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1,344 results for “ribosome”
Capturing single-copy nuclear genes, organellar genomes, and nuclear ribosomal DNA from deep genome skimming data for plant phylogenetics: A case study in Vitaceae
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Data from: Extensive allopolyploidy in the neotropical genus Lachemilla (Rosaceae) revealed by PCR ‐based target enrichment of the nuclear ribosomal DNA cistron and plastid phylogenomics
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A snakemake toolkit for the batch assembly, annotation, and phylogenetic analysis of mitochondrial genomes and ribosomal genes from genome skims of museum collections
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A Pleistocene legacy of gene pools, ecodemes and admixtures of Stuckenia pectinata (L.) Börner as evidenced from microsatellites, complete chloroplast genomes and ribosomal RNA cistron (Europe, Africa)
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Data for publication: Recognition of non-CpG repeats in Alu and ribosomal RNAs by the Z-RNA binding domain of ADAR1 induces A-Z junctions
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Ribosome demand links transcriptional bursts to protein expression noise
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New insights into infrageneric relationships of Lonicera (Caprifoliaceae) as revealed by nuclear ribosomal DNA cistron data and plastid phylogenomics
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Supplemental information and Data for: Colloidal physics modeling reveals how per-ribosome productivity increases with growth rate in E. coli
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Ribosomal stalk proteins RPLP1 and RPLP2 promote biogenesis of flaviviral and cellular multi-pass transmembrane proteins
<p>The ribosomal stalk proteins, RPLP1 and RPLP2 (RPLP1/2), which form the ancient ribosomal stalk, were discovered decades ago but their functions remain mysterious. We had previously shown that RPLP1/2 are exquisitely required for replication of dengue virus (DENV) and other mosquito-borne flaviviruses. Here, we show that RPLP1/2 function to relieve ribosome pausing within the DENV envelope coding sequence, leading to enhanced protein stability. We evaluated viral and cellular translation in RPLP1/2-depleted cells using ribosome profiling and found that ribosomes pause in the sequence coding for the N-terminus of the envelope protein, immediately downstream of sequences encoding two adjacent transmembrane domains (TMDs). We also find that RPLP1/2 depletion impacts a ribosome density for a small subset of cellular mRNAs. Importantly, the polarity of ribosomes on mRNAs encoding multiple TMDs was disproportionately affected by RPLP1/2 knockdown, implying a role for RPLP1/2 in multipass transmembrane protein biogenesis. These analyses of viral and host RNAs converge to implicate RPLP1/2 as functionally important for ribosomes to elongate through ORFs encoding multiple TMDs. We suggest that the effect of RPLP1/2 at TMD associated pauses is mediated by improving the efficiency of co-translational folding and subsequent protein stability.</p>
Supplemental Data for "Shape changes and cooperativity in the folding of central domain of the 16S ribosomal RNA"
<p>This is data set associated with an article "Shape changes and cooperativity in the folding of central domain of the 16S ribosomal RNA" by Naoto Hori, Natalia A. Denesyuk, and D. Thirumalai. See README.txt file for the format of the data set.</p>
Raw data for 'Deciphering molecular details of the RAC-ribosome interaction by EPR spectroscopy'
<p>Raw data, analyzed data, and figure data for 'Deciphering molecular details of the RAC-ribosome interaction by EPR spectroscopy'</p> <p> </p> <p>The folder 'CW' contains continuous wave EPR data.</p> <p>The folder 'DEER' contains raw data and analyzed data for the distance measurements.</p> <p>The folder 'MD' contains molecular dynamics trajectories for the four helix bundle (4HB) of RAC and the proline-induced unfolding (KR_PP).</p> <p>The folder 'MMM' contains distance information obtained by cluster analysis and distance calculation with the MMM package.</p>
FIGURE 6. Fast distance based analysis tree for 16s ribosomal RNA gene. Note total genetic uniformity among 28 in Billions and billions sold: Pet-feeder crickets (Orthoptera: Gryllidae), commercial cricket farms, an epizootic densovirus, and government regulations make for a potential disaster
FIGURE 6. Fast distance based analysis tree for 16s ribosomal RNA gene. Note total genetic uniformity among 28 individuals of G. locorojo from eight "localities" on three continents. See Appendix A for specimen source data.
FIGURE 5 in Two new species of Siconema (Drilonematoidea: Ungellidae) parasitic in earthworms in Vietnam, and systematic relationships as inferred from ribosomal sequence data
FIGURE 5. Phylogram of the relationships between nematodes of the genera Siconema and Homungella tonkinense from Pu Mat National Park and other nematode genera based on the partial sequence of D2D3 expansion segment of LSU rDNA. A—Tree obtained with maximum parsimony and distance (NJ) optimality criteria. Number of bootstrap replicates = 10000; of 718 total characters: 276 characters are constant, 127 variable characters are parsimony-uninformative, number of parsimonyinformative characters = 315. Bootstrap values of MP and NJ analysis (in parentheses) are indicated near appropriate nodes. B—Maximum likelihood analysis, model selected - Model selected: GTR+G+I; – lnL = 6293.3618, Number of bootstrap replicates = 100, Bootstrap values are indicated near appropriate nodes.
FIGURE 4 in Two new species of Siconema (Drilonematoidea: Ungellidae) parasitic in earthworms in Vietnam, and systematic relationships as inferred from ribosomal sequence data
FIGURE 4. Siconema diducuncinum sp. n. SEM images. Female. A: hooks, dorsal view; B: stomatal tube, en face view; C: caudal organ, dorsal view; D: caudal organ, lateral view; E: margin of sub-lateral field. Scale bars in µm.
FIGURE 2 in Two new species of Siconema (Drilonematoidea: Ungellidae) parasitic in earthworms in Vietnam, and systematic relationships as inferred from ribosomal sequence data
FIGURE 2. Siconema ovicallosum sp. n. SEM images. Female. A, B: head hooks, latero-dorsal view; C: caudal organ, ventral view; D: amphid, lateral view. Scale bars in µm.
FIGURE 3 in Two new species of Siconema (Drilonematoidea: Ungellidae) parasitic in earthworms in Vietnam, and systematic relationships as inferred from ribosomal sequence data
FIGURE 3. Siconema diducuncinum sp. n. A & B, female & male in copula; C–H, female; I, J, male. C: pharynx region; C: posterior region; D: hooks; and G, I: hooks into D, G, I: hooks; J: posterior region. Except I, all in lateral position. Scale bars in µm.
FIGURE 1 in Two new species of Siconema (Drilonematoidea: Ungellidae) parasitic in earthworms in Vietnam, and systematic relationships as inferred from ribosomal sequence data
FIGURE 1. Siconema ovicallosum sp. n. A–G, female; H–K, male. A: entire worm; B: pharynx region; C: posterior region; D: vulval region; E: eggs; F: tail tip; G: hooks; H: entire worm; I: pharynx region; J: cloaca; K: caudal organ. All in lateral position. Scale bars in µm.
Supplementary Information: RAPP-containing arrest peptides induce translational stalling by short circuiting the ribosomal peptidyltransferase activity
<p><span><span>The Simulation_files folder contains initial coordinates, input files and output coordinates of the Molecular Dynamics (MD) simulations of wild type and mutants of the Apdp peptide in the ribosome ( region of 35 </span></span>Å around the peptide).</p> <p><span><span>The Uncharged_N-terminal_residues folder includes residue topologies (.rtp file) and hydrogen data bank (.hdb) of the uncharged terminal Alanine and Proline (used for modelling Ala134 and Pro134).</span></span></p> <p><span><span>The Figures folder contains rmsd, distances, rmsf values, and projections on the most dominant conformational modes sampled by the Ala 132 backbone atoms obtained from the MD trajectories.</span></span><span><br></span></p>
FIGURE 12. Rhabdopleura emancipata n in Four new species and a ribosomal phylogeny of Rhabdopleura (Hemichordata: Graptolithina) from New Zealand, with a review and key to all described extant taxa
FIGURE 12. Rhabdopleura emancipata n. sp., A, B, D, E, paratype NIWA 161566; C, paratype 161211: A, B, distal part of a ringed tube, the bracketed section enlarged in B. C, transmitted-light view of a principal tube (stem) with openings of four ringed tubes all around; tentacles of one young zooid partly emergent; note how black stolon changes position within principal tube; cdc = cone of diaphragm complex. D, close-up of exterior surface of a principal tube showing parallel fusellar annuli marked by thin sutures. E, sclerotized tube, with terminal aperture at left, branching off a principal stolon. Scale bars: A, 200 μm; B, 100 μm; C, 400 μm; D, 100 μm; E, 1 mm.
FIGURE 11. Rhabdopleura emancipata n in Four new species and a ribosomal phylogeny of Rhabdopleura (Hemichordata: Graptolithina) from New Zealand, with a review and key to all described extant taxa
FIGURE 11. Rhabdopleura emancipata n. sp., A, B, holotype NIWA 13590; C, E, paratype 161211; D, paratype NIWA162566: A, B, close-up and whole colony (inset); principal tubes are identifiable in A by the dark-brown stolon that passes through them; abundant ringed tubes diverge almost at right angles from principal tubes. C, transmitted-light view of a principal tube (pt) from which two ringed tubes (rt) diverge and, between them, a branch of the principal tube with a bifurcation of the black stolon (bs); other abbreviations: cdc, cone of diaphragm complex; cs, contractile stalk (gymnocaulus) of zooid; fc, fusellar collar; s, septum. D, SEM of a principal tube (pt) (stem), with its aperture at left, and five ringed tubes in various stages of development. E, transmitted-light view of a principal tube (pt) (stem) and its black stolon (bs) in which are three young zooids (z), the middle one of which shows, from below, the opening of a potential ringed tube (ort). Scale bars: A, 3 mm; B, 3 cm; C‒E, 0.5 mm.
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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)
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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.