Find research datasets worth reusing
Search datasets from major research repositories and use ShareScore to quickly assess how well each record supports discovery, access, and reuse.
43
datasets available to search
ShareScore release 0.9.0
Dataset results
43 results for “Nuclear Pore Complex”
Simulations of passive diffusion through the nuclear pore complex
<p>Repository for simulations of passive diffusion through the nuclear pore complex, associated with the manuscript:</p> <p>Simple rules for passive diffusion through the nuclear pore complex. Timney B<em>, </em>Raveh B, Mironska R, Trivedi JM, Kim SJ, Russel D, Wente SR, Sali A, and Rout MP Journal of Cell Biology (2016) DOI: 10.1083/jcb.201601004</p>
CX-MS Datasets for "Comprehensive Structure and Functional Adaptations of the Yeast Nuclear Pore Complex"
<p>This repository contains chemical cross-linking mass spectrometry data of affinity-purified Yeast nuclear pore complexes.</p> <p>Data Files Description:</p> <p>NPC_XL_Identification_Inter_Crosslinked.csv: Inter-protein cross-links identified by pLink 2.</p> <p>NPC_XL_spectra.mgf: MS2 spectra data for the identified cross-links.</p> <p>NPC_XL_proteins.fasta : Protein sequences used for search.</p> <p>Sample Processing:</p> <p>NPCs were immuno-purified from Mlp1 tagged S. cerevisiae strains (Kim et al., 2018). After native elution, 1.0 mM disuccinimidyl suberate (DSS) was added and the sample was incubated at 25ºC for 40 min with shaking (1,200 rpm). The reaction was quenched by adding a final concentration of 50 mM freshly prepared ammonium bicarbonate and incubating for 20 min with shaking (1,200 rpm) at 25ºC. The sample (50 µg) was then concentrated and denatured at 98ºC for 5 min in a solubilization buffer (10% solution of 1-dodecyl-3-methylimidazolium chloride (C12-mim-Cl) in 50 mM ammonium bicarbonate, pH 8.0, 100 mM DTT). After denaturation, the sample was centrifuged at 21,130 g for 10 min and the supernatant was transferred to a 100 kDa MWCO ultrafiltration unit (MRCF0R100, Microcon). The sample was quickly spun at 1,000 g for 2 min and washed twice with 50 mM ammonium bicarbonate. After alkylation (50 mM iodoacetamide), the cross-linked NPC in-filter was digested by trypsin and lysC O/N at 37ºC. After proteolysis, the sample was recovered by centrifugation and peptides were fractionated into 10-12 fractions by using a stage tip self-packed with basic C18 resins (Dr. Masch GmbH). Fractionated samples were pooled prior to LC/MS analysis.</p> <p>Desalted cross-link peptides were dissolved in the sample loading buffer (5% Methanol, 0.2% FA), separated with an automated nanoLC device (nLC1200, Thermo Fisher), and analyzed by an Orbitrap Q Exactive HFX (Pharma mode) mass spectrometer (Thermo Fisher) as previously described (Xiang et al., 2020; Xiang et al., 2021). Briefly, peptides were loaded onto an analytical column (C18, 1.6 μm particle size, 100 Å pore size, 75 μm × 25 cm; IonOpticks) and eluted using a 120-min liquid chromatography gradient. The flow rate was approximately 300 nl/min. The spray voltage was 1.7 kV. The QE HF-X instrument was operated in the data-dependent mode, where the top 10 most abundant ions (mass range 380 – 2,000, charge state 4 - 8) were fragmented by high-energy collisional dissociation (HCD). The target resolution was 120,000 for MS and 15,000 for tandem MS (MS/MS) analyses. The quadrupole isolation window was 1.8 Th; the maximum injection time for MS/MS was set at 200 ms.</p> <p>Data Processing:</p> <p>The raw data were searched with pLink2 (Chen et al., 2019b). An initial MS1 search window of 5 Da was allowed to cover all isotopic peaks of the cross-linked peptides. The data were automatically filtered using a mass accuracy of MS1 ≤ 10 ppm (parts per million) and MS2 ≤ 20 ppm of the theoretical monoisotopic (A0) and other isotopic masses (A+1, A+2, A+3, and A+4) as specified in the software. Other search parameters included cysteine carbamidomethyl as a fixed modification and methionine oxidation as a variable modification. A maximum of two trypsin missed-cleavage sites was allowed. The initial search results were obtained using a default 5% false discovery rate (FDR) expected by the target-decoy search strategy. Spectra were manually verified to improve data quality (Kim et al., 2018; Shi et al., 2014). Cross-linking data were analyzed and plotted with CX-Circos (http://cx-circos.net).</p>
Modeling of the yeast Nuclear Pore Complex
<p>These scripts demonstrate the use of <a href="http://salilab.org/imp">IMP</a> in the modeling of the yeast NPC complex using diverse types of data as described in Seung Joong Kim, et al.'s 2018 NPC article published in Nature.</p> <p><strong>For more information</strong> about how to reproduce this modeling, see the <a href="https://salilab.org/npc2018/">Sali lab website</a> or the README file.</p>
Modeling of the Nup133 subunit of the yeast Nuclear Pore Complex
<p>These scripts demonstrate the use of <a href="https://integrativemodeling.org/">IMP</a>, <a href="https://salilab.org/modeller/">MODELLER</a>, <a href="https://salilab.org/foxs/">FoXS</a>, and <a href="https://salilab.org/allosmod/">AllosMod</a>, and <a href="http://bl1231.als.lbl.gov/saxs_protocols/mes.php">Minimal Ensemble Search</a> in the modeling of the Nup133 protein in the <em>S. cerevisiae</em> Nuclear Pore Complex (NPC). First, MODELLER is used to generate an initial comparative model of Nup133 guided by FoXS fits to SAXS data. Then, the model was subjected to conformational sampling with AllosMod, and finally Minimal Ensemble Search was used to identify four models that together reproduced both the SAXS data and a set of electron microscopy class averages. The final model was also validated against a set of chemical cross-links, that were not used in the modeling.</p> <p><strong>For more information</strong> about how to reproduce this modeling, see the <a href="https://salilab.org/nup133/">Sali lab website</a> or the README file.</p>
Molecular Architecture of the Major Membrane Ring Component of the Nuclear Pore Complex
<p>This repository contains the modeling files and the analysis related to the article <a href="https://www.ncbi.nlm.nih.gov/pubmed/28162953">"Molecular Architecture of the Major Membrane Ring Component of the Nuclear Pore Complex"</a> by Upla et al. in Structure 2017.</p> <p><strong>For more information</strong> about how to reproduce this modeling, see the <a href="https://salilab.org/pom152/">Sali lab website</a> or the README file.</p>
Structure and Function of the Nuclear Pore Complex Cytoplasmic mRNA Export Platform
<p>These scripts demonstrate the use of <a href="https://integrativemodeling.org/">IMP</a>, <a href="https://salilab.org/modeller">MODELLER</a>, and <a href="https://github.com/salilab/pmi">PMI</a> in the modeling of the Nup82 complex using DSS/EDC chemical cross-links and electron microscopy (EM) 2D class averages.</p> <p>First, <a href="https://salilab.org/modeller">MODELLER</a> is used to generate initial structures for the individual components in the Nup82 complex. Then, IMP is used to model these components using DSS/EDC crosslinks and the electron microscopy 2D class averages for the entire Nup82 complex.</p> <p>The modeling protocol will work with a default build of IMP, but for most effective sampling, IMP should be built with <a href="https://integrativemodeling.org/2.5.0/doc/ref/namespaceIMP_1_1mpi.html">MPI</a> so that replica exchange can be used.</p> <p><strong>For more information</strong> about how to reproduce this modeling, see the <a href="https://salilab.org/nup82/">Sali lab website</a> or the README file.</p>
Integrative Structure and Functional Anatomy of a Nuclear Pore Complex
<p>This repository contains the chemical cross-linking mass spectrometry raw data of the nuclear pore complex.</p>
Modeling of the Nup84 subcomplex of the Nuclear Pore Complex
<p>These scripts demonstrate the use of IMP, MODELLER, and PMI in the modeling of the Nup84 complex using 286 DSS/EDC chemical cross-links and an electron microscopy (EM) 2D class average.</p> <p>First, MODELLER is used to generate initial structures for the individual components in the Nup84 complex. Then, IMP is used to model these components using DSS/EDC crosslinks and the electron microscopy 2D class average for the entire Nup84 complex.</p> <p>For more information about how to reproduce this modeling, see <a href="https://salilab.org/nup84">the Sali lab website</a> or the README file.</p>
Data from: The herpes simplex virus pUL16 and pUL21 proteins prevent capsids from docking at nuclear pore complexes
Open the record for dataset details and reuse information.
Integrative modeling of the in-cell architecture of the yeast Nuclear Pore Complex
<p>Repository with source code files and input files utilized for integrative modeling of the in-cell architecture of the yeast Nuclear Pore Complex (ScNPC). All output integrative models of ScNPCs associated with the following work are included:</p> <p>"In-cell architecture of the nuclear pore and snapshots of its turnover. Matteo Allegretti, Christian E. Zimmerli, Vasileios Rantos, Florian Wilfling, Paolo Ronchi, Herman K.H. Fung, Chia-Wei Lee, Wim Hagen, Beata Turonova, Kai Karius, Mandy Börmel, Xiaojie Zhang, Christoph Müller, Yannick Schwab, Julia Mahamid, Boris Pfander, Jan Kosinski, Martin Beck. Nature, 2020"</p> <p>For questions/support please <strong>contact</strong>: <a href="mailto:jan.kosinski@embl.de">jan.kosinski@embl.de</a> or <a href="mailto:vasileios.rantos@embl-hamburg.de">vasileios.rantos@embl-hamburg.de</a></p>
Data for integrative modeling of the Nuclear Pore Complex from Schizosaccharomyces pombe
<p>Repository with input and output files utilized for integrative modeling of the Nuclear Pore Complex from Schizosaccharomyces pombe.</p>
Brownian Dynamics simulations of yeast Nuclear Pore Complex FG repeats
<p>The files in this folder can be used to reproduce the Brownian Dynamics simulations of FG repeats using IMP as described in Kim et al., 2018.</p>
Data from: Cooperative interactions between different classes of disordered proteins play a functional role in the nuclear pore complex of Baker's yeast
Open the record for dataset details and reuse information.
Dissecting the structural dynamics of the nuclear pore complex
<p>Raw mass spectrometry data files for the experiments included in the manuscript "Dissecting the structural dynamics of the nuclear pore complex" by Hakhverdyan et al.</p>
Data from: Extensive reduction of the nuclear pore complex in nucleomorphs
The nuclear pore complex (NPC) is a large macromolecular assembly situated within the pores of the nuclear envelope. Through interactions between its subcomplexes and import proteins, the NPC mediates the transport of molecules into and out of the nucleus and facilitates dynamic chromatin regulation and gene expression. Accordingly, the NPC constitutes a highly integrated nuclear component that is ubiquitous and conserved amongst eukaryotes. Potential exceptions to this are nucleomorphs: highly reduced, relict nuclei that were derived from green and red algae following their endosymbiotic integration into two lineages, the chlorarachniophytes and the cryptophyceans. A previous investigation failed to identify NPC genes in nucleomorph genomes suggesting that these genes have either been relocated to the host nucleus or lost. Here we sought to investigate the composition of the NPC in nucleomorphs by using genomic and transcriptomic data to identify and phylogenetically classify NPC proteins in nucleomorph-containing algae. Although we found NPC proteins in all examined lineages, most of those found in chlorarachniophytes and cryptophyceans were single copy, host-related proteins that lacked signal peptides. Two exceptions were Nup98 and Rae1, which had clear nucleomorph-derived homologues. However, these proteins alone are likely insufficient to structure a canonical NPC and previous reports revealed that Nup98 and Rae1 have other nuclear functions. Ultimately, these data indicate that nucleomorphs represent eukaryotic nuclei without a canonical NPC, raising fundamental questions about their structure and function.
Data from: Ribosomal RNA gene repeats associate with the nuclear pore complex for maintenance after DNA damage
The ribosomal RNA genes (rDNA) comprise a highly repetitive gene cluster. The copy number of genes at this locus can readily change and is therefore one of the most unstable regions of the genome. DNA damage in rDNA occurs after binding of the replication fork blocking protein Fob1 in S phase, which triggers unequal sister chromatid recombination. However, the precise mechanisms by which such DNA double-strand breaks (DSBs) are repaired is not well understood. Here, we demonstrate that the conserved protein kinase Tel1 maintains rDNA stability after replication fork arrest. We show that rDNA associates with nuclear pores, which is dependent on DNA damage checkpoint kinases Mec1/Tel1 and replisome component Tof1. These findings suggest that rDNA-nuclear pore association is due to a replication fork block and subsequent DSB. Indeed, quantitative microscopy revealed that rDNA is relocated to the nuclear periphery upon induction of a DSB. Finally, rDNA stability was reduced in strains where this association with the nuclear envelope was prevented, which suggests its importance for avoiding improper recombination repair that could induce repeat instability.
Data from: Ribosomal RNA gene repeats associate with the nuclear pore complex for maintenance after DNA damage
Open the record for dataset details and reuse information.
Data from: Extensive reduction of the nuclear pore complex in nucleomorphs
Open the record for dataset details and reuse information.
Genome organization regulates nuclear pore complex formation and promotes differentiation during Drosophila oogenesis [CUT&RUN]
GEO Series GSE250350. Drosophila melanogaster. 24 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
Genome organization regulates nuclear pore complex formation and promotes differentiation during Drosophila oogenesis [RNA-seq]
GEO Series GSE248057. Drosophila melanogaster. 8 samples. Type: Expression profiling by high throughput sequencing.
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.