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175
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ShareScore release 0.9.0
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175 results for “Single-molecule”
Thermal Transport through Single-Molecule Junctions - data
<p>Raw data as displayed in the figures of the paper "Thermal Transport through Single-Molecule Junctions", Nanoletters (2019), <a href="https://doi.org/10.1021/acs.nanolett.9b02089">https://doi.org/10.1021/acs.nanolett.9b02089</a></p>
Data for Single-molecule Detection of Modified Amino Acid Regulating Transcriptional Activity
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Data from: Next-generation polyploid phylogenetics: rapid resolution of hybrid polyploid complexes using PacBio single-molecule sequencing
Difficulties in generating nuclear data for polyploids have impeded phylogenetic study of these groups. We describe a high-throughput protocol and an associated bioinformatics pipeline (PURC: "Pipeline for Untangling Reticulate Complexes") that is able to generate these data quickly and conveniently, and demonstrate its efficacy on accessions from the fern family Cystopteridaceae. We conclude with a demonstration of the downstream utility of these data by inferring a multilabeled species tree for a subset of our accessions. We amplified four ~1kb-long nuclear loci and sequenced them in a parallel-tagged amplicon sequencing approach using the PacBio platform. PURC infers the final sequences from the raw reads via an iterative approach that corrects PCR and sequencing errors and removes PCR-mediated recombinant sequences (chimeras). We generated data for all gene copies (homeologs, paralogs, and segregating alleles) present in each of three sets of 50 mostly-polyploid accessions, for four loci, in three PacBio runs (one run per set). From the raw sequencing reads PURC was able to accurately infer the underlying sequences. This approach makes it easy and economical to study the phylogenetics of polyploids, and in conjunction with recent analytical advances, facilitates investigation of broad patterns of polyploid evolution.
Enabling single-molecule localization microscopy in turbid food emulsions
<p>Supplementary and raw data</p>
A Cost-Effective Semi-Ab Initio Approach to Model Relaxation in Rare-Earth Single-Molecule Magnets. Open data set
<p>Data supporting the original figures 2 and 3 of the related publication.</p>
Rotary catalysis of bovine mitochondrial F1-ATPase studied by single-molecule experiments
<p><span>The reaction scheme of rotary catalysis and the torque generation mechanism of bovine mitochondrial F<sub>1</sub> (<i>b</i>MF<sub>1</sub>) were studied in single-molecule experiments. Under ATP-saturated concentrations, high-speed imaging of single 40 nm gold bead attached to the γ subunit of <i>b</i>MF<sub>1</sub> showed two types of intervening pauses during the rotation that were discriminated by <i>short</i> <i>dwell</i> and <i>long dwell</i>. <span>Using ATP</span><span>g</span><span>S as a slowly hydrolyzing ATP derivative as well as using a functional mutant </span><span>b</span><span>E188D with slowed ATP hydrolysis, the two pausing events were distinctively identified. </span>Buffer-exchange experiment with a non-hydrolyzable analog (AMP-PNP) revealed that the <i>long</i><i> dwell</i> corresponds to the catalytic dwell, i.e. the waiting state for hydrolysis, while it remains elusive which catalytic state <i>short pause</i> represents. The angular position of <i>catalytic dwell</i> was determined to be at +80° from <i>ATP-binding angle</i>, mostly consistent with other F<sub>1</sub>s. The position of <i>short dwell </i>was found at 50-60° from <i>catalytic dwell</i>, <i>i.e.</i> +10-20° from <i>ATP-binding angle</i>. This is a distinct difference from human mitochondrial F<sub>1</sub> (<i>h</i>MF<sub>1</sub>) that also shows the intervening dwell that probably corresponding to <i>short dwell</i> of <i>b</i>MF<sub>1</sub>, at +65° from <i>binding pause</i>. Furthermore, we conducted 'stall-and-release' experiments with magnetic tweezers to reveal how the binding affinity and hydrolysis equilibrium are modulated by the g rotation. Similar to thermophilic F<sub>1</sub>, <i>b</i>MF<sub>1</sub> showed a strong exponential increase in ATP affinity while the hydrolysis equilibrium did not change significantly. This indicates that the ATP binding process generates larger torque than hydrolysis process. </span></p>
single-molecule tertiary structure determination reveals RNA folding landscape
<p>Initial release of the 6HB RNA origami 3D density maps, fitting models and EMDB validation reports.</p>
Iterative Machine Learning for Classification and Discovery of Single-molecule Unfolding Trajectories from Force Spectroscopy Data (Raw Data)
<p>Raw data used for the testing of the FUSION Learning algorithm available at <a href="https://github.com/Nash-Lab/Fusion-Learning">https://github.com/Nash-Lab/Fusion-Learning</a>.</p> <p> </p> <ol> </ol>
Single-Molecule Image Sequences of Trichoderma reesei Cel7A and Variants on Cellulose Fibrils
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Data from: Single-molecule RNA detection at depth by hybridization chain reaction and tissue hydrogel embedding and clearing
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Data from: Single-molecule imaging and quantification of the immune-variant adhesin VAR2CSA on knobs of Plasmodium falciparum-infected erythrocytes
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Raw data associated with the article: "Single-molecule DNA sequencing of widely varying GC-content using nucleotide release, capture and detection in microdroplets.", NAR, Puchtler et.al.
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Data from: Next-generation polyploid phylogenetics: rapid resolution of hybrid polyploid complexes using PacBio single-molecule sequencing
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Single-molecule microscopy (SiM-KARTS) and chemical probing (SHAPE) of lncRNA
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Rotary catalysis of bovine mitochondrial F1-ATPase studied by single-molecule experiments
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Data from: Direct sequencing of haplotypes from diploid individuals through a modified emulsion PCR-based single-molecule sequencing approach
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Comparative analysis between single-cell RNA-seq and single-molecule RNA FISH indicates that the pyrimidine nucleobase idoxuridine (IdU) globally amplifies transcriptional noise
GEO Series GSE263194. Homo sapiens. 4 samples. Type: Expression profiling by high throughput sequencing.
A framework to validate fluorescently labeled DNA-binding proteins for single-molecule experiments
GEO Series GSE212751. Bacillus subtilis PY79. 8 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
A subcellular map of translational machinery composition and regulation at the single-molecule level [ALIBi_Nmd3_Gnl3_KD]
GEO Series GSE283892. Mus musculus. 17 samples. Type: Expression profiling by high throughput sequencing.
Single-molecule regulatory architectures captured by chromatin fiber sequencing [DNAseI-seq]
GEO Series GSE146939. Drosophila melanogaster. 1 samples. Type: Other.
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.