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658 results for “non-coding RNA”
retracted and commented papers related to non-coding RNA
<p>This is the dataset related to the research integrity analysis paper of non-coding RNA.</p> <p>The retracted and commented papers related to non-coding RNA and their publication years and citations are presented. It have the following sheets:</p> <ul> <li>Figure 1 <ul> <li>number of publications, retraction and comments of each year</li> </ul> </li> <li>Figure 2 <ul> <li>Percentage of retractions and Percentage of papers for major Prefixes/Keywords</li> </ul> </li> <li>retraction <ul> <li>retracted papers with their citation and related research integrity issue</li> </ul> </li> <li>comment <ul> <li>commented papers with thier citation and pubpeer url</li> </ul> </li> </ul>
Reducing the structure bias of RNA-Seq reveals a large number of non-annotated non-coding RNA Data Archive
<p>[This repository contains the source data for the workflow presented in the manuscript "<strong>Reducing the structure bias of RNA-Seq reveals a large number of non-annotated non-coding RNA</strong>". The workflow can be found here: http://gitlabscottgroup.med.usherbrooke.ca/gaspard/snakemake_blockbuster ]</p> <p>The study of RNA expression is the fastest growing area of genomic research. However, despite the dramatic increase in the number of sequenced transcriptomes, we still do not have accurate estimates of the number and expression levels of non-coding RNA genes. Non-coding transcripts are often overlooked due to incomplete genome annotation. In this study, we use annotation-independent detection of RNA reads generated using a reverse transcriptase with low structure bias to identify non-coding RNA. Transcripts between 20 and 500 nucleotides were filtered and crosschecked with non-coding RNA annotations revealing 115 non-annotated non-coding RNAs expressed in different cell lines and tissues. Inspecting the sequence and structural features of these transcripts indicated that 60% of these transcripts correspond to new tRNA and snoRNA genes. The identified genes exhibited features of their respective families in terms of structure, expression, conservation and response to depletion of interacting proteins. Together, our data reveal a new group of RNA that are difficult to detect using standard gene prediction and RNA sequencing techniques, suggesting that reliance on actual gene annotation and sequencing techniques distort the perceived architecture of the human transcriptome.</p>
Transcriptional stochasticity reveals multiple mechanisms of long non-coding RNA regulation at the Xist – Tsix locus
<p>Data and codes for Figure reprodicbility, image processing and demo.</p>
Long non-coding RNA Neat1 and paraspeckle components are translational regulators in hypoxia
<p>Internal ribosome entry sites (IRESs) drive translation initiation during stress. In response to hypoxia, (lymph)angiogenic factors responsible for tissue revascularization in ischemic diseases are induced by the IRES-dependent mechanism. Here we searched for IRES <em>trans</em>-acting factors (ITAFs) active in early hypoxia in mouse cardiomyocytes. Using knock-down and proteomics approaches, we show a link between a stressed-induced nuclear body, the paraspeckle, and IRES-dependent translation. Furthermore, smiFISH experiments demonstrate the recruitment of IRES-containing mRNA into paraspeckle during hypoxia. Our data reveal that the long non-coding RNA Neat1, an essential paraspeckle component, is a key translational regulator, active on IRESs of (lymph)angiogenic and cardioprotective factor mRNAs. In addition, paraspeckle proteins p54<sup>nrb</sup> and PSPC1 as well as nucleolin and Rps2, two p54<sup>nrb</sup>-interacting proteins identified by mass spectrometry, are ITAFs for IRES subgroups. Paraspeckle thus appears as a platform to recruit IRES-containing mRNAs and possibly host IRESome assembly. Polysome PCR array shows that Neat1 isoforms regulate IRES-dependent translation and, more widely, translation of mRNAs involved in stress response.</p>
Long non-coding RNA Neat1 and paraspeckle components are translational regulators in hypoxia
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Supplementary material 2 from: Rosenblad MA, Larsson E, Walker A, Thongklang N, Wurzbacher C, Nilsson RH (2022) Evidence for further non-coding RNA genes in the fungal rDNA region. MycoKeys 90: 203-213. https://doi.org/10.3897/mycokeys.90.84866
List of absolute positions of the rRNA and ncRNA genes in the six sequences released with this study
Data from: The non-coding RNA CcnA modulates the master cell cycle regulators CtrA and GcrA in Caulobacter crescentus
<p>Bacteria are powerful models for understanding how cells divide and accomplish global regulatory programs. In <em>Caulobacter crescentus</em>, a cascade of essential master regulators supervises the correct and sequential activation of DNA replication, cell division and development of different cell types. Among them, the response regulator CtrA plays a crucial role coordinating all those functions. Here, for the first time we describe the role of a novel factor named CcnA, a cell cycle regulated ncRNA located at the origin of replication, presumably activated by CtrA and responsible for the accumulation of CtrA itself. In addition, CcnA may be also involved in the inhibition of translation of the S-phase regulator, GcrA, by interacting with its 5' untranslated region (5'-UTR). Performing <em>in vitro</em> experiments and mutagenesis, we propose a mechanism of action of CcnA based on liberation (<em>ctrA</em>) or sequestration (<em>gcrA</em>) of their ribosome-binding site (RBS). Finally, its role may be conserved in other alphaproteobacterial species, such as <em>Sinorhizobium</em> <em>meliloti</em>, representing indeed a potentially conserved process modulating cell cycle in <em>Caulobacterales </em>and<em> Rhizobiales</em>. </p>
Implication of Long Non-coding RNA HOTTIP Haplotype on Liver Cancer Metastasis
ClinicalTrials.gov study NCT06544005. IPD Sharing: UNDECIDED. Countries: 1. Publications: 12.
Circulating Non-coding RNA in Acute Ischemic Stroke with Endovascular Treatment (EVTRNA)
ClinicalTrials.gov study NCT04230785. IPD Sharing: YES. Countries: 1. Publications: 1.
Circulating Non-coding RNA in Acute Ischemic Stroke (AISRNA)
ClinicalTrials.gov study NCT04175691. IPD Sharing: YES. Countries: 1. Publications: 5.
Implication of Long Non-coding RNA CCDC144NL-AS1/Micro RNA-143-3p Axis Expression Level as Novel Signature in Colorectal Cancer
ClinicalTrials.gov study NCT06427278. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Biochemical Role of Long Non-coding RNA MALAT 1 and Serum Tumor Necrosis Factor Alpha in Bronchial Asthma Patients.
ClinicalTrials.gov study NCT06459895. IPD Sharing: Not stated. Countries: 1. Publications: 3.
Data from: The non-coding RNA CcnA modulates the master cell cycle regulators CtrA and GcrA in Caulobacter crescentus
Open the record for dataset details and reuse information.
Supplementary material 1 from: Rosenblad MA, Larsson E, Walker A, Thongklang N, Wurzbacher C, Nilsson RH (2022) Evidence for further non-coding RNA genes in the fungal rDNA region. MycoKeys 90: 203-213. https://doi.org/10.3897/mycokeys.90.84866
Details of the sequence processing steps.
Study of Long Non-coding RNA SNHG15 as a Novel Biomarker in HBV Associated HCC
ClinicalTrials.gov study NCT05840133. IPD Sharing: NO. Countries: 0. Publications: 7.
Total RNA sequencing in multiple Sus Scrofa tissues reveals novel long non-coding RNAs functioning in skeletal muscle development
GEO Series GSE73763. Sus scrofa. 13 samples. Type: Expression profiling by high throughput sequencing.
Long non-coding RNA and mRNA transcriptomic profiles after ischemia-reperfusion injury in rat spinal cord.
GEO Series GSE138966. Rattus norvegicus. 6 samples. Type: Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing.
The long non-coding RNA LUCAT1 is a negative feedback regulator of the Interferon Response in humans (IAV and HSV dataset)
GEO Series GSE145449. Homo sapiens. 10 samples. Type: Expression profiling by high throughput sequencing.
Long non-coding RNA NEAT1 promotes sarcoma metastasis by regulating RNA splicing pathways
GEO Series GSE139574. Mus musculus. 20 samples. Type: Expression profiling by high throughput sequencing.
Non-coding RNA and mRNA expression profile in multi-drug resistance of colorectal cancer
GEO Series GSE173606. Homo sapiens. 9 samples. Type: Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing.
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.