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.
179
datasets available to search
ShareScore release 0.9.0
Dataset results
179 results for “data matrix”
Data from: Sorting states of environmental DNA: Effects of isolation method and water matrix on recovery of membrane-bound, dissolved, and adsorbed states of eDNA
Open the record for dataset details and reuse information.
Generating an expression matrix for droplet single-cell RNA-seq (dscRNA-seq) data
<p>This tutorial is adapted from the 'Generating an expression matrix' training session at the EBI (https://www.ebi.ac.uk/training/events/2019/single-cell-rna-seq-analysis-questions-clusters).</p>
Colorectal cancer scRNA-seq 10xG-format data matrix
<p>Metastatic colorectal cancer (CRC) is a major cause of cancer-related death and incidence is rising in the younger population (<50 years). Current chemotherapies can achieve response rates above 50%, but immunotherapies have limited value for patients with microsatellite-stable (MSS) cancers. The present study investigates the impact of chemotherapy on the tumor immune microenvironment. We treat human liver metastases slices with 5-Fluorouracil (5FU) plus either irinotecan or oxaliplatin, then perform single-cell transcriptome analyses. Results from eight cases reveal two cellular subtypes with divergent responses to chemotherapy. Susceptible tumors are characterized by a stemness signature, an activated interferon pathway, and suppression of PD-1 ligands in response to 5FU+irinotecan. Conversely, immune checkpoint TIM-3 ligands are maintained or up-regulated by chemotherapy in CRC with an enterocyte-like signature, and combining chemotherapy with TIM-3 blockade leads to synergistic tumor killing. Together, our analyses highlight chemo-modulation of the immune microenvironment and provide a framework for combined chemo-immunotherapies. </p>
easyMF: A Web Platform for Matrix Factorization-based Biological Discovery from Large-scale Transcriptome Data
<p>With the development of high-throughput experimental technologies, large-scale RNA sequencing (RNA-Seq) data have been and continue to be produced, but have led to challenges in extracting relevant biological knowledge hidden in the produced high-dimensional gene expression matrices. Here, we present easyMF, a user-friendly web platform that aims to facilitate biological discovery from large-scale transcriptome data through matrix factorization (MF). The easyMF platform enables users with little bioinformatics experience to streamline transcriptome analysis from raw reads to gene expression and to decompose expression matrix from thousands of genes to a handful of metagenes. easyMF also offers a series of functional modules for metagene-based exploratory analysis with an emphasis on functional gene discovery. As a modular, containerized and open-source platform, easyMF can be customized to satisfy users’ specific demands and deployed as a web server for broad applications. easyMF is freely available at https://github.com/cma2015/easyMF. We demonstrated the application of easyMF with four case studies using 940 RNA sequencing datasets from maize (<em>Zea mays </em>L<em>.</em>).</p>
Replication Data for "Inverse-designed low-index-contrast structures on silicon photonics platform for vector-matrix multiplication"
<p>COMSOL files and Python post-processing code.</p>
Simulation data for paper "Evaluation of Fendiline Treatment in VP40 System with Nucleation-Elongation Process: A Computational Model of Ebola Virus Matrix Protein Assembly"
<p>This is the original simulation data sets for paper "Evaluation of Fendiline Treatment in VP40 System with Nucleation-Elongation Process: A Computational Model of Ebola Virus Matrix Protein Assembly".</p>
Data from: A myristoyl switch at the plasma membrane triggers cleavage and oligomerization of Mason-Pfizer monkey virus matrix protein
<p>Here we present NMR and MS data used in article A myristoyl switch at the plasma membrane triggers cleavage and oligomerization of Mason-Pfizer monkey virus matrix protein. NMR data contain full set of assignment experiments used to partially assign signals of non-myristoylated wt M-PMV MAPPHis, H-N HSQC spectra or myristoylated M-PMV MAPPHis wt, A79V and I51A mutants and results from TALOS+ program used to calculate the secondary structure of C-terminal part of both mristoylated and non-myristoylated wt MAPPHis. The MS data contain MS data measured both for non-labeled samples of myristoylated M-PMV MAPPHis wt, A79V and I51A mutants and non-myristoylated MAPPHis, as well as data measured on these proteins after deuterium exchange.</p>
Data for "Heat treatment and fiber drawing effect on the matrix structure and fluorescence lifetime of Er- and Tm-doped silica optical fibers"
<p>Includes data for absorption and attenuation measurements and calculations, profiles of refractive index and concentrations, TEM images, XRD patters, and data for fluorescence decay curves presented in the graphs.</p>
The Protective Function of Directed Asymmetry in the Pericellular Matrix Enveloping Chondrocytes (Supporting Data)
<p>This dataset contains the images necessary to reproduce the study "The Protective Function of Directed Asymmetry in the Pericellular Matrix Enveloping Chondrocytes (DOI: 10.1007/s10439-021-02900-1)"</p>
Images and data accompanying article: Remarkable response of hollow thermoplastic microspheres-elastomer matrix composites in uniaxial tension.
<p><strong>Images and data accompanying article:<br> Remarkable response of hollow thermoplastic microspheres-elastomer matrix composites in uniaxial tension.*</strong><br> <em>By Michel Coret, Erwan Verron & Pierre Rublon</em><br> <strong>(<a href="http://hal.archives-ouvertes.fr/hal-03480982">https://hal.archives-ouvertes.fr/hal-03480982</a>)</strong></p> <p><br> <strong>Abstract of the article</strong><br> In the last few years, the mechanical response of hollow thermoplastic micro-spheres-elastomer matrix composites has been investigated. The large majority of the studies focuses on their compressive properties and particularly on the stress-strain response. In the present paper, large strain uniaxial tension experiments are conducted on thermoplastic microspheres filled polyurethane elastomer. Six volume fractions of microspheres are considered. Thanks to a two-camera setup and digital image correlation measurements, the volumetric response of the materials is extensively analyzed. As a major result, the remarkable volumetric behaviour is highlighted: the hydrostatic pressure vs. volume change curves admit several extrema that may be read as the macroscopic signature of the complex microstructural phenomena involved during deformation. Moreover, it is shown that the size of the volumetric loading-unloading hysteresis loop is directly related to the volume fraction of microspheres in the materials.<br> Experimental test methodology is described within the article. The objective of the deposit is to share data.</p> <p><strong>Description of the deposit</strong><br> <strong>Objectives:</strong></p> <p>The objective of this deposit is to share all the data needed to retrieve the results presented in the article (<a href="http://hal.archives-ouvertes.fr/hal-03480982">https://hal.archives-ouvertes.fr/hal-03480982</a>). This deposit do not explain any experimental methodology, that can be found in the article.</p> <p><strong>Data overview:</strong></p> <ol> <li>The images taken during the tests (raw data)</li> <li>Force and displacement measured by the tensile machine (raw data).</li> <li>Surface strain field on face and lateral sides of the tensile specimen (obtain by Digital Image Correlation)</li> <li>Averaged and filtered</li> </ol> <p><strong>Data description:</strong><br> 1. Image directories:<strong> "YY/MM/DD_poro_xx_spec_nn"</strong></p> <ul> <li> YY/MM/DD: date of the test</li> <li> xx: specimen porosity (can be one of these values [0, 05, 10, 15, 20, 25] in %)</li> <li> nn: Specimen number</li> </ul> <p> In each directory you will find:</p> <ul> <li> YY/MM/DD_poro_xx_spec_nn-aaaaa_0.tif (face side *aaaaa* image)</li> <li> YY/MM/DD_poro_xx_spec_nn-bbbbb_1.tif (lateral side *bbbbb* image</li> <li> YY/MM/DD_poro_xx_spec_nn.csv (Synchronized analogic data with images) <ul> <li>Column A: Image n°</li> <li>Columns B & C: Image file name</li> <li>Columns D & E: Timestamp</li> <li>Columns F & G: Analog data (Volts)</li> <li>Column H: Position of the jack (millimeter)</li> <li>Column I: Measured force (N)</li> </ul> </li> </ul> <p>2. Scalar data directory: <strong>Data_csv/</strong></p> <ul> <li><strong>DIC</strong>: strain average results from digital image correlation on face side (axis xy) and lateral side (axis yz) <ul> <li>Column A: Image n°</li> <li>Column B, C, D (Hencky strains): exx, eyy & exy</li> <li>Column E, F (Hencky eigen strains): e1 & e2</li> </ul> </li> </ul> <p> </p> <ul> <li><strong>Machine</strong>: displacement and force from tensile machine for each image <ul> <li>Column A: Image n°</li> <li>Columns B & C: Image file name</li> <li>Columns D & E: Timestamp</li> <li>Columns F & G: Analog data (Volts)</li> <li>Column H: Position of the jack (millimeter)</li> <li>Column I: Measured force (N)</li> </ul> </li> </ul> <p> </p> <ul> <li><strong>Post</strong>: Average + smoothed data for each porosities <ul> <li>Column A: Longitudinal stretch <span class="math-tex">\(\lambda\)</span></li> <li>Column B: Nominal stress P</li> <li>Column C: Lateral stretch ratio <span class="math-tex">\(\lambda_w=\lambda_t\)</span><br> </li> </ul> </li> </ul>
Data matrix for ALTERNATIVE project deliverable D3.1
<p>The evaluation of epidemiological evidence was carried out in project ALTERNATIVE by a systematic review of the literature. The project defined the literature search strategy and build a data matrix from the collected evidence. The matrix consists of all the variables collected from each selected evidence and is presented in separate tables. This file presents the original data matrix.</p>
Data matrix for ALTERNATIVE project deliverable D3.2
<p>The toxicological data matrix provides a framework for the derived results of the targeted literature study that was carried out in project ALTERNATIVE. Included are 3 tables. Table 1 (1<sup>st</sup> sheet) provides an overview of the included toxicants, as well as physicochemical properties and the total number of results for every toxicant. In table 2 (2<sup>nd</sup> sheet), a list of all potency estimates can be found (318 in total). Table 3 (3<sup>rd</sup> tab) provides the summarized main findings of included cardiotoxicity studies.</p>
Data matrix for phylogeography of Euphorbia jolkinii
<p>In this study, we conducted phylogenomic analyses on the plastome and genome-wide nuclearSNP of <em>Euphorbia jolkinii</em> and its relative. We archived the data matrix for the analyses.</p>
Data matrix for phylogeography of sea hibiscus (Hibiscus tiliaceus) group
<p><span>Long-distance dispersal (LDD) of seeds plays an important role in the plant migration to a new habitat and maintaining gene flow among populations. Pantropical plants with sea-drifted seeds have achieved their global distribution by LDD. However, the spatiotemporal processes to achieve the wide distribution and the role of LDD in it have not yet been investigated.</span></p> <p><span> In this study, we conducted phylogenomic analyses on the plastome, genome-wide nuclear SNP, and low-copy gene data of <em>Hibiscus tiliaceus</em> and its relatives. We conducted shotgun sequencing for extracting plasome sequence and MIG-seq for a genome-wide SNPs genotyping.</span></p> <p><span>The dated phylogeny showed that global expansion started approximately four million years ago (MYA), and species diversification occurred 1 MYA. Plastome phylogeny suggested the non-monophyly of the haplotypes in the two widely distributed coastal species, <em>H. tiliaceus </em>and <em>H. pernambucensis</em>. In contrast, genome-wide nuclear SNP phylogenies clearly illustrated genetic segregation among species and/or geographical regions. Ancestral polymorphisms in chloroplast genomes shared among distinct species have remained below the range of rapid expansion and speciation of marginal populations. This study demonstrated that the LDD of sea-drifted seeds contributed to the rapid expansion and pantropical distribution of sea hibiscus, and adaptation to local environment or isolation by regional effect after LDD promoted speciation, suppressing gene flow.</span></p>
Data from: CoZr nanocomposites in a ceramic-metal AlOx(OH)y/Al matrix with different Co/Zr ratio and its potential for syngas processing
<p>Data from article in Dalton Transaction</p>
Q matrix data for the problems studied using Flexible-PEPS simulator.
<p>How to read the Q matrix:<br><br>Load the dictionary, say as "main_dictionary".</p> <p>Q_dictionary=main_dictionary['Q_dict']</p> <p>Q_dictionary['(x,y)']=value_xy<br><br>value_xy is the Q matrix strength between the vertices (x, y), here x, y are integers starting from 1, to N, where N is the number of qubits (number of variables) in the system.</p>
Data Matrix Theme-Specific Analysis of the Recommendation on Science and Scientific Researchers (RSSR): Open Access, Open Data, and Open Science
<p>This Table sets out findings from the mapping exercise conducted as part of the objectives of subtask 6.1 of the RRING project.</p> <p>Aim: Alignment of RRI to advance the UN SDGs.</p> <p>Objectives:</p> <ul> <li>Mapping the RSSR to the SDGs </li> </ul> <p>Mapping the RSSR to the SDGs is aimed at providing new perspectives, ideas and approaches that can help to improve the operationalization and implementation of each SDG, <em>by facilitating the integration of RRI (or RRI-like) practices in the SDGs, to make them more achievable.</em> The impact of the new perspectives, ideas and approaches in SDG operationalization and implementation will be aimed at the level of <em>national and international policy (making); future research and innovation projects (in industry and academia); as well as education and training of researchers, policy makers and other stakeholders.</em></p> <p>Two documents were used for this task:</p> <ul> <li>2017 Recommendation on Science and Scientific Researchers ([RSSR], UNESCO), and</li> <li>the United Nations 2030 Agenda for Sustainable Development with the 17 Sustainable Development Goals (SDGs).</li> </ul>
Raw, unprocessed SEM data images for: Figure 1: Scanning electron microscope images of "type-1 bone collagen" demineralized bone matrix fibrils
<p>Raw, unprocessed SEM data images for Figure 1 of the manuscript: Scanning electron microscope images of "type-1 bone collagen" demineralized bone matrix fibrils. (A) Fibrils from the <em>B</em>. <em>taurus</em> extant long bone control. Prominent banding (~67nm) is present that is characteristic of type-1 collagen protein fibrils (Boatman et al., 2019; Gottardi et al., 2016; Lin et al., 1993; Rabotyagova et al., 2008; Tzaphlidou, 2005). (B) Permafrost YG 610.2397 <em>M</em>. <em>primigenius</em> demineralized bone matrix fibrils. An ~67nm banding pattern on the fibrils is also observed but is somewhat less distinct in comparison to that of the extant <em>B</em>. <em>taurus</em> specimen. (C) Observed fibril structures in the temperate MOR 91.72 <em>M</em>. <em>columbi</em> specimen. Fibril banding is generally absent, suggesting the original chemical state of the type-1 collagen fibrils/sequences is substantially altered.</p>
Mygalomorph spiders: Discrete data matrix of burrow construction behavior and somatic morphology
<p>Mygalomorph spiders (trapdoor spiders and their kin) have long been associated with high levels of homoplasy, and many convergent features can be intuitively associated with different behavioral niches. This dataset includes two discrete behavioral characters and 55 somatic morphological characters (scored from adult females), for 110 genera of mygalomorph spiders, along with a complete reference list and exemplar list used when constructing the dataset. This dataset was used to reconstruct the evolution of burrowing behavior in the Mygalomorphae, compare the influence of behavior and evolutionary history on somatic morphology, and test hypotheses of correlated evolution between specific morphological features and behavior. The results revealed the simplicity of the mygalomorph adaptive landscape, with opportunistic, web-building taxa at one end, and burrowing/nesting taxa with structurally-modified burrow entrances (e.g., a trapdoor) at the other. Shifts in behavioral niche, in both directions, are common across the evolutionary history of the Mygalomorphae, and several major clades include taxa inhabiting both behavioral extremes. Somatic morphology is heavily influenced by behavior, with taxa inhabiting the same behavioral niche often more similar morphologically than more closely-related but behaviorally-divergent taxa.</p>
Optimizing Sparse Matrix-Matrix Multiplication for the GPU supplementary data
<p>This contains the matrices for the SpGEMM tests presented in "Optimizing Sparse Matrix-Matrix Multiplication for the GPU", by Steven Dalton, Nathan Bell, and Luke N. Olson.</p> <p>Each A matrix from Table 3 has an companion matrix P in the directory. The storage scheme appends "_P" to the end of the A matrix filename.<br> </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.