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264 results for “Single molecule”
Dataset supporting the paper "Doublet-Singlet-Doublet Transition in a Single Organic Molecule Magnet On-Surface Constructed with up to 3 Aluminum Atoms. Nano Letters 21, 8317 (2021)"
<p>Dataset corresponding to theoretical calculations in the paper "Doublet-Singlet-Doublet Transition in a Single Organic Molecule Magnet On-Surface Constructed with up to 3 Aluminum Atoms" Nano Letters 21, 8317 (2021), <a href="https://doi.org/10.1021/acs.nanolett.1c02881">https://doi.org/10.1021/acs.nanolett.1c02881</a></p> <p>List of files:</p> <p>Several folders corresponding to the figures of the paper. They contain:</p> <ul> <li>.siesta files: STM images in WsXM format (http://www.wsxm.eu/) simulated using STMpw (<a href="https://doi.org/10.5281/zenodo.3581159">https://doi.org/10.5281/zenodo.3581159</a>).</li> <li>CONTCAR and POSCAR files: relaxed structures in VASP format. They can be visualized with VESTA (<a href="https://jp-minerals.org/vesta/en/">https://jp-minerals.org/vesta/en/</a>).</li> <li>.agr: grace files (<a href="https://plasma-gate.weizmann.ac.il/Grace/">https://plasma-gate.weizmann.ac.il/Grace/</a>).<br> </li> </ul>
Datasets for "Single-molecule and super-resolved imaging deciphers membrane behaviour of onco-immunogenic CCR5"
<p><strong>Flow cytometry</strong></p> <p>Modality / instrument: <em>Flow cytometer</em> <em>(CytoFLEX LX, Beckman Coulter)</em></p> <p>File format:<em> FCS + XIT (CytExpert, Beckman Coulter).</em></p> <p>Samples and acquisitions:</p> <p>Fluorescent fusions in live Chinese Hamster ovary (CHO) cells.</p> <table> <tbody> <tr> <td> <p><em>File</em></p> </td> <td> <p><em>Cell line</em></p> </td> <td> <p><em>Runs</em></p> </td> <td> <p><em>Cells counted</em></p> </td> </tr> <tr> <td> <p>CONTROL.fcs</p> </td> <td> <p>CHO wild-type</p> </td> <td> <p>1</p> </td> <td> <p>7000</p> </td> </tr> <tr> <td> <p>GFP-CCR5.fcs</p> </td> <td> <p>CHO-GFP-CCR5</p> </td> <td> <p>1</p> </td> <td> <p>7000</p> </td> </tr> <tr> <td> <p>Exp_20220916_1_GFP.xit</p> </td> <td> <p>N/A - metadata</p> </td> </tr> </tbody> </table> <p>Approx. size 6 MB</p> <p> </p> <p><strong>PaTCH microscopy images</strong></p> <p>Imaging modality / instrument: <em>Brightfield</em> + <em>PaTCH fluorescence microscopy</em></p> <p>Image format:<em> OME TIFF (16 bit) + MicroManager metadata files</em></p> <p>Microscope settings:</p> <p><em>488 nm triggered excitation; split red/green detection, cropped to green (GFP) channel only; 10 ms/frame laser exposure; 13.5 ms/frame-to-frame; 53 nm/px. Photometrics Prime95b CMOS.</em></p> <p>Samples and acquisitions:</p> <p>Fluorescent fusions of GFP-CCR5 receptor in live CHO cells imaged with and without 100 nM CCL5 ligand. Each subfolder corresponds to a field of view and contains one brightfield and one PaTCH acquisition of the same cell.</p> <table> <tbody> <tr> <td> <p>Folder</p> </td> <td> <p>Condition</p> </td> <td> <p>Fields of view</p> </td> </tr> <tr> <td> <p>AC6 CONTROL sc</p> </td> <td> <p>CCL5-</p> </td> <td> <p>11</p> </td> </tr> <tr> <td> <p>AC6 CCL5 sc</p> </td> <td> <p>CCL5+ (100 nM)</p> </td> <td> <p>10</p> </td> </tr> </tbody> </table> <p>Approx. size before compression: 14 GB</p> <p> </p> <p><strong>Structured illumination microscopy - volumetric stacks</strong></p> <p>Imaging modality / instrument: <em>SIM fluorescence microscopy (custom setup at NPL based on Olympus IX71)</em></p> <p>Image format:<em> OME TIFF (16 bit) with intrinsic metadata (voxel size)</em></p> <p>Microscope settings: <em>638 nm excitation; 60x/1.3 NA; Flash 4.0, Hamamatsu Photonics. For additional details see the reference below (Hunter et al, bioRxiv).</em></p> <p>Samples and acquisitions:</p> <p>Dylight 650-MC-5 labeled CCR5 receptor in fixed CHO-CCR5 cells, imaged with and without 100 nM CCL5 ligand. Each acquisition is of a unique field of view and contains one SIM reconstruction as an XYZ volumetric stack. ‘Basal membrane’ acquisitions consist of 5 slices at 200 nm z-intervals across the range of the basal membrane. ‘Whole cell' acquisitions are made up of 7 slices with 500 nm z-interval ranging from just below the basal membrane to just above the apical membrane. </p> <table> <tbody> <tr> <td>Folder</td> <td>Subfolder/condition</td> <td>Fields of view</td> </tr> <tr> <td>Basal membrane</td> <td>CCL5-</td> <td>5</td> </tr> <tr> <td>Basal membrane</td> <td>CCL5+ (100 nM)</td> <td>6</td> </tr> <tr> <td>Whole cells</td> <td>CCL5-</td> <td>5</td> </tr> <tr> <td>Whole cells</td> <td>CCL5+ (100 nM)</td> <td>8</td> </tr> </tbody> </table> <p>Approx. size before compression: 300 MB</p>
Single-molecule DNA methylation patterns of full-length human-specific LINE-1 (L1HS) retrotransposons in a panel of cell lines.
<p>We used bs-ATLAS-seq to comprehensively map the genomic location and assess the DNA methylation status of full-length human-specific LINE-1 elements (L1HS). The approach capture region 1-210 of L1HS elements, which corresponds to the most 5' end of its promoter sequence. This was performed in a panel of 12 human primary or transformed cell lines (BJ, IMR90, MRC5, H1, K562, HCT116, HeLa S3, HepG2, MCF7, HEK-293, HEK-293T, 2102Ep), many being shared with the encode project.</p> <p>These datasets provide a visualization for DNA methylation patterns at the single molecule level for each L1HS loci.</p>
Super-Resolved FRET Imaging by Confocal Fluorescence-Lifetime Single-Molecule Localization Microscopy
<p>FRET-based methods are a special tool for detecting interactions between (bio)molecules and their immediate environment. The spatial distribution of molecular interactions and functional states can be seen using FLIM (Fluorescence Lifetime IMaging) and FRET imaging. The spatial information, accuracy, and dynamic range of the observed signals are, however, constrained by the fact that conventional FLIM and FRET imaging only provides average information over an ensemble of molecules within a diffraction-limited volume. On the other hand, conventional Single Molecule Localization Microscopy (SMLM) relies on highly sensitive multi-pixel detectors (e.g. sCMOS or EM-CCD) whose time resolution is not suitable for fluorescence lifetime measurements.</p> <p>Here, we demonstrate a method for obtaining super-resolved FRET imaging using confocal fluorescence-lifetime single-molecule localization microscopy. The proof of concept was carried out using a DNA origami sample for performing DNA-PAINT measurements in combination with fluorogenic probes for reducing background signal. With this method, We show that FRET events separated by sub-diffraction distances can be distinguished based on lifetime modifications.</p>
Single molecule nanotribology: understanding friction and adhesion at a single molecule level
<p>Data presented in the annual conference SAOG2019 (Surface Science and Thin Films Community of Switzerland 2019). </p> <p>Here we discuss the effect of molecular vibrations on its friction properties. This is intended to provide an overview of the results published in the following peer-reviewed freely available papers:<br> Nature Communications 10, 685 (2019). [DOI:10.1038/s41467-019-08531-4 ]<br> Nano Lett. 20, 652 (2020). [DOI: 10.1021/acs.nanolett.9b04418]<br> (Please cite them, if you found this information useful.)</p> <p> </p>
Addressable Nanoantennas with Cleared Hotspots for Single-Molecule Detection on a Portable Smartphone Microscope
<p>The advent of highly sensitive photodetectors and the development of photostabilization strategies made detecting the fluorescence of single molecules a routine task in many labs around the world. However, to this day, this process requires cost-intensive optical instruments due to the truly nanoscopic signal of a single emitter. Simplifying single-molecule detection would enable many exciting applications, <em>e.g.</em> in point-of-care diagnostic settings, where costly equipment would be prohibitive. Here, we introduce addressable NanoAntennas with Cleared HOtSpots (NACHOS) that are scaffolded by DNA origami nanostructures and can be specifically tailored for the incorporation of bioassays. Single emitters placed in the NACHOS emit up to 461-fold (average of 89±7-fold) brighter enabling their detection with a customary smartphone camera and an 8-US-dollar objective lens. To prove the applicability of our system, we built a portable, battery-powered smartphone microscope and successfully carried out an exemplary single-molecule detection assay for DNA specific to antibiotic-resistant <em>Klebsiella pneumonia</em> „on the road “. Here we demonstrate the raw data on which our findings based on.</p>
Widespread Polycistronic Transcripts in Fungi Revealed by Single-Molecule mRNA Sequencing
<p>Genes in prokaryotic genomes are often arranged into clusters and co-transcribed into poly- cistronic RNAs. Isolated examples of polycistronic RNAs were also reported in some higher eukaryotes but their presence was generally considered rare. Here we developed a long- read sequencing strategy to identify polycistronic transcripts in several mushroom forming fungal species including Plicaturopsis crispa, Phanerochaete chrysosporium, Trametes ver- sicolor, and Gloeophyllum trabeum. We found genome-wide prevalence of polycistronic transcription in these Agaricomycetes, involving up to 8% of the transcribed genes. Unlike polycistronic mRNAs in prokaryotes, these co-transcribed genes are also independently transcribed. We show that polycistronic transcription may interfere with expression of the downstream tandem gene. Further comparative genomic analysis indicates that polycis- tronic transcription is conserved among a wide range of mushroom forming fungi. In sum- mary, our study revealed, for the first time, the genome prevalence of polycistronic transcription in a phylogenetic range of higher fungi. Furthermore, we systematically show that our long-read sequencing approach and combined bioinformatics pipeline is a generic powerful tool for precise characterization of complex transcriptomes that enables identifica- tion of mRNA isoforms not recovered via short-read assembly.</p>
Data and code for "Tweezepy: A Python package for calibrating forces in single-molecule video-tracking instruments"
<p>Data and code for "Tweezepy: A Python package for calibrating forces in single-molecule video-tracking instruments."</p> <p>Data includes representative real and simulated bead trajectories used in the manuscript.</p> <p>Code includes all simulations, analysis, and plot details for the Figures in the manuscript. </p> <p>See included README.txt for more details.</p>
Single molecule videos related to "MCM complexes are barriers that restrict cohesin-mediated loop extrusion" Part 2/3
<p>Videos of cohesin translocation and collisions between translocating cohesin and MCMs under physiological salt conditions collected with MicroManager 1.4 as tif image sequences. Vidoes of DNA stained with SYTOX Orange after collection of cohesin translocation are included as separate image sequences.</p>
Single molecule videos related to "MCM complexes are barriers that restrict cohesin-mediated loop extrusion" Part 1/3
<p>Videos of collisions between translocating cohesin and MCMs under high salt conditions collected with MicroManager 1.4 as tif image sequences. Vidoes of DNA stained with SYTOX Orange after collection of cohesin translocation are included as separate image sequences.</p>
Single molecule videos related to "MCM complexes are barriers that restrict cohesin-mediated loop extrusion" Part 3/3
<p>Videos of collisions between translocating cohesin and MCM containing the YDF motif under physiological salt conditions collected with MicroManager 1.4 as tif image sequences. Videos of DNA stained with SYTOX Orange after collection of cohesin translocation are included as separate image sequences.</p>
Dynamic FRET example videos related to "Mars, a molecule archive suite for reproducible analysis and reporting of single-molecule properties from bioimages"
<p>Videos of dynamic switching between iso-I and iso-II conformations of a holiday junction at 50 mM Magnesium resulting in high and low FRET from Cy3 and Alexa647 labels positioned on the arms. Holiday junctions are surface immobilized through a biotin attachment and imaged using TIRF microscopy. The camera sensor is split using a dual view so that the acceptor emission is on the top and the donor emission is on the bottom. Videos from each position are provided as compressed zip files containing a sequence of tif files and associated metadata text file. Image sequences were collected using Micro-Manager 2.0 using ALEX or alternating laser excitation with alternating 637 and 532 pulses separated as two different channels. Beam profile images are provided for 637 and 532 excitation allowing for correction of the non-uniform beam profiles. The following 2D affine transformation matrix can be used to transform from the top acceptor emission region to the bottom donor emission region during processing.</p> <p>Affine 2D transformation from top to bottom: (m00, m01, m02, m10, m11, m12), (1.00276, 0.000208, 1.01236, 0.000267, 1.00312, 507.21025)</p> <p>A detailed image processing workflow for this dataset using Mars can be found under the example section at <a href="https://duderstadt-lab.github.io/mars-docs/">https://duderstadt-lab.github.io/mars-docs/</a> or directly at <a href="https://duderstadt-lab.github.io/mars-docs/examples/FRET_dynamic/">https://duderstadt-lab.github.io/mars-docs/examples/FRET_dynamic/</a></p>
Single molecule dataset for article: Multistep orthophosphate release tunes actomyosin energy transduction
<table> <tbody> <tr> <td> <p>Dataset (single molecule movies) that is behind the results in the article's Figure 2 and Figure 3.</p> <p>MATLAB scripts used to analyze the dataset. </p> </td> </tr> </tbody> </table> <p> </p>
Single-molecule FRET reveals multiscale chromatin dynamics modulated by HP1α-Fig. 2def
<p>smTIRF-FRET Data for Fig 2, for "Single-molecule FRET reveals multiscale chromatin dynamics modulated by HP1α"</p>
Single-molecule FRET reveals multiscale chromatin dynamics modulated by HP1α-Fig. 7cde
<p>smTIRF-FRET Data for Fig 7, for "Single-molecule FRET reveals multiscale chromatin dynamics modulated by HP1α"</p>
Dataset supporting the paper "Bipolar single-molecule electroluminescence and electrofluorochromism. Physical Review Research 5, 033027 (2023)"
<p>Dataset corresponding to theoretical calculations in the paper "Bipolar single-molecule electroluminescence and electrofluorochromism. Physical Review Research 5, 033027 (2023)" DOI: https://doi.org/10.1103/PhysRevResearch.5.033027</p> <p>Please cite as:</p> <p>Tzu-Chao Hung, Roberto Robles, Brian Kiraly, Julian H. Strik, Bram A. Rutten, Alexander A. Khajetoorians, Nicolas Lorente and Daniel Wegner. Dataset supporting the paper "Bipolar single-molecule electroluminescence and electrofluorochromism. Physical Review Research 5, 033027 (2023)" DOI:10.5281/zenodo.13768737</p> <p>List of files:</p> <p>Several folders corresponding to the figures of the paper. They contain:</p> <p>CONTCAR files: relaxed structures in VASP format. They can be visualized with VESTA (https://jp-minerals.org/vesta/en/).</p> <p>.agr: grace files (https://plasma-gate.weizmann.ac.il/Grace/).</p> <p>Image files in png format.</p>
Dataset supporting the paper "Single-Spin Sensing: A Molecule-on-Tip Approach. ACS Nano 18, 13829 (2024)"
<p>Dataset corresponding to theoretical calculations in the paper "Single-Spin Sensing: A Molecule-on-Tip Approach" ACS Nano 18, 13829 (2024) DOI: https://doi.org/10.1021/acsnano.4c02470</p> <p>Please cite as:</p> <p>Alex Fétida, Olivier Bengone, Michelangelo Romeo, Fabrice Scheurer, Roberto Robles, Nicolás Lorente, and Laurent Limot. Dataset supporting the paper "Single-Spin Sensing: A Molecule-on-Tip Approach. ACS Nano 18, 13829 (2024)" DOI: 10.5281/zenodo.13774118</p> <p>List of files:</p> <p>Several folders corresponding to the figures of the paper. They contain:</p> <p>CONTCAR files: relaxed structures in VASP format. They can be visualized with VESTA (https://jp-minerals.org/vesta/en/).</p> <p>.agr: grace files (https://plasma-gate.weizmann.ac.il/Grace/).</p> <p>Image files in png format.</p>
Ha-SingleMoleculeLab's data for publication: Linking folding dynamics and function of SAM/SAH riboswitches at the single molecule level
<p>This upload is the raw data that support our findings sent to review on Nucleic Acids Research, corresponding to each individual figure. The paper title is " Linking folding dynamics and function of SAM/SAH riboswitches at the single molecule level".</p>
A survey of the sorghum transcriptome using single-molecule long reads
<p>Alternative splicing and alternative polyadenylation (APA) of pre-mRNAs greatly contribute to transcriptome diversity, coding capacity of a genome and gene regulatory mechanisms in eukaryotes. Second-generation sequencing technologies have been extensively used to analyze transcriptomes. However, a major limitation of short-read data is that it is difficult to accurately predict full-length splice isoforms. Here we sequenced the sorghum transcriptome using Pacific Biosciences single molecule real time long-read isoform sequencing and developed a pipeline called TAPIS (Transcriptome Analysis Pipeline for Isoform Sequencing) to identify full-length splice isoforms and APA sites. Our analysis reveals transcriptome-wide full-length isoforms at an unprecedented scale with over 11,000 novel splice isoforms. Additionally, we uncover APA of ~11,000 expressed genes and more than 2,100 novel genes. These results greatly enhance sorghum gene annotations and aid in studying gene regulation in this important bioenergy crop. The TAPIS pipeline will serve as a useful tool to analyze Iso-Seq data from any organism.</p>
Single molecule experimental data for intensity histograms in Gilburt et al, Angewandte 2017
<p>Raw and partially processed single molecule intensity histogram data for the following publication:</p> <p>James A H Gilburt, Hajrah Sarkar, Peter Sheldrake, Julian Blagg, Liming Ying, Charlotte A Dodson (2017) Dynamic equilibrium of the Aurora-A kinase activation loop revealed by single molecule spectroscopy. <em>Angewandte Chemie</em></p> <p><strong><em>Please cite our publication in any use of this data.</em></strong></p>
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.