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21,281 results for “molecular”
Molecular dynamics simulations of the interaction of wild type human CYP2J2 with arachidonic acid (POSES 1 and 2)
<p><strong>Description of files in this dataset:</strong></p> <p><strong>MD_wt_CYP2J2_AA_StateX_repeatY.zip</strong> : Series of zipped directories for molecular dynamics simulations of arachidonic acid in the active site of wild type CYP2J2. X is the docking pose number that constitutes the starting point of the simulation (the 6 lowest-energy poses from docking were selected as the starting points of the simulations - this dataset is State(pose) 1). Y is the repeat (each simulation was repeated 4 times, hence there are 4 repeats per pose). </p> <p>Each directory contains the following sub-directories:</p> <p>001.leap : Amber parameter and coordinate files; PDBs; ligands; leap commands</p> <p>002.min : Minimisation stage</p> <p>003.heat : Heating stage</p> <p>004.equil: Equilibration stage</p> <p>005.md : Production stage</p> <p>006.analysis : Basic energy graphs</p> <p>007.cpptraj: Contains only the file strip.md.nc (Amber trajectories stripped of water in netCDF format)</p>
Molecular dynamics simulations of the interaction of wild type human CYP2J2 with arachidonic acid (POSES 5 and 6)
<p><strong>Description of files in this dataset:</strong></p> <p><strong>MD_wt_CYP2J2_AA_StateX_repeatY.zip</strong> : Series of zipped directories for molecular dynamics simulations of arachidonic acid in the active site of wild type CYP2J2. X is the docking pose number that constitutes the starting point of the simulation (the 6 lowest-energy poses from docking were selected as the starting points of the simulations - this dataset is State(pose) 1). Y is the repeat (each simulation was repeated 4 times, hence there are 4 repeats per pose). </p> <p>Each directory contains the following sub-directories:</p> <p>001.leap : Amber parameter and coordinate files; PDBs; ligands; leap commands</p> <p>002.min : Minimisation stage</p> <p>003.heat : Heating stage</p> <p>004.equil: Equilibration stage</p> <p>005.md : Production stage</p> <p>006.analysis : Basic energy graphs</p> <p>007.cpptraj: Contains only the file strip.md.nc (Amber trajectories stripped of water in netCDF format)</p>
Molecular dynamics simulations of the interaction of the double mutant human CYP2J2 (R117A and R111A) with arachidonic acid (POSES 1-3)
<p><strong>Description of files in this dataset:</strong></p> <p><strong>MD_mutR111A_R117A_CYP2J2_AA_StateX_repeatY.zip</strong> : Series of zipped directories for molecular dynamics simulations of arachidonic acid in the active site of the double R111A + R117A mutant CYP2J2. X is the docking pose number that constitutes the starting point of the simulation (the 6 lowest-energy poses from docking were selected as the starting points of the simulations - this dataset is State(pose) 1). Y is the repeat (each simulation was repeated 3 times, hence there are 3 repeats per pose). </p> <p>Each directory contains the following sub-directories:</p> <p>001.leap : Amber parameter and coordinate files; PDBs; ligands; leap commands</p> <p>002.min : Minimisation stage</p> <p>003.heat : Heating stage</p> <p>004.equil: Equilibration stage</p>
Molecular dynamics simulations of the interaction of mutant human CYP2J2 (R117A) with arachidonic acid (POSES 1-4)
<p><strong>Description of files in this dataset:</strong></p> <p><strong>MD_mutR117A_CYP2J2_AA_StateX_repeatY.zip</strong> : Series of zipped directories for molecular dynamics simulations of arachidonic acid in the active site of the R117A mutant CYP2J2. X is the docking pose number that constitutes the starting point of the simulation (the 6 lowest-energy poses from docking were selected as the starting points of the simulations - this dataset is State(pose) 1). Y is the repeat (each simulation was repeated 3 times, hence there are 3 repeats per pose). </p> <p>Each directory contains the following sub-directories:</p> <p>001.leap : Amber parameter and coordinate files; PDBs; ligands; leap commands</p> <p>002.min : Minimisation stage</p> <p>003.heat : Heating stage</p> <p>004.equil: Equilibration stage</p> <p>005.md : Production stage</p> <p>006.analysis : Basic energy graphs</p> <p>007.cpptraj: Contains only the file strip.md.nc (Amber trajectories stripped of water in netCDF format)</p>
Molecular dynamics simulations of the interaction of mutant human CYP2J2 (R111A) with arachidonic acid (POSES 4-6)
<p><strong>Description of files in this dataset:</strong></p> <p><strong>MD_mutR111A_CYP2J2_AA_StateX_repeatY.zip</strong> : Series of zipped directories for molecular dynamics simulations of arachidonic acid in the active site of the R111A mutant CYP2J2. X is the docking pose number that constitutes the starting point of the simulation (the 6 lowest-energy poses from docking were selected as the starting points of the simulations - this dataset is State(pose) 1). Y is the repeat (each simulation was repeated 3 times, hence there are 3 repeats per pose). </p> <p>Each directory contains the following sub-directories:</p> <p>001.leap : Amber parameter and coordinate files; PDBs; ligands; leap commands</p> <p>002.min : Minimisation stage</p> <p>003.heat : Heating stage</p> <p>004.equil: Equilibration stage</p> <p>005.md : Production stage</p> <p>006.analysis : Basic energy graphs</p> <p>007.cpptraj: Contains only the file strip.md.nc (Amber trajectories stripped of water in netCDF format)</p>
Molecular dynamics simulations of the interaction of wild type human CYP2J2 with EPA (POSES 1-4)
<p><strong>Description of files in this dataset:</strong></p> <p><strong>MD_wt_CYP2J2_EPA_StateX_repeatY.zip</strong> : Series of zipped directories for molecular dynamics simulations of eicosapentaenoic acid (EPA) in the active site of wild type CYP2J2. X is the docking pose number that constitutes the starting point of the simulation (the 4 lowest-energy poses from docking were selected as the starting points of the simulations - this dataset is State(pose) 1). Y is the repeat (each simulation was repeated 3 times, hence there are 3 repeats per pose). </p> <p>Each directory contains the following sub-directories:</p> <p>001.leap : Amber parameter and coordinate files; PDBs; ligands; leap commands</p> <p>002.min : Minimisation stage</p> <p>003.heat : Heating stage</p> <p>004.equil: Equilibration stage</p> <p>005.md : Production stage</p> <p>006.analysis : Basic energy graphs</p> <p>007.cpptraj: Contains only the file strip.md.nc (Amber trajectories stripped of water in netCDF format)</p>
Molecular dynamics simulations of the interaction of the quadruple mutant human CYP2J2 (R111A + R117A + R382A + R446A) with arachidonic acid (POSES 4-6)
<p><strong>Description of files in this dataset:</strong></p> <p><strong>MD_quadmut_CYP2J2_AA_StateX_repeatY.zip</strong> : Series of zipped directories for molecular dynamics simulations of arachidonic acid in the active site of the quadruple (R111A + R117A+R382A+R446A) mutant CYP2J2. X is the docking pose number that constitutes the starting point of the simulation (the 6 lowest-energy poses from docking were selected as the starting points of the simulations - this dataset is State(pose) 1). Y is the repeat (each simulation was repeated 3 times, hence there are 3 repeats per pose). </p> <p>Each directory contains the following sub-directories:</p> <p>001.leap : Amber parameter and coordinate files; PDBs; ligands; leap commands</p> <p>002.min : Minimisation stage</p> <p>003.heat : Heating stage</p> <p>004.equil: Equilibration stage</p>
Example dataset for openPMD-conform molecular dynamics data (MD domain extension)
<p>This dataset results from the molecular dynamics (MD) simulation of the photon-sample interaction. The photons are propagated through the SASE1 beamline and the SPB-SFX instrument at European XFEL, with an initial energy of 5 keV. The sample is the two-nitrogenase iron protein (2nip) with 4348 atoms. The simulation is performed with a demo version of XMDYN. The datasets were rewritten from the original XMDYN output into an hdf5 format that complies with the openPMD metadata standard for particle and mesh data and the proposed domain extension of this standard for MD data. The dataset "pure_2nip_pmi_out.opmd.h5" conforms the openPMD metadata MD domain extension strictly, while the dataset "pure_2nip_pmi_out.opmd.ff.h5" stores form factor results additionally for SingFEL diffraction simulation.</p> <p>This dataset is part of the Deliverable D5.1 in Workpackage 5 (Virtual Neutron and X-ray Laboratory) of the Photon and Neutron Open Science Cloud (PaNOSC).</p> <p>This project has received funding from the European Union's Horizon 2020 research and innovation programme under grant agreement No. 823852.<br> </p>
Evaluating Changes in the Local Protein Physicochemical En-vironment induced by Molecular Dynamics Simulation
<p><span>Mutation of a single amino acid residue may significantly affect the structure and function of an entire protein. The effect of single amino acid substitutions can be assessed by examining the physicochemical environment surrounding the amino acid of interest, an emerging form of quantification of which is multidimensional tensors. However, the effect with respect to a protein variant’s inherent dynamics in tensor space is rarely assessed despite the potential importance of this form of analysis in revealing local physicochemical properties of the protein and response to mutation. Using the wild-type and 936 mutant structures of the protein domain 1pga, the present research evaluated the effects of local protein context and single amino acid substitutions on molecular dynamics simulation-derived structural distributions via the use of tensors capturing a range of biochemical properties. It was observed that the extent of simulated </span><span>physicochemical</span><span> variation local to a substituted amino acid is positively associated with local mechanical stiffness, loss of protein thermostability and decreased local hydrophobicity. In addition, it was observed that the largest tensor variation occurs in densely-packed, hydrophobic core-associated regions of protein structures. In summary, the pattern of tensor change aligns with prior knowledge about protein stability and physicochemical properties.</span></p>
Dataset from "Venomous Peptides: Molecular Origin of the Toxicity of Snake Venom PLA2‑like Peptides"
<p>Dataset from "Venomous Peptides: Molecular Origin of the Toxicity of Snake Venom PLA2‑like Peptides", containing the most relevant all-atom output trajectories and input files ran with GROMACS 2021:</p> <p>1) <strong>pure_membrane_systems.7z</strong> - pure bilayer systems (AA1, AA2, AA5), including equilibration, calcium insertion, and umbrella sampling simulations;</p> <p>2) <strong>single_peptide_systems.7z</strong> - single peptide-containing systems (AA3, AA4, AA6), including equilibration, calcium insertion, and umbrella sampling simulations;</p> <p>3) <strong>multiple_peptide_systems.7z</strong> - multiple peptide-containing systems (AA7, AA8), including equilibration, calcium insertion, and umbrella sampling simulations.</p> <p>We have included the input files (.mdp), system topology (.top and .itp), initial and final structure files (.gro), the index file (.ndx), and the portable binary run input files (.tpr). We have also included the output trajectories of systems AA3, AA4, AA6-8 in .xtc format, and spaced every 500 ps.</p> <p>System composition is given in Table Z1. More details can be found in the related publication.</p> <p><strong>Table Z1. Simulated systems' details, including name, composition (in number of lipid and peptide molecules), number of atoms composing the systems, simulation (sim.) time, and total umbrella sampling (US) time.</strong> </p> <table> <tbody> <tr> <td><strong>System</strong></td> <td><strong>POPC/POPS/Peptide</strong></td> <td><strong>no. atoms (a)</strong></td> <td><strong>sim. time (µs)</strong></td> <td><strong>US time (µs)</strong></td> </tr> <tr> <td><strong>AA1</strong></td> <td>128/0/0</td> <td>40,226</td> <td>0.3</td> <td>10.8</td> </tr> <tr> <td><strong>AA2</strong></td> <td>0/128/0</td> <td>39,458</td> <td>0.3</td> <td>10.8</td> </tr> <tr> <td><strong>AA3</strong></td> <td>128/0/1</td> <td>40,504</td> <td>0.5</td> <td>32.3</td> </tr> <tr> <td><strong>AA4</strong></td> <td>0/128/1</td> <td>39,724</td> <td>0.5</td> <td>32.3</td> </tr> <tr> <td><strong>AA5</strong></td> <td>96/32/0</td> <td>40,034</td> <td>1.0</td> <td>-</td> </tr> <tr> <td><strong>AA6</strong></td> <td>96/32/1</td> <td>40,300</td> <td>1.0</td> <td>-</td> </tr> <tr> <td><strong>AA7</strong></td> <td>96/32/5</td> <td>41,364</td> <td>1.0</td> <td>10.8</td> </tr> <tr> <td><strong>AA8</strong></td> <td>96/32/13</td> <td>55,128</td> <td>2.0</td> <td>10.8</td> </tr> </tbody> </table> <p>(a) for the US simulations, the total number of atoms was reduced in 1 because two sodium ions were substituted by a single calcium ion.</p>
Plasmodesmata Act as Unconventional Membrane Contact Sites Regulating Inter-Cellular Molecular Exchange in Plants.
<p>This table contains peaks aera values from LC-MS for lipidomic quantification of PIP and PIP2. These data were used for Pérez-Sancho, Jessica and Smokvarska, Marija and Glavier, Marie and Sritharan, Sujith and Dubois, Gwennogan and Dietrich, Victor and Platre, Matthieu and Li, Ziqiang Patrick and Paterlini, Andrea and Moreau, Hortense and Fouillen, Laetitia and Grison, Magali S. and Cana-Quijada, Pepe and Moraes, Tatiana Sousa and Immel, Françoise and Wattelet, Valerie and Ducros, Mathieu and Brocard, Lysiane and Chambaud, Clément and Zabrady, Matej and Luo, Yongming and Busch, Wolfgang and Tilsner, Jens and Helariutta, Yrjö and Russinova, Jenny and Taly, Antoine and Jaillais, Yvon and Bayer, Emmanuelle, Plasmodesmata Act as Unconventional Membrane Contact Sites Regulating Inter-Cellular Molecular Exchange in Plants. </p>
'Invisible' Molecular Dynamics Revealed for a Conformationally Chiral π-Stacked Perylene Bisimide Foldamer
<p>Additional data to report <a href="https://doi.org/10.1002/anie.202414069">https://doi.org/10.1002/anie.202414069</a>:</p> <p><a name="_Hlk172654864"></a>Whilst energetic and kinetic aspects of folding processes are meanwhile well understood for natural biomacromolecules, the folding dynamics in so far studied artificial foldamer counterparts remain largely unexplored. This is due to the low energy barriers between their conformational isomers that make the dynamic processes undetectable with conventional methods such as UV/vis absorption, fluorescence, and NMR spectroscopy, making such processes ‘invisible’. Here we present an asymmetric perylene bisimide dimer (bis-PBI <strong>1</strong>) that possesses conformational chirality in its folded state. Owing to the large interconversion barrier (≥ 116 kJ mol<sup>–1</sup>), four stereoisomers could be separated and isolated. Since the interconversion between these stereoisomers requires the foldamer to first open and then to re-fold, the transformation of one stereoisomer into others allowed us to ‘visualize’ the dynamics of folding with time and determine its lifetimes and the energetic barriers associated with the folding process. Supported by quantum chemical calculations, we identified the open structure to be only a fleeting metastable state of higher energy. Our experimental observation of the kinetics associated with the molecular dynamics in the PBI foldamer advances the fundamental understanding of folding in synthetic foldamers and paves the way for the design of smart functional materials.</p>
Direct molecular evidence for an ancient, conserved developmental toolkit controlling post-transcriptional gene regulation in land plants
<p>In plants, miRNA production is orchestrated by a suite of proteins that control transcription of the pri-miRNA gene, post-transcriptional processing and nuclear export of the mature miRNA. Post-transcriptional processing of miRNAs is controlled by a pair of physically-interacting proteins, HYL1 and DCL1. However, the evolutionary history and structural basis of the HYL1-DCL1 interaction is unknown. Here we use ancestral sequence reconstruction and functional characterization of ancestral HYL1 <em>in vitro</em> and in <em>Arabidopsis thaliana </em>to better understand the origin and evolution of the HYL1-DCL1 interaction and its impact on miRNA production and plant development. We found the ancestral plant HYL1 evolved high affinity for both double-stranded RNA (dsRNA) and its DCL1 partner before the divergence of mosses from seed plants (~500 Ma), and these high-affinity interactions remained largely conserved throughout plant evolutionary history. Structural modeling and molecular binding experiments suggest that the second of two double-stranded RNA-binding motifs (DSRMs) in HYL1 may interact tightly with the first of two C-terminal DCL1 DSRMs to mediate the HYL1-DCL1 physical interaction necessary for efficient miRNA production. Transgenic expression of the nearly 200 Ma-old ancestral flowering-plant HYL1 in <em>A. thaliana</em> was sufficient to rescue many key aspects of plant development disrupted by HYL1<sup>-</sup> knockout and restored near-native miRNA production, suggesting that the functional partnership of HYL1-DCL1 originated very early in and was strongly conserved throughout the evolutionary history of terrestrial plants. Overall, our results are consistent with a model in which miRNA-based gene regulation evolved as part of a conserved plant ‘developmental toolkit’.</p>
Molecular Dynamics Simulation of SARS-CoV-2 Spike Protein
<p>Trajectory data corresponding to the manuscript, tentatively titled "Distant Residues Modulate the Conformational Opening in SARS-CoV-2 Spike Protein"</p> <p>Authors: Dhiman Ray, Ly Le, Ioan Andricioaei</p> <p>Affiliation: University of California Irvine, USA</p> <p>Description: Multiple unbiased simulations of 40 ns were performed for the SARS-CoV-2 spike protein. Frames are saved at 50 ps interval. The initial structures were generated from umbrella sampling simulation starting from PDB ID: 6VSB and 6VXX. The index at the end of filename stands for the umbrella sampling window from which the trajectory was initiated. The indices are not continuous as not all the umbrella sampling windows were used to start trajectories. Additionally 3 trajectories, each of length 80 ns, are included for the closed, partially open and fully open state. The topology is provided as a PDB file ("spike_dry.pdb").</p> <p>The trajectories are for the spike head only structure obtained from the CHARMM-GUI Covid-19 archive. No solvent or ions are included in the trajectory or the topology.</p> <p>Update: Additional trajectories and PDB files for D614G mutant added. Each trajectory is 40 ns long. The PDB files are named 6VXX_mutant_dry.pdb and 6VSB_mutant_dry.pdb for the closed and partially open state.</p> <p>Pre-print available: https://doi.org/10.1101/2020.12.07.415596</p>
Mutually Beneficial Combination of Molecular Dynamics Computer Simulations and Scattering Experiments - DATA
<p>Specular reflectivities of the SoyPC bilayer stack measured at the vertical reflectometer MARIA at Heinz Maier-Leibnitz Zentrum (MLZ) in Garching, Germany.</p> <p>Offspecular reflectivity map (log scale) of the multilayer sample as a function of theangle of incidence (θi) and of the reflection angle (θi).</p> <p>Specular reflectivities of the Si/SiO<sub>2</sub>/DMPC/H2O at 4 different contrasts (H<sub>2</sub>O, D<sub>2</sub>O, SMW and 4MW)</p> <p>Small-angle neutron scattering of the unilamellar SoyPC</p>
A collection of molecular formula databases for HERMES
<p>A compilation of different molecule databases ready to be used in <a href="https://www.biorxiv.org/content/10.1101/2021.03.08.434466v1">HERMES</a>. We have compiled different open-access DBs and adapted their format to the HERMES requisite columns. Since all databases share the "Name" and "MolecularFormula" columns, merges between databases can be easily generated.</p> <p>More databases and merges will be added in the future. If you have any suggestions or want to contribute, feel free to contact us!</p> <p>All rights reserved to the original authors of the databases.</p> <p>Description of the files:</p> <ul> <li>ECMDB.csv: Entries from <a href="https://ecmdb.ca/"><em>E. coli</em> Metabolome Database</a>. 3760 compounds.</li> <li>Merge_KEGG_ECMDB.csv: a merge between all metabolites from <a href="https://www.genome.jp/kegg/pathway.html">KEGG pathways</a> associated to E.coli K12 with the ECMDB.csv from above. 6107 compounds.</li> <li>Merge_LipidMaps_LipidBlast.csv: a merge between lipid entities from <a href="https://www.lipidmaps.org/resources/databases/index.php">LipidMaps</a> LMSD and the metadata (just Name and Molecular Formula) of <a href="https://fiehnlab.ucdavis.edu/projects/LipidBlast">LipidBlast</a> entries. 163453 compounds.</li> <li>norman.xls: Entries from <a href="https://www.norman-network.com/nds/susdat/susdatSearchShow.php">NORMAN SusDat</a>, containing common and emerging drugs, pollutants, etc. 52019 compounds.</li> <li>PubChemLite_31Oct2020.csv Adapted column names from <a href="https://zenodo.org/record/4183801">https://zenodo.org/record/4183801</a>. 371,663 compounds related to exposomics.</li> <li>MS1_2ID.csv. Merge of HMDB, ChEBI and NORMAN compounds. 183911 compounds related to Human Metabolism, drugs, etc..</li> <li>COCONUT_NP.csv: parsed collection of entries from the COlleCtion of Open Natural ProdUcTs (<a href="https://coconut.naturalproducts.net/">COCONUT</a>).406752 compounds.</li> <li>DiTriPeptides.csv: a list of all theoretically possible dipeptides (400) and tripeptides (8000) and their associated molecular formulas. 8400 compounds.</li> </ul>
A molecular taxonomy of tumors independent of tissue-of-origin
<p>This tarball contains the pre-processed data in .Rda files required to compile our manuscript entitled "A molecular taxonomy of tumors independent of tissue-of-origin"</p>
Coarse-grained molecular dynamics simulations of SARS-CoV-2 envelope protein E in the pentameric form
<p>The trajectories of coarse-grained (CG) molecular dynamics (MD) simulations of<br> 1) unmodified (FeigLab_NMR; FeigLab_PentamerNoPTM_POPC_Martini3b: 5 μs; 5 μs); <br> 2) palmitoylated (FeigLab_PentamerCYSP43; PentamerCYSP44_POPC_Martini3b: 5 μs; 5 μs); <br> SARS-CoV-2 E protein pentamer in a POPC bilayer.</p> <p>The trajectory of CG MD of system containing 2 pentamers in the membrane buckled in a single direction (BuckledMembrane_FeigLab_2xPentamerNoPTM_POPC_Martini3b: 1 μs).</p> <p>FeigLab_Pentamer: https://github.com/feiglab/sars-cov-2-proteins/blob/master/Membrane/E_protein.pdb<br> FeigLab_NMR_Pentamer is assembled based on the transmembrane domain determined by NMR (PDB ID: 7K3G) and FeigLab model for the rest.</p>
Molecular characterization and genetic diversity of four undescribed novel oleaginous Mortierella alpina strains from Libya
<p>A large number of undiscovered fungal species still exist on earth, which can be useful for bioprospecting, particularly for single cell oil (SCO) production. <em>Mortierella</em> is one of the significant genera in this field and contains about hundred species. Moreover, <em>M. alpina </em>is the main single cell oil producer / arachidonic acid producer at commercial scale under this genus.</p>
Dataset related to article "Molecular Studies and ex vivo Complement assay on Endothelium Highlight the Genetic Complexity of Atypical Hemolytic Uremic Syndrome: The Case of a Pedigree With a Null CD46 Variant".
<p><em>The files contain raw data related to the article "Molecular Studies and ex vivo Complement assay on Endothelium Highlight the Genetic Complexity of Atypical Hemolytic Uremic Syndrome: The Case of a Pedigree With a Null CD46 Variant", available from <a href="https://www.frontiersin.org/articles/10.3389/fmed.2020.579418/full">https://www.frontiersin.org/articles/10.3389/fmed.2020.579418/ful</a>l.</em></p> <p>File <strong>"Genetic and clinical data"</strong>:</p> <ul> <li>In the sheet "485 aHUS patients" are reported data obtained from the screening of 485 unrelated patients with aHUS including rare variants (RVs) in complement disease-associated genes (<em>CFH, CD46, CFI, C3, CFB </em>and <em>THBD</em>), the presence of <em>CFH-CFHR</em> genomic rearrangements and/or anti-FH antibodies.</li> <li>In the sheet "Pedigrees with c.286+2T>G" are listed all pedigrees carrying the c.286+2T>G variant, the diseases status of all subjects and the age of disease onset of patients. In bold are indicated pedigrees (n=7) used to study the penetrance of aHUS in c.286+2T>G carriers.</li> <li>In the sheet "Haplotypes" are reported genotypes used to evaluate the association between the presence of <em>CFH-H3</em> and <em>CD46<sub>GGAAC</sub></em> risk haplotypes and aHUS. Results of this analysis are reported in Table 3 of the published paper.</li> <li>In the sheet "Raw data Fig.2" are reported data of "platelet count" and "serum creatinine" of the proband used to elaborate Figure 2.</li> </ul> <p>In the file <strong>"C3 and C5b-9 deposition"</strong> is reported the quantification of serum-induced C3 and C5b-9 deposition on human microvascular endothelial cell line (HMEC-1). The fluorescent staining was evaluated with Image J and expressed as pixel<sup>2 </sup>per field analyzed. The fields with the lowest and highest values were excluded from calculation. These values were used to elaborate data included in Table 2 and in Figure 5.</p> <p>In the file <strong>"CD46 protein expression"</strong> are reported data of CD46 expression on peripheral blood mononuclear cells (PBMCs) isolated from the proband, his relatives and healthy volunteers. Data of specific expression of CD46 (evaluated for SCR1 or for SCR4 as reported in the materials and methods section) are indicated as median fluorescence intensity (MFI) percentage compared with the control.</p> <p>In the ppt file <strong>"cDNA amplification and sequencing results"</strong> is reported:</p> <ul> <li>the agarose gel image of the amplified cDNA from the control (ctr), the proband (IV-8) and his healthy father (III-7).</li> <li>Electropherograms obtained from the cDNA sequencing of the control (ctr), the proband (IV-8) and his healthy father (III-7).</li> </ul> <p>Additional data will be made available by the authors, without undue reservation, to any qualified researcher. </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.