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ShareScore release 0.9.0
Dataset results
162 results for “Nucleic Acid”
Scalable acoustic virtual stirrer for enhanced interfacial enzymatic nucleic acid reactions
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NMR raw data for: DTX3L ubiquitin ligase ubiquitinates single-stranded nucleic acids
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Dataset for "Energy landscapes of deoxyxylo- and xylo-nucleic acid octamers"
<p>Dataset for "Energy landscapes of deoxyxylo- and xylo-nucleic acid octamers"</p> <p>contains:</p> <p>- database for PATHSAMPLE for XyNA and dXyNA ds octamers</p> <p>- corresponding free energy databases</p> <p>- curves results for fastest right- to left-handed paths</p> <p>- library files</p> <p>- example structures (pdb and rst format)</p>
Supplemental data for Structural dynamics of therapeutic nucleic acids with phosphorothioate backbone modification, Carlesso et al.
<p>Description of the parameterization strategy for phosphorothioate-modified therapeutic nucleic acids, and files related to the system preparation, MD trajectories and analysis.</p>
Cotton-based nucleic acid extraction
<p><strong>Abstract</strong>: Nucleic acid amplification technique (NAAT)-assisted detection is the primary intervention for pathogen molecular diagnostics. However, NAATs such as quantitative real-time polymerase chain reaction (qPCR) require prior purification or extraction of target nucleic acid from the sample of interest since the latter often contains polymerase inhibitors. Similarly, genetic disease screening is also reliant on the successful extraction of pure patient genomic DNA from the clinical sample. However, such extraction techniques traditionally utilize spin-column techniques that in turn require centralized high-speed centrifuges. This hinders any potential deployment of qPCR- or PCR-like NAAT methods in resource-constrained settings. The development of instrument-free nucleic acid extraction methods, especially those utilizing readily available materials would be of great interest and benefit to NAAT-mediated molecular diagnosis workflows in resource-constrained settings. In this report, we screened medical-grade cotton, a readily available over-the-counter biomaterial to extract <em>E. coli</em> genomic DNA (gDNA) spiked in 30%, 45%, and 60% serum. The extraction was carried out in a completely instrument-free manner using cotton and a sterilized toothpick and was completed in 30 min (with using chaotropic salt) or 10 min (without using chaotropic salt). The quality of the extracted DNA was then probed using PCR followed by agarose gel analysis, qPCR, and sequencing. Our method demonstrated that the high-quality DNA extraction could be performed both with or without using a chaotropic salt, albeit with a difference in the quality of the extracted DNA</p>
input files for " Martini bead form factors for nucleic-acids and their application in the refinement of protein/nucleic-acid complexes against SAXS data".
<p>input files for " Martini bead form factors for nucleic-acids and their application in the refinement of protein/nucleic-acid complexes against SAXS data", cf plumed-nest</p>
ProtNAff: Protein-bound Nucleic Acid filters and fragment libraries
<p>This dataset contains the library produced by the ProtNAff tool for the paper.</p> <p>The files are in the numpy format matrix.</p> <p>There are files for the reduced and the all atoms fragments.</p>
Dataset to manuscript "Trans-cis isomerization kinetics of cyanine dyes reports on the folding states of exogeneous RNA G-quadruplexes in live cells" accepted for publication in Nucleic Acids Research
<p><strong>This folder contains all raw data underlying the results presented in a manuscript, accepted for publication in Nucleic Acids Research, and entitled:</strong></p> <p> </p> <p><strong><em>Trans</em></strong><strong>-<em>cis</em> isomerization kinetics of cyanine dyes reports on the folding states of exogeneous RNA G-quadruplexes in live cells </strong></p> <p> </p> <p><strong>Authored by:</strong></p> <p>Akira Kitamura<sup>2,*</sup>, Johan Tornmalm<sup>1,*</sup>, Baris Demirbay<sup>1</sup>, Joachim Piguet<sup>1</sup>, Masataka Kinjo<sup>2</sup>, Jerker Widengren<sup>1+</sup></p> <p> </p> <p><sup>1</sup> Experimental Biomolecular Physics, Department of Applied Physics, Royal Institute of Technology (KTH), Stockholm, Sweden</p> <p><sup>2</sup> Laboratory of Molecular Cell Dynamics, Faculty of Advanced Life Science, Hokkaido University, Sapporo, Japan</p> <p><sup>* </sup>Contributed equally</p> <p><sup>+</sup> To whom correspondence should be addressed. Email: jwideng@kth.se. Tel: +46-8-7907813</p> <p> </p> <p><strong>The data files are grouped into the different techniques used to generate them, and refer to the figures/tables in the manuscript where the extracted results are presented. </strong></p> <p> </p> <p><strong>ABSTRACT</strong></p> <p>Guanine (G)-rich nucleic acids are prone to assemble into four-stranded structures, so-called G-quadruplexes. Abnormal GGGGCC repeat elongations, and in particular their folding states, are associated with amyotrophic lateral sclerosis and frontotemporal dementia. Due to methodological constraints however, most studies of G quadruplex structures are restricted to <em>in vitro</em> conditions. Evidence of how GGGGCC repeats form into G-quadruplexes <em>in vivo</em> is sparse. We devised a readout strategy, exploiting the sensitivity of <em>trans</em>-<em>cis</em> isomerization of cyanine dyes to local viscosity and sterical constraints. Thereby, folding states of cyanine-labeled RNA, and in particular G-quadruplexes, can be identified in a sensitive manner. The isomerization kinetics, monitored via fluorescence blinking generated upon transitions between a fluorescent <em>trans</em> isomer and a non-fluorescent <em>cis</em> isomer, was first characterized for RNA with GGGGCC repeats in aqueous solution using fluorescence correlation spectroscopy and transient state (TRAST) monitoring. With TRAST, monitoring the isomerization kinetics from how the average fluorescence intensity varies with laser excitation modulation characteristics, we could then detect folding states of fluorescently tagged RNA introduced into live cells.</p>
Model files for "Modeling Protein-Nucleic Acid Complexes with Extremely Large Conformational Changes using Flex-LZerD"
<p>Models in PDB format generated for "Modeling Protein-Nucleic Acid Complexes with Extremely Large Conformational Changes using Flex-LZerD" by domain-based docking and flexible fitting. See summary Table 2.</p>
Case studies from doubleHelix: nucleic acid sequence identification, assignment and validation tool for cryo-EM and crystal structure models
<p>Case studies from "doubleHelix: nucleic acid sequence identification, assignment and validation tool for cryo-EM and crystal structure models"</p>
Activation of Therapeutic Nucleic Acids from a Mechanoresponsive Drug Carrier by Low-intensity Imaging Ultrasound
<p>Data sets used for main figures of the manuscript entitled 'Activation of Therapeutic Nucleic Acids from a Mechanoresponsive Drug Carrier by Low-intensity Imaging Ultrasound'.</p>
Stability of Nucleic Acid Bases in Concentrated Sulfuric Acid: Implications for the Habitability of Venus' Clouds
<p><strong>Supplementary datasets for the article accepted in PNAS entitled: </strong>Stability of Nucleic Acid Bases in Concentrated Sulfuric Acid: Implications for the Habitability of Venus’ Clouds.</p> <p>Dataset S1. Dataset S1 contains original UV-Vis data. </p> <p>The folder “UV-VIS_plots-data-code-tables DATASET S1.zip” contains the original UV-Vis data</p> <p>Dataset S2. Dataset S2 contains original NMR data. </p> <p>The folder “ORIGINAL NMR DATA_DATASET S2.zip” contains the original NMR data.<br> </p>
The appendix for evaluating the impact of large-scale nucleic acid testing and home quarantine on COVID-19 prevention and control: a dynamic modeling approach
<p><strong>Appendix I</strong>: The program of evaluating the impact of large-scale nucleic acid testing and home quarantine on COVID-19 prevention and control: a dynamic modeling approach</p> <p><strong>Appendix II</strong>: The sensitivity analysis of evaluating the impact of large-scale nucleic acid testing and home quarantine on COVID-19 prevention and control: a dynamic modeling approach</p>
The Dangers of Using Cq to Quantify Nucleic Acid in Biological Samples: A Lesson From COVID-19 - supplementary data
<p>Dataset in relation to </p> <p>Evans, Daniel, Cowen, Simon, Kammel, Martin, O'Sullivan, Denise M, Stewart, Graham, Grunert, Hans-Peter, Moran-Gilad, Jacob, Verwilt, Jasper, In, Jiwon, Vandesompele, Jo, Harris, Kathryn, Hong, Ki Ho, Storey, Nathaniel, Hingley-Wilson, Suzie, Dühring, Ulf, Bae, Young-Kyung, Foy, Carole A, Braybrook, Julian, Zeichhardt, Heinz, & Huggett, Jim F. (2021). The Dangers of Using Cq to Quantify Nucleic Acid in Biological Samples: A Lesson From COVID-19. Clinical Chemistry, 68(1), 153–162. https://doi.org/10.1093/clinchem/hvab219 </p>
A mechanoresponsive nucleic acid scaffold to control biological systems by biocompatible ultrasound
<p>Data sets used for main figures of the manuscript entitled 'A mechanoresponsive nucleic acid scaffold to control biological systems by biocompatible ultrasound'.</p>
Primary Organoid Models and Combined Nucleic Acids Therapeutics for Anti-HPV Treatments
ClinicalTrials.gov study NCT04278326. IPD Sharing: Not stated. Countries: 1. Publications: 5.
Micro Ribosomal Nucleic Acid 155 in Non Hodgkin Lymphoma
ClinicalTrials.gov study NCT03185325. IPD Sharing: NO. Countries: 1. Publications: 4.
Effect of Monosodium L-Glutamate (MSG) and Nucleic Acid (IMP) on Satiety and Food Intake
ClinicalTrials.gov study NCT01761045. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Ontario-wide Cancer TArgeted Nucleic Acid Evaluation
ClinicalTrials.gov study NCT02906943. IPD Sharing: YES. Countries: 1. Publications: 2.
Corona Virus Disease 2019 Patients Whose Nucleic Acids Changed From Negative to Positive
ClinicalTrials.gov study NCT04333589. IPD Sharing: Not stated. Countries: 1. Publications: 1.
ScienceDex guides
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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.