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.
2,481
datasets available to search
ShareScore release 0.7.1
Dataset results
2,481 results for “zebrafish”
Loss of alpha Ba-crystallin, but not alpha A-crystallin, increases age-related cataract in the zebrafish lens
<p>The vertebrate eye lens is an unusual organ in that most of its cells lack nuclei and the ability to replace aging protein. The small heat shock protein α-crystallins evolved to become key components of this lens, possibly because of their ability to prevent aggregation of aging protein that would otherwise lead to lens opacity. Most vertebrates express two α-crystallins, αA- and αB-crystallin, and mutations in each are linked to human cataract. In a mouse knockout model, only the loss of αA-crystallin led to early-stage lens cataract. We have used the zebrafish as a model system to investigate the role of α-crystallins during lens development. Interestingly, while zebrafish express one lens-specific αA-crystallin gene (<em>cryaa</em>), they express two αB-crystallin genes, with one evolving lens specificity (<em>cryaba</em>) and the other retaining the broad expression of its mammalian ortholog (<em>cryabb</em>). In this study, we used individual mutant zebrafish lines for all three α-crystallin genes to determine the impact of their loss on age-related cataract. Surprisingly, unlike mouse knockout models, we found that the loss of the αBa-crystallin gene <em>cryaba</em> led to an increase in lens opacity compared to <em>cryaa</em> null fish at 24 months of age. Loss of αA-crystallin did not increase the prevalence of cataract. We also used single-cell RNA-Seq and RT-qPCR data to show a shift in the lens expression of zebrafish α-crystallins between 5 and 10 days post fertilization (dpf), with 5 and 6 dpf lenses expressing <em>cryaa</em> almost exclusively, and expression of <em>cryaba</em> and <em>cryabb</em> becoming more prominent after 10 dpf. These data show that <em>cryaa</em> is the primary α-crystallin during early lens development, while the protective role for <em>cryaba</em> becomes more important during lens aging. This study is the first to quantify cataract prevalence in wild-type aging zebrafish, showing that lens opacities develop in approximately 25% of fish by 18 months of age. None of the three α-crystallin mutants showed a compensatory increase in the expression of the remaining two crystallins, or in the abundant βB1-crystallin. Overall, these findings indicate an ontogenetic shift in the functional importance of individual α-crystallins during zebrafish lens development. Our finding that the lens-specific zebrafish αBa-crystallin plays the leading role in preventing age-related cataract adds a new twist to our understanding of vertebrate lens evolution.</p>
Dataset for Uncovering multiscale structure in the variability of larval zebrafish navigation
<p>Datasets needed for recreating the figures from the paper "Uncovering multiscale structure in the variability of larval zebrafish navigation"</p>
Annotated and processed 3D confocal microscopy images of dorsal aorta in wild-type and Endoglin-deficient zebrafish embryos at 48 hpf and 72 hpf
<p>This repository contains the original 3D confocal microscopy images that were used for the analysis of vessel geometry and endothelial cell morphology in the dorsal aorta of wild-type and Endoglin-deficient zebrafish embryos at 48 hours post fertilization (hpf) and 72 hpf in the article <a href="https://www.biorxiv.org/content/10.1101/2024.02.19.580931">Novel mathematical approach to accurately quantify 3D endothelial cell morphology and vessel geometry based on fluorescently marked endothelial cell contours: Application to the dorsal aorta of wild-type and Endoglin-deficient zebrafish embryos</a>. In this article, we developed a novel mathematical approach that allows to consistently estimate 3D vessel geometry and endothelial cell surface morphology using only information from endothelial cell contours. For the article's analysis, endothelial cell contours were manually annotated on Pecam1-EGFP-labeled cell junctions. Furthermore, dorsal aorta cross-sections were outlined on Dextran Texas Red-perfused vessel lumens. Further details are provided in the article's Materials and methods section.</p> <p>This repository contains 14 images of 7 wild-type embryos, each imaged at 48hpf and 72hpf. Furthermore, 12 images of 6 Endoglin-deficient embryos, each imaged at 48hpf and 72hpf are included. These combined files (called "analysis data" in the article) are stored in "eng_wt_data.zip". Secondly, images of 2 wild-types at 72hpf with repeated cell contour annotation and outlined vessel lumens (called "validation data" in the article) are located in "wt_angiogram_data.zip". The provided files are stored in Imaris format and can be inspected using the free <a href="https://imaris.oxinst.com/imaris-viewer">Imaris Viewer software</a>.</p> <p>To allow inspection of the endothelial cell contours that we manually annotated for the article's analysis and compare them against the intermediate results of our novel mathematical approach, i.e., contour enrichments by neighboring cells, contour smoothing splines and their projections onto the estimated vessel surfaces, we imported these contours into the Imaris files. Note that the contours' coordinates in these files are slightly less precise than in our article's analysis and thus are intended for visual inspection. To exactly reproduce the results in our article, refer to the files in <a href="https://doi.org/10.5281/zenodo.10549101">our other Zenodo repository</a>.</p>
Gene biomarkers for the assessment of thyroid-disrupting activity in zebrafish embryos
<p>We have conducted an exposure study on zebrafish embryos using thyroidal active compounds. Based on OECD guideline 236, freshly fertilized zebrafish embryos were exposed to two sublethal concentrations of triiodothyronine (T3), 6-Propyl-2-thiouracil (6-PTU), methimazole (MMI) and iopanoic acid (IOP) until 96 hours post fertilization. RNA was extracted and sequenced to identify thyroid-related gene expression patterns. .</p> <p>The uploaded data archive consists of three major data types:<br>1. MultiQC reports from raw RNA-Seq read processing and QC<br>2. Result tables from differential gene expression analysis (DGEA) with DESeq2 (apeglm shrunk results indicated by "reslfs")<br>3. Result tables from Overrespresentation Analysis (ORA) with clusterProfiler</p> <p>Gene count normalization and DGEA was conducted with DESeq2 (<a href="https://genomebiology.biomedcentral.com/articles/10.1186/s13059-014-0550-8">Love et al., 2014</a>, DOI 10.1186/s13059-014-0550-8). Three biological replicates per condition, exposure treatments were compared with respect to the control group in a pairwise fashion, applying Wald’s t-test. P values were corrected for multiple testing with independent hypothesis weighting (IHW) (<a href="https://www.nature.com/articles/nmeth.3885">Ignatiadis et al., 2016</a>, DOI 10.1038/nmeth.3885 ) after Benjamini-Hochberg (BH). To improve the signal to statistical noise ratio, the obtained log<sub>2</sub>-fold change (lfc) values were shrunk with the apeglm method described by Zhu and colleagues (<a href="https://academic.oup.com/bioinformatics/article/35/12/2084/5159452?login=true">2019</a>, DOI 10.1093/bioinformatics/bty895 ) before DGEA result tables were subjected to ORA via clusterProfiler (<a href="https://www.liebertpub.com/doi/10.1089/omi.2011.0118">Yu et al., 2012</a>, DOI 10.1089/omi.2011.0118).</p> <p>The ArrayExpress accession numbers E-MTAB-14185 (IOP), E-MTAB-14184 (MMI), E-MTAB-14183 (T3) and E-MTAB-9054 (6-PTU), provide access to the raw and DESeq2 normalized gene count matrices upon which these analysis were performed. Genes were annotated through the biomaRt package (<a href="https://www.nature.com/articles/nprot.2009.97.pdf?origin=ppub">Durinck et al., 2009</a>, DOI 10.1038/nprot.2009.97 ) in R (<a href="https://www.r-project.org/">R Core Team 2021</a>).</p>
One-cell-stage to 21-somite-stage development of a zebrafish embryo
<p>These videos show the development of a zebrafish embryo from one-cell-stage to 21-somite-stage. Unedited videos, as well as a sped-up version are available. The sped-up version includes text indicating the developmental stages, as well as how many hours post fertilization each stage occurs at a temperature of 28.5°C.</p> <p>Videos were recorded and edited by Mona Wellhäusser and Timo Schreiber in the research group headed by Lennart Hilbert at the Institute of Biological and Chemical Systems, Karlsruhe Institute of Technology. Videos were acquired using an Olympus SZX7 zoom stereo transmitted light microscope, equipped with an Olympus SZX2-ILLTQ base, an Olympus DF Plapo 1X-4 stereo objective, as well as an Olympus EP50 camera.</p> <p>The imaging dish was constructed from a 35 mm glass bottom dish glued into the middle of a 90 mm Petri dish using clear nail polish. Fertilized zebrafish eggs were placed into the glass bottom dish, the imaging dish was filled to the brim with E3 medium (5 mM NaCl, 0.17 mM KCl, 0.33 mM CaCl2, 0.33 mM MgSO4), then sealed with an upside-down Petri dish lid for recording. 'Microscopy_Setup.png' illustrates the microscopy dish construction (illustration created in biorender.com).</p>
Dynamic interplay of cNHEJ and MMEJ pathways of DNA double-strand break repair during embryonic development in zebrafish.
<p><span>Fastq sequences from zebrafish embryos corresponding to 9 amplicons sequenced by </span><span>Illumina MiSeq. DNA sample were obtained from non-treated wildtype controls (ctrl) or from wildtype (WT), polq mutants, lig3 mutant or lig4 mutant injected with Cas9 protein and a pool of 5 or 4 different sgRNA (numbered from 1#1 to 5#2). Each target site corresponds to one amplicon. </span></p>
Confocal imaging raw data files of autophagy analysis in optn and p62 zebrafish mutants during Mycobacterium marinum infection
<p>Association of fluorescent Mycobacterium marinum bacteria with Ubiquitin immunolabelling and GFP-Lc3 signal in zebrafish larvae carrying mutations in the selective autophagy receptors optnineurin and p62. Data deposited are Leica LIF files belonging bioRxiv 415463; doi: https://doi.org/10.1101/415463</p>
Zebrafish Phenotype Ontology
<p>Current release of Zebrafish Phenotype Ontology</p>
Zebrafish shoal dataset
<p>Data, figures and videos about zebrafish (<em>Danio rerio</em>) shoal experiments where different population sizes (2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 individuals) and environmental conditions (0, 1, 2 floating objects) were investigated.</p> <p>This dataset is attached to the PhD thesis: "Influence de la population et de l'environnement sur la dynamique en banc du poisson-zèbre (<em>Danio rerio</em>): expériences et développement d'outils d'analyse", Bette S. (2019), Université libre de Bruxelles </p>
Zebrafish behavioral profiling identifies ligands, targets, and neurons related to sedation and paradoxical excitation
<p>Anesthetics are generally associated with sedation, but some anesthetics can also increase brain and motor activity — a phenomenon known as paradoxical excitation. Previous studies have identified GABAA receptors as the primary targets of most anesthetic drugs, but how these compounds produce paradoxical excitation is poorly understood. To identify and understand such compounds, we applied a behavior-based drug profiling approach. Here, we show that a subset of central nervous system depressants cause paradoxical excitation in zebrafish. Using this behavior as a readout, we screened thousands of compounds and identified dozens of hits that caused paradoxical excitation. Many hit compounds modulated human GABAA receptors, while others appeared to modulate different neuronal targets, including the human serotonin-6 receptor. Ligands at these receptors generally decreased neuronal activity, but paradoxically increased activity in the caudal hindbrain. Together, these studies identify ligands, targets, and neurons affecting sedation and paradoxical excitation in vivo in zebrafish.</p>
Contributions of mirror-image hair cell orientation to mouse otolith organ and zebrafish neuromast function
<p>Dataset for Ono et al., 2024.<br>Contains all source data from the Tarchini laboratory, including illustrative images and raw data for quantification, as well as the data file containing statistical analysis. It also contains the data file produced by the Cullen laboratory reporting behavioral data. </p>
Data from: The laboratory domestication of zebrafish: from diverse populations to inbred substrains
<p>We know from human genetic studies that practically all aspects of biology are strongly influenced by the genetic background, as reflected in the advent of 'personalized medicine'. Yet, with few exceptions, this is not taken into account when using laboratory populations as animal model systems for research in these fields. Laboratory strains of zebrafish (Danio rerio) are widely used for research in vertebrate developmental biology, behaviour and physiology, for modelling diseases, and for testing pharmaceutic compounds in vivo. However, all of these strains are derived from artificial bottleneck events and therefore are likely to represent only a fraction of the genetic diversity present within the species.</p> <p>Here we use Restriction site-Associated DNA sequencing (RAD-seq) to genetically characterize wild populations of zebrafish from India, Nepal and Bangladesh, and to compare them to previously published data on four common laboratory strains. We measured nucleotide diversity, heterozygosity and allele frequency spectra, and find that wild zebrafish are much more diverse than laboratory strains. Further, in wild zebrafish there is a clear signal of GC-biased gene conversion that is missing in laboratory strains. We also find that zebrafish populations in Nepal and Bangladesh are most distinct from all other strains studied, making them an attractive subject for future studies of zebrafish population genetics and molecular ecology. Finally, isolates of the same strains kept in different laboratories show a pattern of ongoing differentiation into genetically distinct substrains. Together, our findings broaden the basis for future genetic, physiological, pharmaceutic and evolutionary studies in Danio rerio.</p>
Phenotypic architecture of sociality and its associated genetic polymorphisms in zebrafish
<p>Sociality is often seen as a single phenotypic trait, but it relies on motivational and cognitive components implemented by specific causal mechanisms. Hence, these components may have evolved independently, or may have been linked by phenotypic correlations driven by a shared selective pressure for increased social competence. Furthermore, these components may be domain-specific or of general domain across social and non-social contexts. Here we have characterized the phenotypic architecture of sociality in zebrafish, which has been increasingly used as a model organism in social neuroscience. For this purpose, we have behaviorally phenotyped zebrafish from different wild type lines in four tests: social tendency, social and non-social recognition, and open-field test. Our results indicate that: (1) sociality has two main components that are independent from each other (social tendency and social recognition), hence not supporting the occurrence of a sociality syndrome; (2) both social traits are phenotypically linked to non-social traits (non-social exploration and non-social memory, respectively), forming two general behavioral modules, general inspection and general recognition, and suggesting that sociality traits have been co-opted from general-domain motivational and cognitive traits. Moreover, the study of the association between genetic polymorphisms (i.e. single nucleotide polymorphisms, SNPs) and each behavioral module further supports this view, since several SNPs from a list of candidate "social" genes, are statistically associated with the general inspection (motivational), but not with a general recognition (cognitive), behavioral module. The SNPs associated with general inspection are widespread across different chromosomes and include neurotransmitters, neuromodulators, and synaptic plasticity genes, suggesting that this behavioral module is regulated by multiple genes, each of them with small effects. Together, these results support the occurrence of general domain motivational and cognitive behavioral modules in zebrafish, which have been co-opted for the social domain.</p>
Thermal modulation of Zebrafish exploratory statistics reveals constraints on individual behavioral variability
<p><span><strong>Background</strong>: </span>Variability is a hallmark of animal behavior. It contributes to survival by endowing individuals and populations with the capacity to adapt to ever-changing environmental conditions. Intra-individual variability is thought to reflect both endogenous and exogenous modulations of the neural dynamics of the central nervous system. However, how variability is internally regulated and modulated by external cues remains elusive. Here we address this question by analyzing the statistics of spontaneous exploration of freely swimming zebrafish larvae, and by probing how these locomotor patterns are impacted when changing the water temperatures within an ethologically relevant range.<br> <br> <span><strong>Results</strong>: </span>We show that, for this simple animal model, five short-term kinematic parameters - interbout interval, turn amplitude, travelled distance, turn probability and orientational flipping rate - together control the long-term exploratory dynamics. We establish that the bath temperature consistently impacts the means of these parameters, but leave their pairwise covariance unchanged. These results indicate that the temperature merely controls the sampling statistics within a well-defined kinematic space delineated by this robust statistical structure. At a given temperature, individual animals explore the behavioral space over a timescale of tens of minutes, suggestive of a slow internal state modulation that could be externally biased through the bath temperature. By combining these various observations into a minimal stochastic model of navigation, we show that this thermal modulation of locomotor kinematics results in a thermophobic behavior, complementing direct gradient-sensing mechanisms.<br> <br> <span><strong>Conclusions</strong>: </span>This study establishes the existence of a well-defined locomotor space accessible to zebrafish larvae during spontaneous exploration, and quantifies self-generated modulation of locomotor patterns. Intra-individual variability reflects a slow diffusive-like probing of this space by the animal. The bath temperature in turn restricts the sampling statistics to sub-regions, endowing the animal with basic thermophobicity. This study suggests that in Zebrafish, as well as in other ectothermic animals, ambient temperature could be used to efficiently manipulate internal states in a simple and ethological way.</p>
Microscopy data: interaction of the gene ripply1 with RNA polymerase II clusters during early zebrafish embryo development
<p>Microscopy image data containing fluorescently labeled gene loci, recruited RNA polymerase II, and elongating RNA polymerase II.</p> <p>This data set is for the gene <em>ripply1</em> and is obtained from fixed zebrafish embryos, collected at the developmental stages oblong, sphere, dome, 30% epiboly, and 50% epiboly (indicated in the file names). Data were recorded using an instant-SIM microscope (iSIM, VisiTech UK) with a 100X TIRF oil immersion objective (Nikon, NA 1.49, CFI SR HP Apo TIRF 100XAC Oil). Two independent experiments were performed (IF1, IF2 in the file name), for each experiment, two samples were prepared per stage and experiment (001, 002 in the file name).</p> <p>The image data are in the ND2 format (Nikon proprietary) and can be imported using the BioFormats importer (Open Microscopy Environment).</p>
Microscopy data: interaction of the gene klf2b with RNA polymerase II clusters during early zebrafish embryo development
<p>Microscopy image data containing fluorescently labeled gene loci, recruited RNA polymerase II, and elongating RNA polymerase II.</p> <p>This data set is for the gene <em>klf2b</em> and is obtained from fixed zebrafish embryos, collected at the developmental stages oblong, sphere, dome, 30% epiboly, and 50% epiboly (indicated in the file names). Data were recorded using an instant-SIM microscope (iSIM, VisiTech UK) with a 100X TIRF oil immersion objective (Nikon, NA 1.49, CFI SR HP Apo TIRF 100XAC Oil). Two independent experiments were performed (IF1, IF2 in the file name), for each experiment, one or two samples were prepared per stage and experiment (001, 002 in the file name).</p> <p>The image data are in the ND2 format (Nikon proprietary) and can be imported using the BioFormats importer (Open Microscopy Environment).</p>
Microscopy data: interaction of the gene foxd5 with RNA polymerase II clusters during early zebrafish embryo development
<p>Microscopy image data containing fluorescently labeled gene loci, recruited RNA polymerase II, and elongating RNA polymerase II.</p> <p>This data set is for the gene <em>foxd5</em> and is obtained from fixed zebrafish embryos, collected at the developmental stages oblong, sphere, dome, 30% epiboly, and 50% epiboly (indicated in the file names). Data were recorded using an instant-SIM microscope (iSIM, VisiTech UK) with a 100X TIRF oil immersion objective (Nikon, NA 1.49, CFI SR HP Apo TIRF 100XAC Oil). Two independent experiments were performed (IF1, IF2 in the file name), for each experiment, two or three samples were prepared per stage and experiment (001, 002 in the file name).</p> <p>The image data are in the ND2 format (Nikon proprietary) and can be imported using the BioFormats importer (Open Microscopy Environment).</p>
Microscopy data: interaction of the gene gadd45ga with RNA polymerase II clusters during early zebrafish embryo development
<p>Microscopy image data containing fluorescently labeled gene loci, recruited RNA polymerase II, and elongating RNA polymerase II.</p> <p>This data set is for the gene <em>gadd45ga</em> and is obtained from fixed zebrafish embryos, collected at the developmental stages oblong, sphere, dome, 30% epiboly, and 50% epiboly (indicated in the file names). Data were recorded using an instant-SIM microscope (iSIM, VisiTech UK) with a 100X TIRF oil immersion objective (Nikon, NA 1.49, CFI SR HP Apo TIRF 100XAC Oil). Two independent experiments were performed (IF1, IF2 in the file name), for each experiment, two samples were prepared per stage and experiment (001, 002 in the file name).</p> <p>The image data are in the ND2 format (Nikon proprietary) and can be imported using the BioFormats importer (Open Microscopy Environment).</p>
Microscopy data: interaction of the gene drll2 with RNA polymerase II clusters during early zebrafish embryo development
<p>Microscopy image data containing fluorescently labeled gene loci, recruited RNA polymerase II, and elongating RNA polymerase II.</p> <p>This data set is for the gene <em>drll2</em> and is obtained from fixed zebrafish embryos, collected at the developmental stages oblong, sphere, dome, 30% epiboly, and 50% epiboly (indicated in the file names). Data were recorded using an instant-SIM microscope (iSIM, VisiTech UK) with a 100X TIRF oil immersion objective (Nikon, NA 1.49, CFI SR HP Apo TIRF 100XAC Oil). Two independent experiments were performed (IF1, IF2 in the file name), for each experiment, two samples were prepared per stage and experiment (001, 002 in the file name).</p> <p>The image data are in the ND2 format (Nikon proprietary) and can be imported using the BioFormats importer (Open Microscopy Environment).</p>
Microscopy data: interaction of the gene iscub with RNA polymerase II clusters during early zebrafish embryo development
<p>Microscopy image data containing fluorescently labeled gene loci, recruited RNA polymerase II, and elongating RNA polymerase II.</p> <p>This data set is for the gene <em>iscub</em> and is obtained from fixed zebrafish embryos, collected at the developmental stages oblong, sphere, dome, 30% epiboly, and 50% epiboly (indicated in the file names). Data were recorded using an instant-SIM microscope (iSIM, VisiTech UK) with a 100X TIRF oil immersion objective (Nikon, NA 1.49, CFI SR HP Apo TIRF 100XAC Oil). Two independent experiments were performed (IF1, IF2 in the file name), for each experiment, two samples were prepared per stage and experiment (001, 002 in the file name).</p> <p>The image data are in the ND2 format (Nikon proprietary) and can be imported using the BioFormats importer (Open Microscopy Environment).</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.