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2,489 results for “Sars-CoV-2”
The RNA demethylase FTO controls m6A marking on SARS-CoV-2 and classifies COVID-19 severity in patients
GEO Series GSE201626. Chlorocebus sabaeus. 12 samples. Type: Other.
Chromatin disruptions in pathophysiologically relevant gene promoters underlie unique SARS-Cov-2 nucleocapsid-mediated gene regulation
GEO Series GSE290042. Homo sapiens. 48 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
SARS-CoV-2 nsp13 restricts episomal DNA transcription and hepatitis B virus infection
GEO Series GSE200511. Homo sapiens. 7 samples. Type: Expression profiling by high throughput sequencing.
Differences in syncytia formation by SARS-CoV-2 variants modify host chromatin accessibility and cellular senescence via TP53 [RNA-Seq]
GEO Series GSE241891. Homo sapiens; Chlorocebus sabaeus. 20 samples. Type: Expression profiling by high throughput sequencing.
Role of Top1 and 3D Genome structure in SARS-CoV-2 infection [Hi-C]
GEO Series GSE162612. Homo sapiens. 6 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
Two-component intranasal vaccine against SARS-CoV-2 Omicron variant
GEO Series GSE279004. Mus musculus. 6 samples. Type: Expression profiling by high throughput sequencing; Other.
An ex vivo human precision-cut lung slice platform provides insight into SARS-CoV-2 pathogenesis and antiviral drug efficacy
GEO Series GSE226702. Homo sapiens. 9 samples. Type: Expression profiling by high throughput sequencing.
Non-occupational and occupational factors associated with specific SARS-CoV-2 antibodies among Hospital Workers – a multicentre cross-sectional study
<p>Variables and baseline data from this cross-sectional study. Manuscript currently available as preprint: https://medrxiv.org/cgi/content/short/2020.11.10.20229005v1.</p>
Dataset related to the article "Evidence of SARS-CoV-2 transcriptional activity in cardiomyocytes of COVID-19 patients without clinical signs of cardiac involvement"
<p>This record contains raw data related to the article "Evidence of SARS-CoV-2 transcriptional activity in cardiomyocytes of COVID-19 patients without clinical signs of cardiac involvement"</p> <p> </p> <p>Article abstract:</p> <p><strong>Abstract:</strong> <strong>Aims: </strong>A considerable proportion of patients affected by coronavirus respiratory disease (COVID-19) develop cardiac injury. The viral impact in cardiomyocytes deserves, however, further investigations, especially in asymptomatic patients. <strong>Methods: </strong>We investigated for SARS-CoV-2 presence and activity in heart tissues of 6 consecutive COVID-19 patients deceased for respiratory failure showing no signs of cardiac involvement and with no history of heart disease. Cardiac autopsy samples were collected within 2 hours after death, and then analysed by digital PCR, Western blot, immunohistochemistry, immunofluorescence, RNAScope, and transmission electron microscopy assays. <strong>Results</strong>: The presence of SARS-CoV-2 into cardiomyocytes was invariably detected in all assays. A variable pattern of cardiomyocytes injury was observed, spanning from absence of cell death and subcellular alterations hallmarks, to intracellular oedema and sarcomere ruptures. In addition, we found active viral transcription in cardiomyocytes, by detecting both sense and antisense SARS-CoV-2 spike RNA. <strong>Conclusions: </strong>In this autopsy cases analysis of patients with no clinical signs of cardiac involvement, the presence of SARS-CoV-2 into cardiomyocytes has been detected, determining variable patterns of intracellular damage. These findings suggest the need of a cardiologic surveillance in survived COVID-19 patients not displaying a cardiac phenotype<em>.</em></p>
Supplementary (MD): Repurposing Alzheimer's Therapeutics: A Computational Approach to Identifying Potential SARS-CoV-2 Mpro Inhibitors
<p>100 ns Molecular Dynamic Simulation Trajectories for Compound 2, 3, 6, 7, and 8 </p>
Bioinformática para el análisis de SARS-CoV-2 para principiantes: Módulo_2
Open the record for dataset details and reuse information.
Preliminary Evidence for IL-10-Induced ACE2 mRNA Expression in Lung-Derived and Endothelial Cells: Implications for SARS-Cov-2 ARDS Pathogenesis
<p>Angiotensin-converting enzyme 2 (ACE2) is a receptor for the spike protein of SARS-COV-2 that allows viral binding and entry and is expressed on the surface of several pulmonary and non-pulmonary cell types, with induction of a "cytokine storm" upon binding. Other cell types present the receptor and can be infected, including cardiac, renal, intestinal, and endothelial cells. High ACE2 levels protect from inflammation. Despite the relevance of ACE2 levels in COVID-19 pathogenesis, experimental studies to comprehensively address the question of ACE2 regulations are still limited. A relevant observation from the clinic is that, besides the pro-inflammatory cytokines, such as IL-6 and IL-1β, the anti-inflammatory cytokine IL-10 is also elevated in worse prognosis patients. This could represent somehow a "danger signal", an alarmin from the host organism, given the immuno-regulatory properties of the cytokine. Here, we investigated whether IL-10 could increase ACE2 expression in the lung-derived Calu-3 cell line. We provided preliminary evidence of ACE2 mRNA increase in cells of lung origin <em>in vitro</em>, following IL-10 treatment. Endothelial cell infection by SARS-COV-2 is associated with vasculitis, thromboembolism, and disseminated intravascular coagulation. We confirmed ACE2 expression enhancement by IL-10 treatment also on endothelial cells. The sartans (olmesartan and losartan) showed non-statistically significant ACE2 modulation in Calu-3 and endothelial cells, as compared to untreated control cells. We observed that the antidiabetic biguanide metformin, a putative anti-inflammatory agent, also upregulates ACE2 expression in Calu-3 and endothelial cells. We hypothesized that IL-10 could be a danger signal, and its elevation could possibly represent a feedback mechanism fighting inflammation. Although further confirmatory studies are required, inducing IL-10 upregulation could be clinically relevant in COVID-19-associated acute respiratory distress syndrome (ARDS) and vasculitis, by reinforcing ACE2 levels.</p>
Supplementary material for The divergent pattern of SARS-CoV-2 variant prevalence and transmission dynamics in the Brazilian island of Ilhabela
<p>The number of new cases per epidemiological week for each region, the VOC surveillance data and the GISAID ids from the genomes used in the phylogenetic analysis can be found in this Supplementary Material.</p>
SARS-CoV-2 virus seems to induce O-glycosylation and other metabolic dysfunctions which might predispose new-onset diabetes
<p>COVID-2019 pandemic has caused huge damage to human health, and some individuals are more prone to severe manifestations, such as type-2 diabetic patients. The correlation between diabetes and severe manifestations have been under investigation, and molecular findings may highlight some pathophysiological pathways. The present study aimed to identify plasma metabolites in patients affected by type-2 diabetes and COVID-19, concomitantly, using an untargeted metabolomic approach. We employed high-resolution mass spectrometry analysis to annotate 10 metabolites, with N-acetyl-D-glucosamine among them; it is involved with O-glycosylation, which is enhanced in diabetic conditions. SARS-CoV-2 Spike proteins depend on glycosylation, what seems to be overstimulated upon infection. Interestingly, N-acetyl-D-glucosamine was found in part of the non-diabetic COVID-19 patients, indicating that SARS-CoV-2 might induce new-onset diabetes through glycosylation. Besides, the identified biomarkers seem to be all interconnected and represent a global perception of metabolic alterations in a Diabetic-COVID-19 scenario, highlighting new targets for further pharmacological interventions.</p>
Data Deposit for "Ligation-based Assay for Variant-Typing without Sequencing: Application to SARS-CoV-2 Variants of Concern"
<p>No description provided.</p>
Comparison of two RNA extraction methods for the molecular detection of SARS-CoV-2 from nasopharyngeal swab samples
<p>The database includes the raw data of the article “Comparison of two RNA Extraction Methods for the Molecular Detection of SARS-CoV-2 from nasopharyngeal swab samples”.</p> <p>Aim of this work was to compare a two commercially available kit for viral RNA extraction from human swab samples that differ mainly for time consuming (9 min. vs 35 min.) in order to improve SARS-CoV-2 diagnostic workflow.</p> <p>The database contains the data obtained by the following evaluations:</p> <p>a) RNA analysis for the evaluation of quality and quantity by nanodrop instrument</p> <p>b) Real Time PCR analysis of SARS-CoV-2 genes and internal control.</p> <p>The two procedures evaluated gave similar analytical results in terms of extracted RNA analysis and Real Time PCR data for gene expression.</p>
Dissecting CD8+ T cell pathology of severe SARS-CoV-2 infection by single-cell immunoprofiling
<p>SARS-CoV-2 infection results in varying disease severity, ranging from asymptomatic infection to severe illness. A detailed understanding of the immune response to SARS-CoV-2 is critical to unravel the causative factors underlying differences in disease severity and to develop optimal vaccines against new SARS-CoV-2 variants. We combined single-cell RNA and T cell receptor sequencing with CITE-seq antibodies to characterize the CD8+ T cell response to SARS-CoV-2 infection at high resolution and compared responses between mild and severe COVID-19. We observed a population of exhausted CD8+ T cells in severe SARS-CoV-2 infection and identified a population of NK-like, terminally differentiated CD8+ effector T cells characterized by expression of FCGR3A (encoding CD16). Further characterization of NK-like CD8+ T cells revealed heterogeneity among CD16+ NK-like CD8+ T cells and profound differences in cytotoxicity, exhaustion, and NK-like differentiation between mild and severe disease conditions. We propose a model in which differences in the surrounding inflammatory milieu lead to crucial differences in NK-like differentiation of CD8+ effector T cells, ultimately resulting in the appearance of NK-like CD8+ T cell populations of different functionality and pathogenicity. Our in-depth characterization of the CD8+ T cell-mediated response to SARS-CoV-2 infection provides a basis for further investigation of the importance of NK-like CD8+ T cells in COVID-19 severity.</p>
Subjects who have developed SARS-CoV-2 specific IgM-S after vaccination show a longer humoral immunity and a lower frequency of infection
<p>We analysed anti-SARS-CoV-2 spike (S) protein (IgG-S), anti-nucleocapsid IgG (IgG-N) and anti-Spike IgM (IgM-S) in 1872 vaccinees at the first dose (D1; w0), after three weeks at the second dose (D2; w3) at three (w6) and 23 weeks (w29) after D2; 109 subjects where further tested at the booster dose (D3, w44), at three weeks (w47) and six months (w70) after D3. Two-level linear regression models were used to evaluate the differences in IgG-S levels.</p>
Dataset for "Analytical and clinical performances of seven direct detection assays for SARS-CoV-2"
<p>This dataset represent raw data for the unpublished article "Analytical and clinical performances of seven direct detection assays for SARS-CoV-2".</p>
Dataset related to article "Recognition and inhibition of SARS-CoV-2 by humoral innate immunity pattern recognition molecules"
<p>This record contains raw data related to article “Recognition and inhibition of SARS-CoV-2 by humoral innate immunity pattern recognition molecules"</p> <p>The humoral arm of innate immunity includes diverse molecules with antibody-like functions, some of which serve as disease severity biomarkers in coronavirus disease 2019 (COVID-19). The present study was designed to conduct a systematic investigation of the interaction of human humoral fluid-phase pattern recognition molecules (PRMs) with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Of 12 PRMs tested, the long pentraxin 3 (PTX3) and mannose-binding lectin (MBL) bound the viral nucleocapsid and spike proteins, respectively. MBL bound trimeric spike protein, including that of variants of concern (VoC), in a glycan-dependent manner and inhibited SARS-CoV-2 in three in vitro models. Moreover, after binding to spike protein, MBL activated the lectin pathway of complement activation. Based on retention of glycosylation sites and modeling, MBL was predicted to recognize the Omicron VoC. Genetic polymorphisms at the MBL2 locus were associated with disease severity. These results suggest that selected humoral fluid-phase PRMs can play an important role in resistance to, and pathogenesis of, COVID-19, a finding with translational implications.</p>
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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.