculus. 4 samples. Type: Expression profiling by high throughput sequencing.
An ultraconserved snoRNA-like element in long noncoding RNA CRNDE promotes ribosome biogenesis and cell proliferation (CRISPRi screen) [786-O]
GEO Series GSE270847. Homo sapiens. 4 samples. Type: Other.
VILMIR is a trans-acting long noncoding RNA that enhances the host interferon response in human epithelial cells
GEO Series GSE305270. Homo sapiens. 18 samples. Type: Expression profiling by high throughput sequencing.
The long noncoding RNA expression profile of hepatocellular carcinoma identified by microarray analysis
GEO Series GSE55191. Homo sapiens. 6 samples. Type: Expression profiling by array; Non-coding RNA profiling by array.
Allele-selective Transcriptome Recruitment to Polysomes Primed for Translation: Protein-coding and Noncoding RNAs, and RNA Isoforms
GEO Series GSE66135. Homo sapiens. 6 samples. Type: Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing; Genome variation profiling by high throughput sequencing.
The nuclear cap-binding complex regulates subcellular RNA processing and surveillance of coding and noncoding RNAs
GEO Series GSE291993. Arabidopsis thaliana. 18 samples. Type: Other; Expression profiling by high throughput sequencing.
The long noncoding RNA expression profile of human intervertebral disc degeneration identified by microarray analysis
GEO Series GSE56081. Homo sapiens. 10 samples. Type: Non-coding RNA profiling by array; Expression profiling by array.
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.