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7,515 results for “screenings”
Systematic reconstruction of molecular pathway signatures using scalable single-cell perturbation screens
<p>This repo contains Seurat objects, differential expression analysis results, and pathway gene lists for the manuscript "Systematic reconstruction of molecular pathway signatures using scalable single-cell perturbation screens"<br>List of files:</p> <p>1. Seurat_object_IFNB_Perturb_seq.rds: Seurat object of the Perturb-seq data for Interferon-beta pathway<br>2. Seurat_object_IFNG_Perturb_seq.rds: Seurat object of the Perturb-seq data for Interferon-gamma pathway<br>3. Seurat_object_TNFA_Perturb_seq.rds: Seurat object of the Perturb-seq data for TNF-alpha pathway<br>4. Seurat_object_TGFB1_Perturb_seq.rds: Seurat object of the Perturb-seq data for TGF-beta1 pathway<br>5. Seurat_object_INS_Perturb_seq.rds: Seurat object of the Perturb-seq data for insulin pathway<br>6. Pathway_genelist.rds: The pathway gene lists from MultiCCA analysis<br>7. Pathway_Exclusive_genelist.rds: The pathway exclusive gene lists generated from Pathway_genelist.rds<br>8. HClust_Pathway_celltype_specific_genelist.rds: The cell-line specific pathway gene lists from hierarchical clustering analysis independently done on each cell line<br>9. DE_results_all_pathway.zip: The DE test results for all the regulators, cell lines, and pathways (from Mixscale weighted DE test.)<br>10. Bulk_RNAseq_Seurat_object_IFNG_and_TGFB_stim.rds: Seurat object for the bulk RNA-seq data for interferon-gamma and TGF-beta stimulation experiments<br>11. Parse_Guide_Capture_Protocol.pdf: The guide RNA capture protocol developed for Parse Evercode Whole Transcriptome kit</p>
A High-Performance Data Processing Workflow to Incorporate Effect-Directed Analysis in Suspect and Nontarget Screening [Feature Tables]
<p>This repository is supplementary to the manuscript "High-Performance Data Processing Workflow Incorporating Effect-Directed Analysis for Feature Prioritization in Suspect and Nontarget Screening" (DOI: 10.1021/acs.est.1c04168) and includes an overview of all measured chemical features and annotations in a waste water treatment plant (WWTP) effluent, dust standard reference material (SRM) 2585 and fetal calf serum (FCS) sample.</p> <p>Samples were measured using liquid chromatography - high resolution mass spectrometry (LC-HRMS) and fractionated into 80 micro-fractions encompassing a couple of seconds from the chromatographic run. The fractions were tested for their bioactivity in the antibiotics and the TTR-binding assay. The samples were processed separately using one, two, and three technical replicates in positive and negative ion mode. The first excel sheet includes all measured chemical features, suspect screening annotation, and corresponding bioassay responses. The second sheet includes all possible isomer annotations from the CECscreen database (DOI: <a href="https://doi.org/10.5281/zenodo.3956586">10.5281/zenodo.3956586</a>) for the annotated features. </p>
Metadata on EUbOPEN multiplex chemogenomic compound screen, wave 1
<p>This is the metadata about EUbOPEN multiplex chemogenomic compound screen, wave 1. The corresponding image data is found at <a href="https://www.ebi.ac.uk/biostudies/studies/S-BIAD145">https://www.ebi.ac.uk/biostudies/studies/S-BIAD145</a>.</p> <p>To compile the metadata Excel file into filelists, please use the Python scripts at: <a href="https://doi.org/10.5281/zenodo.6325622">https://doi.org/10.5281/zenodo.6325622</a>.</p> <p> </p>
Dataset for Dynamics of Solid-Electrolyte Interphase Formation on Silicon Electrodes Revealed by Combinatorial Electrochemical Screening
<p>This dataset provides the raw data to the manuscript</p> <p>"<strong>Dynamics of Solid-Electrolyte Interphase Formation on Silicon Electrodes Revealed by Combinatorial Electrochemical Screening"</strong></p> <p>published in Angewandte Chemie International Edition (2022): <a href="https://doi.org/10.1002/anie.202207184">https://doi.org/10.1002/anie.202207184</a></p> <p>Specifically, the following measurements are provided:</p> <ul> <li>Electrochemical measurements for combinatorial preparation of solid-electrolyte layers under different conditions and repetitions ("SECCM/")</li> <li>Raman spectra obtained using SHINERS for all the prepared conditions and repetitions ("SHINERS/")</li> <li>Atomic force microscopy data for each SEI layer ("AFM/")</li> <li>Energy-dispersive X-ray spectroscopy data ("EDX/")</li> </ul>
Diagnostic accuracy of a set of clinical and radiological criteria for screening of COVID-19 using RT-PCR as the reference standard - Dataset
<p>Dataset of a cohort whose summary is described below.</p> <p>Abstract</p> <p><strong>Objective:</strong> To evaluate the accuracy, sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV) of a set of clinical-radiological criteria for COVID-19 screening in patients with severe acute respiratory failure (SARF) admitted to intensive care units (ICUs), using reverse-transcriptase polymerase chain reaction (RT-PCR) as the reference standard. <strong>Method: </strong>Diagnostic accuracy study including a historical cohort of 1009 patients consecutively admitted to ICUs across six hospitals in Curitiba (Brazil) from March to September, 2020. The sample was stratified into groups by the strength of suspicion for COVID-19 (strong <em>versus</em> weak) using parameters based on three clinical and radiological (chest computed tomography) criteria. The diagnosis of COVID-19 was confirmed by RT-PCR (referent). <strong>Results:</strong> With respect to RT-PCR, the proposed criteria had 98.5% (95% confidence interval [95% CI] 97.5–99.5%) sensitivity, 70% (95% CI 65.8–74.2%) specificity, 85.5% (95% CI 83.4–87.7%) accuracy, PPV of 79.7% (95% CI 76.6–82.7%) and NPV of 97.6% (95% CI 95.9–99.2%). <strong>Conclusion: </strong>The proposed set of clinical-radiological criteria were accurate in identifying patients with strong <em>versus</em> weak suspicion for COVID-19 and had high sensitivity and considerable specificity with respect to RT-PCR. These criteria may be useful for screening COVID-19 in patients presenting with SARF.</p>
Coswara: A respiratory sounds and symptoms dataset for remote screening of SARS-CoV-2 infection
<p>Coswara is a dataset containing diverse set of respiratory sounds and rich meta-data from COVID-19 positive and Non-COVID subjects.</p>
Dataset underlying the publication: "Organic contaminants in bio-based fertilizer treated soil: Target and suspect screening approaches" DOI: 10.1016/j.chemosphere.2023.139261
<p>Dataset underlying the publication "Organic contaminants in bio-based fertilizer treated soil: Target and suspect screening approaches" DOI: 10.1016/j.chemosphere.2023.139261.</p>
Dataset for the Casein kinase II subunit alpha antibody screening study
<p><strong>This antibody characterization dataset is related to the F1000 research article openly available at F1000Research.</strong></p> <p><em>This project contains the following underlying data included in a study aiming at characterizing ten antibodies for Casein kinase II subunit alpha protein. The study is available on Zenodo (<a href="https://doi.org/10.5281/zenodo.10818214">https://doi.org/10.5281/zenodo.10818214</a>). </em></p> <p><em>The Dataset is in the format of a zip file. Once downloaded, please expand the zip file to access the folders containing the underlying data for Western blot (Wb), immunoprecipitation (IP) and immunofluorescence (IF).</em></p>
Joint AstraZeneca-Cancer Research Horizons Functional Genomics Centre's CRISPRn library benchmark screens: gRNA counts and associated metadata
<p>Genome-wide CRISPR sgRNA libraries have emerged as transformative tools to systematically probe gene function. While these libraries have been iterated over time to be more efficient, their large size limits their use in some applications. Here, we benchmarked publicly available genome-wide single-targeting sgRNA libraries and evaluated dual targeting as a strategy for pooled CRISPR loss-of-function screens. We leveraged this data to design two minimal genome-wide human CRISPR-Cas9 libraries that are 50% smaller than other libraries and that preserve specificity and sensitivity, thus enabling broader deployment at scale. </p>
Dataset for the Rab3A antibody screening study
<p>This dataset contains the following underlying data included in a study aimed at characterizing sixteen commercial antibodies for Rab3A (UniProt ID P20336) protein. </p>
Dataset for the Huntingtin antibody screening study
<p><strong><span>This antibody characterization dataset is related to the F1000 research article openly available at F1000Research.</span></strong></p> <p><em>This dataset contains underlying data from a study that evaluated twenty commercial antibodies agaisnt Huntingtin in western blot, immunoprecipitation and immunofluorescence. The study is accessible on our Zenodo community (<a href="https://doi.org/10.5281/zenodo.11582780">https://doi.org/10.5281/zenodo.11582780</a>) and serves as a research tool to facilitate reproducible and reliable Huntingtin resarch.</em></p> <p><em>The Dataset is in the format of a zip file. Once downloaded, please expand the zip file to access the folders containing the underlying data for Western blot (Wb), immunoprecipitation (IP) and immunofluorescence (IF). </em></p>
Dataset for the stimulator of interferon genes protein (STING1) antibody screening study
<p><strong>This antibody characterization dataset is related to the F1000 research article openly available at F1000Research.</strong></p> <p><em>This dataset contains the following underlying raw data for a study which characterized sixteen antibodies for the stimulator of interferon genes protein (STING1) in western blot, immunoprecipitation and immunofluorescence. The corresponding study is accessible on the YCharOS community on Zenodo (<a href="https://doi.org/10.5281/zenodo.11582350">https://doi.org/10.5281/zenodo.11582350</a>).</em></p> <p><em>The Dataset is in the format of a zip file. Once downloaded, please expand the zip file to access the folders containing the underlying data for Western blot (Wb), immunoprecipitation (IP) and immunofluorescence (IF).</em></p>
Dataset for the Fc receptor gamma-chain (FCER1G) antibody screening study
<p>This dataset contains the following underlying raw data for a study which characterized seven antibodies for the Fc receptor gamma chain (FCER1G) in western blot and immunoprecipitation. The corresponding study is openly accessible on the YCharOS community within Zenodo (DOI: 10.5281/zenodo.10845536).</p>
Supplementary material: Efficient in vivo screening method for the identification of C4 photosynthesis inhibitors based on cell suspensions of the single-cell C4 plant Bienertia sinuspersici
<p>Data described in Minges et al. (2019) Efficient <em>in vivo</em> screening method for the identification of C<sub>4</sub> photosynthesis inhibitors based on cell suspensions of the single-cell C<sub>4</sub> plant <em>Bienertia sinuspersici</em>. doi: <a href="https://doi.org/10.3389/fpls.2019.01350">10.3389/fpls.2019.01350</a></p> <p> </p>
Dataset for the CSNK1A1 antibody screening study
<p><strong>This antibody characterization dataset is related to the F1000 research article openly available at F1000Research.</strong></p> <p><em>This Dataset contains the following underlying data for a study which evaluated ten CSNK1A1 antibodies by western blot, immunoprecipitation and immunofluorescence using a knockdown cell line as an isogenic control. The original study is also available on the Zenodo YCharOS community (<a href="https://doi.org/10.5281/zenodo.11618594">https://doi.org/10.5281/zenodo.11618594</a>).</em></p> <p><em>The Dataset is in the format of a zip file. Once downloaded, please expand the zip file to access the folders containing the underlying data for Western blot (Wb), immunoprecipitation (IP) and immunofluorescence (IF).</em></p>
Dataset for the Rab10 antibody screening study
<p><strong>This antibody characterization dataset is related to the F1000 research article openly available at F1000Research.</strong></p> <p>This Dataset contains the following underlying data for a study which evaluated eight Rab10 antibodies by western blot, immunoprecipitation and immunofluorescence using a knockdown cell line as an isogenic control. The original study is also available on the Zenodo YCharOS community (<a href="https://doi.org/10.5281/zenodo.13684961">https://doi.org/10.5281/zenodo.13684961</a>).</p> <p><em>The Dataset is in the format of a zip file. Once downloaded, please expand the zip file to access the folders containing the underlying data for Western blot (Wb), immunoprecipitation (IP) and immunofluorescence (IF).</em></p>
S69 | LUXPEST | Pesticide Screening List for Luxembourg
<p>This is the collection associated with list S69 LUXPEST Pesticide Screening List for Luxembourg on the NORMAN Suspect List Exchange.</p> <p><a href="https://www.norman-network.com/nds/SLE/">https://www.norman-network.com/nds/SLE/</a></p> <p>A pesticide screening list for Luxembourg, compiled from multiple sources by Jessy Krier, uni.lu. Dataset DOI: 10.5281/zenodo.3862688.</p> <p>NOTE: the presence of pesticides on this list means that they are potentially relevant for Luxembourg and surrounding regions, but does not imply that they have been detected in Luxembourg. This list has been compiled to enable the efficient screening of data using the background knowledge contained within this list.</p> <p>The sources used were:</p> <p>Classification links & Authorization in Luxembourg</p> <p>https://ec.europa.eu/food/plant/pesticides/eu-pesticides-database/public/?event=activesubstance.selection&language=EN</p> <p>https://sitem.herts.ac.uk/aeru/bpdb/search.htm</p> <p>https://sitem.herts.ac.uk/aeru/ppdb/en/search.htm<br> <br> Origin:</p> <p>ASTA: https://saturn.etat.lu/tapes/tapes_de_lst_pdt.jsp?sel=_</p> <p>SWISSPEST16: https://comptox.epa.gov/dashboard/chemical_lists/swisspest</p> <p>Structure mapping: CompTox Batch Search with CID mapping via PubChem; InChIs were generated from SMILES by OpenBabel. MS_READY SMILES were used for mass spectral screening; parent forms were used for structural information and to map classification content.</p> <p>Update 29/7/2021: TP permission information updated.<br> </p>
NON-ANESTHESIOLOGIST ADMINISTERED PROPOFOL SEDATION IN SCREENING COLONOSCOPY
<p> </p> <p>These data came from a. prospective cohort study about cardiorespiratory complications in colorectal cancer screening colonoscopy, comparing two sedation schemes: traditional sedation with fentanyl and midazolam, versus combined Propofol sedation administered by non-anesthesiologists. These screening colonoscopies were performed between 2018 and 2019. We used the ASA and Ramsay scales to evaluate comorbidities and sedation levels. Cardiopulmonary adverse events were defined as: systolic blood pressure<90 mmHg, oxygen saturation <90% or disrrythmia lasting for more than 60 seconds..We recorded the management and outcomes of all these unplanned events. Other data as age, gender and body mass index were recorded as well., We have stored our data as a csv fyle. </p> <p> </p>
Supplemental data for "Computational screening of chemically active metal center in coordinated dipyridyl tetrazine network"
<p>Atomic coordinates of structures used in N. Ud Din, D. Le, T. S. Rahman "Computational screening of chemically active metal center in coordinated dipyridyl tetrazine network", J. Phys.: Condens. Matter .(2023). DOI: 10.1088/1361-648X/acb8f3</p>
Genome-wide screen reveals Rab12 GTPase as a critical activator of pathogenic LRRK2 kinase
<p>Primary data associated with the figure 1 of the manuscript "<strong>Genome wide screen reveals Rab12 GTPase as a critical activator of pathogenic LRRK2 kinase" </strong>(Herschel S. Dhekne, Francesca Tonelli, Wondwossen M. Yeshaw, Claire Y. Chiang, Charles Limouse, Ebsy Jaimon, Elena Purlyte, Dario Alessi, and Suzanne Pfeffer). </p> <p>These include </p> <p>- data (annotated .tiff exports) from Metamorph acquired spinning disk confocal microscope</p> <p>- sequencing data as fastq files .gz files from Hiseq or Miseq next generation sequencing, </p> <p>- graphs made using GraphPad Prism (.pzf files).</p> <p>- flow cytometry .fcs files and workspace files</p> <p>- <a href="https://zenodo.org/api/files/de4d1da1-785a-4f55-a542-876647a2a5ad/Figure%201-%20file%20names%20legend.xlsx">Figure 1- file names legend.xlsx</a> excel sheet explaining the details</p>
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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.