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108 results for “ion channel”
Data from: Positive selection on sperm ion channels in a brooding brittle star: consequence of life-history traits evolution
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Data from: A functionally conserved mechanism of modulation via a vestibule site in pentameric ligand-gated ion channels
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Ion channel open
Drawing uploaded to scidraw.io on: 12 March 2020
Ion channel
Drawing uploaded to scidraw.io on: 23 January 2020
Targeting the potassium ion channel genes SK and SH as a novel approach for control of insect pests: efficacy and biosafety
<p>Numerical data that underlies tables, graphs and statistics of the Pest Management Science article from Alshukri et al., 2019: "Targeting the potassium ion channel genes SK and SH as a novel approach for control of insect pests: efficacy and biosafety".</p>
Data from: Convergence of ion channel genome content in early animal evolution
Multicellularity has evolved multiple times, but animals are the only multicellular lineage with nervous systems. This fact implies that the origin of nervous systems was an unlikely event, yet recent comparisons among extant taxa suggest that animal nervous systems may have evolved multiple times independently. Here, we use ancestral gene content reconstruction to track the timing of gene family expansions for the major families of ion-channel proteins that drive nervous system function. We find that animals with nervous systems have broadly similar complements of ion-channel types but that these complements likely evolved independently. We also find that ion-channel gene family evolution has included large loss events, two of which were immediately followed by rounds of duplication. Ctenophores, cnidarians, and bilaterians underwent independent bouts of gene expansion in channel families involved in synaptic transmission and action potential shaping. We suggest that expansions of these family types may represent a genomic signature of expanding nervous system complexity. Ancestral nodes in which nervous systems are currently hypothesized to have originated did not experience large expansions, making it difficult to distinguish among competing hypotheses of nervous system origins and suggesting that the origin of nerves was not attended by an immediate burst of complexity. Rather, the evolution of nervous system complexity appears to resemble a slow fuse in stem animals followed by many independent bouts of gene gain and loss.
Computational Data for "A conserved peptide binding pocket in HyNaC/ASIC ion channels"
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Biophysical characterization of calcium-binding and modulatory-domain dynamics in a pentameric ligand-gated ion channel
<p><strong>Molecular dynamics simulations</strong></p> <p>Trajectories and related files.</p>
Novel role of TRPM4 ion channel in exocytosis
<p>Under physiological conditions, the widely expressed calcium-activated TRPM4 channel conducts sodium into the cell. This sodium influx depolarizes the plasma membrane and reduces the driving force for calcium entry. Aberrant expression or function of TRPM4 has been reported in various diseases, including different types of cancer. TRPM4 is localized mainly in the plasma membrane, but is also found in intracellular vesicles, which can undergo exocytosis. In this study, we show that calcium-induced exocytosis in the colorectal cancer cell line HCT116 is dependent on TRPM4. In addition, findings from prostate cancer cell lines point to a more general role for TRPM4 in calcium-induced exocytosis in cancer cells. Furthermore, calcium-induced exocytosis depends on TRPM4 ion conductivity. Additionally, an increase in intracellular calcium results in the delivery of TRPM4 to the plasma membrane. This process also depends on TRPM4 ion conductivity. TRPM4-dependent exocytosis and delivery of TRPM4 to the plasma membrane is mediated by SNARE proteins. Finally, we provide evidence that calcium-induced exocytosis depends on TRPM4 ion conductivity not within the plasma membrane, but rather in TRPM4-containing vesicles.</p>
Rhodopsin-bestrophin fusion proteins from unicellular algae form gigantic pentameric ion channels - additional data
<p>This repository stores additional data files for the article Rozenberg, Kaczmarczyk, Matzov, Vierock et al (2022) "<a href="https://doi.org/10.1038/s41594-022-00783-x">Rhodopsin-bestrophin fusion proteins from unicellular algae form gigantic pentameric ion channels</a>".</p> <p>The files included are as follows:</p> <ul> <li>Inputs.zip - all input files to <a href="https://github.com/BejaLab/RRB">the workflow</a> (also available there)</li> <li>Species phylogenies: <ul> <li>Chlorophyte_orthogroups.zip, Haptophyte_orthogroups.zip, Dinoflagellate_orthogroups.zip - zip files with the orthogroups used in species phylogeny. Each folder corresponds to an orthogroup (busco orthogroups for chlorophytes and dinoflagellate, proteinortho orthogroups for haptophytes): <ul> <li>mafft.faa - mafft alignment</li> <li>trimal.faa - trimal trimmed alignment</li> <li>iqtree.treefile and iqtree.log - iqtree tree and log file</li> <li>treeshrink.treefile - treeshrink pruned tree</li> </ul> </li> </ul> </li> <li>Structural_alignment.zip includes structural alignments of the bestrhodopsin's rhodopsin and bestrophin domains with reference sequences: <ul> <li>rhodopsins.aln and bestrophins.aln- raw alignments from t_coffee</li> <li>rhodopsins_modified.fasta and bestrophins_modified.fasta - curated alignments</li> <li>rhodopsins.gff and bestrophins.gff - secondary structure features for the sequences</li> </ul> </li> <li>Global phylogeny of bestrophins and rhodopsins: <ul> <li>Bestrophins_global_sequences.zip - sequence data for the bestrophin global phylogeny: <ul> <li>uniref50.txt - uniref50 tabular data matching bestrophins (Pfam PF01062)</li> <li>ur50_long.cdhit, ur50_long.cdhit.clstr - cdhit clustering (50% identity)</li> <li>ur50_trim.faa - filtered and trimmed alignment used as input to iqtree</li> </ul> </li> <li>Bestrophins_global_phylogeny.zip - global bestrophin phylogeny. Subfolders corresponding to different runs with names corresponding to the seed values, each containing iqtree output files, in particular the newick ur50.treefile files.</li> <li>Rhodopsins_global_phylogeny.fasta, Rhodopsins_global_phylogeny.fasta.trimmed - alignment of rhodopsin sequences and its trimmed version as used for rhodopsin bestrophin phylogeny</li> <li>Rhodopsins_global_phylogeny.zip - global rhodopsin phylogeny. Subfolders corresponding to different runs with names corresponding to the seed values, each containing iqtree output files, in particular the newick rhodopsins.treefile files</li> <li>Rhodopsins_global_phylogeny_interproscan.zip - results of interproscan analysis of the rhodopsin sequences used for global phylogeny</li> </ul> </li> </ul>
Data from: Trans-toxin ion-sensitivity of charybdotoxin-blocked potassium-channels reveals unbinding transitional states
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Data from: Acid-sensing ion channels emerged over 600 MYA and are conserved throughout the deuterostomes
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Data from: Convergence of ion channel genome content in early animal evolution
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Data from: Common internal allosteric network links anesthetic binding sites in a pentameric ligand-gated ion channel
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Ion Channel Expression Patterns in Glioblastoma Stem Cells with Functional and Therapeutic Implications for Malignancy
GEO Series GSE89623. Homo sapiens. 69 samples. Type: Expression profiling by high throughput sequencing.
Multiscale profiling of tyrosine kinase inhibitor cardiotoxicity reveals mechanosensitive ion channel PIEZO1 as cardioprotective [snMultiome]
GEO Series GSE309754. Mus musculus. 3 samples. Type: Expression profiling by high throughput sequencing.
The human ion channel TRPM2 modulates cell survival in neuroblastoma through E2F1 and FOXM1
GEO Series GSE197243. Homo sapiens. 16 samples. Type: Expression profiling by high throughput sequencing.
Multiscale profiling of tyrosine kinase inhibitor cardiotoxicity reveals mechanosensitive ion channel PIEZO1 as cardioprotective
GEO Series GSE309753. Mus musculus. 3 samples. Type: Expression profiling by high throughput sequencing.
The human ion channel TRPM2 modulates migration and invasion in neuroblastoma through regulation of integrin expression
GEO Series GSE203660. Homo sapiens. 4 samples. Type: Expression profiling by high throughput sequencing.
Molecular Remodeling of Ion Channels in Human Atrial and Ventricular Myocytes Associated with Ischemic Cardiomyopathy
GEO Series GSE17294. Homo sapiens. 11 samples. Type: Expression profiling by array.
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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.