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Dataset results
264 results for “Single molecule”
Single molecule motility data of DYNEIN-DYNACTIN-HOOK3-KIF1C (DDHK) complexes plus various controls
<p>Single molecule motility data of DYNEIN-DYNACTIN-HOOK3-KIF1C (DDHK) complexes plus various controls leaving out components or using truncated motors without motor domains (KS - KIF1C stalk; Dt - Dynein tail).</p>
Dataset: Comparative analysis of the coordinated motion of Hsp70s from different organelles observed by single molecule three-color FRET
<p>Dataset: Comparative analysis of the coordinated motion of Hsp70s from different organelles observed by single molecule three-color FRET</p>
Raw data: The NEOtrap – en route with a new single-molecule technique
<p>NEOtrap raw data shown in:</p> <p>The NEOtrap – en route with a new single-molecule technique. Schmid, Dekker (2021) iScience.</p> <p>Incl. bead trapping and ClpP trapping as specified.</p>
Single molecule tracking videos: SOX18 and its dominant-negative mutant SOX18RaOp
<p>Few genetically dominant mutations involved in human disease have been fully explained at the molecular level. In cases where the mutant gene encodes a transcription factor, the dominant-negative mode of action of the mutant protein is particularly poorly understood. Here, we studied the genome-wide mechanism underlying a dominant-negative form of the SOX18 transcription factor (SOX18<sup>RaOp</sup>) responsible for both the classical mouse mutant <u>Ra</u>gged <u>Op</u>ossum and the human genetic disorder Hypotrichosis-Lymphedema-Telangiectasia-Renal Syndrome. Combining three single-molecule imaging assays in living cells together with genomics and proteomics analysis, we found that SOX18<sup>RaOp</sup> disrupts the system through an accumulation of molecular interferences which impair several functional properties of the wild-type SOX18 protein, including its target gene selection process. The dominant-negative effect is further amplified by poisoning the interactome of its wild-type counterpart, which perturbs regulatory nodes such as SOX7 and MEF2C. Our findings explain in unprecedented detail the multi-layered process that underpins the molecular aetiology of dominant-negative transcription factor function.</p>
Single-molecule junction spontaneously restored by DNA zipper
<p>Date set for "Single-molecule junction spontaneously restored by DNA zipper" published in Nature Commun, DOI : 10.1038/s41467-021-25943-3.</p>
Observation of robust energy transfer in the photosynthetic protein allophycocyanin using single-molecule pump-probe spectroscopy - single-molecule photon stream
<p>Photon stream used in the article "<em>Observation of robust energy transfer in the photosynthetic protein allophycocyanin using single-molecule pump-probe spectroscopy" </em> to analyze single-molecule fluorescence emission. Detected emission for single-molecule pump-probe experiments with an associated instrument response function (IRF) and background fluoresence (BG). Each detected photon is described by its time within the collected photon stream and its time relative to the excitation laser. Data is organized by sample and by date. Also included is an .xlsx document with fitted timescales for all included molecules and Matalb structure titled 'FinalDataAndStatistics.mat', which includes the final data, and statistics for the data used within the paper.</p>
Force-tuned Avidity of Spike Variant-ACE2 Interactions viewed on the Single-Molecule Level - MD simulations Dataset
<p>Models of SARS-CoV-2 virus spike protein bound to 1-3 of ACE2 receptors embedded in lipid nanodisks. Systems include all files in GROMACS format needed to reproduce simulations performed in the "Force-tuned Avidity of Spike Variant-ACE2 Interactions viewed on the Single-Molecule Level" article.</p> <p> </p> <table> <caption>Details</caption> <thead> <tr> <th scope="col">system</th> <th scope="col">box size (x-y-z) [nm]</th> <th scope="col">Number of atoms</th> </tr> </thead> <tbody> <tr> <td>Spike +<br> 1x ACE2, full length</td> <td>33.44834 28.96711 57.95573</td> <td>5,665,217</td> </tr> <tr> <td>Spike +<br> 1x ACE2, truncated</td> <td>28.05757 24.29856 46.74417</td> <td>3,203,907</td> </tr> <tr> <td>Spike +<br> 2x ACE2, truncated</td> <td>28.30864 21.23141 48.40873</td> <td>2,936,398</td> </tr> <tr> <td>Spike +<br> 3x ACE2, truncated</td> <td>28.32733 21.24544 48.30436</td> <td>2,936,588</td> </tr> </tbody> </table>
Mechanism of receptor assembly via the pleiotropic adipokine Leptin - single molecule tracking - raw data
<p>This dataset contains the raw single-molecule image data that was analyzed in the manuscript "Mechanism of receptor assembly via the pleiotropic adipokine Leptin"</p>
Data deposition for "Reliability and accuracy of single-molecule FRET studies for characterization of structural dynamics and distances in proteins"
<p>The deposited data for the publication "Reliability and accuracy of single-molecule FRET studies for characterization of structural dynamics and distances in proteins".</p> <p>Data contains folder and sub-folders for the raw data, Main excel sheet named as "MasterTable_FRET-Challenge-Protein-Dynamics_Nat_Meth_Agam et al" has most of the data used in the publication. Another excel sheets "Data List for FIgures for Agam et al_revised" and "Data List for Supplmentary FIgures for Agam et al_revised" have the information regarding the Figure-wise data description and where the respective data locates.</p>
Fibertools: fast and accurate m6A calling using single-molecule long-read sequencing (ML data)
<p>Fibertools is a convolutional neural network that permits the fast and accurate identification of endogenous and exogenous N6-methyladenine (m6A)-marked bases using single-molecule long-read sequencing.<strong> </strong>This dataset (ML data) provides training and validation data for training fibertools supervised and semi-supervised CNN models for three long-read chemistries.</p>
Spatial Mapping and Host Linking of Mobile Genetic Elements in Complex Microbiomes - Optimization of single molecule MGE FISH
<p>We used <em>Escherichia coli </em>transformed with pJKR-H-tetR plasmids encoding an inducible <em>GFP</em> gene as a model system to assess and optimize MGE-FISH on a confocal microscope. We designed FISH probes for the non-coding strand of the <em>GFP</em> gene, used non-transformed <em>E. coli </em>as a negative control, and tested six different FISH protocols.<strong> </strong></p>
Label-free adaptive optics single-molecule localization microscopy for whole zebrafish
<p>The specimen-induced aberration has been a major factor limiting the imaging depth of single-molecule localization microscopy (SMLM). Here, we report the application of label-free wavefront sensing adaptive optics to SMLM for deep-tissue super-resolution imaging. The proposed system measures complex tissue aberrations from intrinsic reflectance rather than fluorescence emission and physically corrects the wavefront distortion more than three-fold stronger than the previous limit. This enables us to resolve sub-diffraction morphologies of cilia and oligodendrocytes in whole zebrafish as well as dendritic spines in thick mouse brain tissues at the depth of up to 102 μm with localization number enhancement by up to 37 times and localization precision comparable to aberration-free samples. The proposed approach can expand the application range of SMLM to whole zebrafish that cause the loss of localization points owing to severe tissue aberrations.</p>
High-temperature magnetic blocking in a monometallic dysprosium azafullerene single-molecule magnet
<p>Single-molecule magnets (SMMs) showing magnetic blocking near or above liquid nitrogen temperature have recently been achieved by inducing exceptionally strong and axial crystal fields via double decker ligands. However, further enhancing the performance at higher temperatures becomes a formidable task. Here we provide an alternative strategy to advance towards this goal by entrapping a single dysprosium(III) ion within a nitrogen-substituted carbon cage. In this structure of Dy@C<sub>81</sub>N, Dy<sup>III</sup> is asymmetrically coordinated by one side to a hexagonal carbon ring of the azafullerene, while lacking any coordination ligand on the other side. Despite the very weak crystal field resulting from this very unusual low-coordination environment, this compound exhibits a high blocking temperature (<em>T</em><sub>B</sub>, defined as <em>T</em>(t<sub>100s</sub>)) of 45 K. Its extraordinary magnetic behavior is attributed to the minimal number of vibrations that couple to its spin states, being also responsible for the unusual slow Raman relaxation mechanism observed at high temperatures.</p>
Pacbio single molecule sequencing
<p>As a leading genomics company, CD Genomics provides next-generation sequencing and bioinformatics services to pharmaceutical and biotech companies, as well as academic and government agencies around the world, relying on advanced sequencing instruments and rich project experience. We are offering long-read sequencing services from PacBio and Oxford Nanopore, giving researchers a wide range of cutting-edge sequencing services to suit the particular needs of any project. Here, we offer long-read sequencing services which are based on <a href="https://longseq.cd-genomics.com/pacbio-smrt-sequencing-technology.html">PacBio single molecule sequencing</a> technology, the Sequel II System. This technology can produce highly accurate (> 99.9% average concordance accuracy) long sequences up to 30 kb long, helping to identify biologically important structural variants, RNA splice site isoforms of cDNA, and provide insights into hard-to-sequence regions of the genome, among others.</p>
Single-molecule and bulk fluorescence and biolayer interferometry on the NAD-II riboswitch and its interactions with NMN
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Single molecule tracking videos: SOX18 and its dominant-negative mutant SOX18RaOp
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Single-molecule analysis of the entire perfringolysin O pore formation pathway
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Single molecule image sequences of Thermothielavioides terrestris AA9E (TtAA9E) on cellulose in oxygen scavenging systems
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Single-molecule localization microscopy reveals the molecular organization of endogenous membrane receptors
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Reference genes for quantitative Arabidopsis single molecule RNA fluorescence in situ hybridization
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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.