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”
Asymmetric mechanotransduction by hair cells of the zebrafish lateral line (Part 1/2)
Open the record for dataset details and reuse information.
Whole-brain mapping in adult zebrafish and identification of the functional brain network underlying the novel tank test
Open the record for dataset details and reuse information.
Data from: Contributions of mirror-image hair cell orientation to mouse otolith organ and zebrafish neuromast function: Part 1/2, Zebrafish data
Open the record for dataset details and reuse information.
Data from: Paternal starvation affects metabolic gene expression during zebrafish offspring development and life-long fitness
Open the record for dataset details and reuse information.
Data from: Kif1a and intact microtubules maintain synaptic-vesicle populations at ribbon synapses in zebrafish hair cells
Open the record for dataset details and reuse information.
Restoration of cone circuit functionality in the regenerating adult zebrafish retina
Open the record for dataset details and reuse information.
Fluorescent microscopy images of larval zebrafish of either TraNac, Nacre or WT background
<p><strong>The images show larval zebrafish at 5 days post-fertilization using fluorescent microscopy. The fish are either of Nacre, TraNac, or WT background. The fluorescent channels are either GFP, YFP or mCherry. </strong></p>
Data from: Zebrafish retinal ganglion cells asymmetrically encode spectral and temporal information across visual space
<p>In vertebrate vision, the tetrachromatic larval zebrafish permits non-invasive monitoring and manipulating of neural activity across the nervous system in vivo during ongoing behaviour. However, despite a perhaps unparalleled understanding of links between zebrafish brain circuits and visual behaviours, comparatively little is known about what their eyes send to the brain via retinal ganglion cells (RGCs). Major gaps in knowledge include any information on spectral coding, and information on potentially critical variations in RGC properties across the retinal surface corresponding with asymmetries in the statistics of natural visual space and behavioural demands. Here, we use in vivo two photon (2P) imaging during hyperspectral visual stimulation as well as photolabeling of RGCs to provide a functional and anatomical census of RGCs in larval zebrafish. We find that RGCs' functional and structural properties differ across the eye and include a notable population of UV-responsive On-sustained RGCs that are only found in the acute zone, likely to support visual prey capture of UV-bright zooplankton. Next, approximately half of RGCs display diverse forms of colour opponency including many that are driven by a pervasive and slow blue-Off system - far in excess of what would be required to satisfy traditional models of colour vision. In addition, most information on spectral contrast was intermixed with temporal information. Taken together, our results suggest that zebrafish RGCs send a diverse and highly regionalised time-colour code to the brain.</p>
I2K2020 Data for "Quantification of the 3D brain vasculature in zebrafish light sheet fluorescence microscopy data"
<p>Example data for the I2K2020 tutorial "Quantification of the 3D brain vasculature in zebrafish light sheet fluorescence microscopy data" (https://www.janelia.org/you-janelia/conferences/from-images-to-knowledge-with-imagej-friends/virtual-workshop-program)</p> <p>"Readme" file for data description included in folder.</p> <p><strong>Background:</strong> Zebrafish transgenic lines and light sheet fluorescence microscopy (LSFM) allow unrivalled insights into vascular development <em>in vivo</em> and 3D. The vascular architecture can be used to describe physiological status. However, assessment of the vasculature still relies on individual visual assessment rather than objective quantification. Thus, an image analysis pipeline is required to allow data assessment in 3D robustly and sensitively, while being able to handle LSFM data.</p> <p>Kugler et al have produced an image analysis workflow to quantify the zebrafish brain vasculature in 3D (https://www.biorxiv.org/content/10.1101/2020.08.06.239905v2).</p> <p><strong>Aim</strong>: In this tutorial we will use the analysis workflow produced by Kugler et al to examine and quantify the zebrafish brain vasculature in 3D with a hands-on practical (https://github.com/ElisabethKugler/ZFVascularQuantification).</p>
Data from: Are acute and acclimated thermal effects on metabolic rate modulated by cell size? A comparison between diploid and triploid zebrafish larvae
Being composed of small cells may carry energetic costs related to maintaining ionic gradients across cell membranes as well as benefits related to diffusive oxygen uptake. Here we test the hypothesis that these costs and benefits of cell size in ectotherms are temperature dependent. To study the consequences of cell size for whole-organism metabolic rate we compared diploid and triploid zebrafish larvae differing in cell size. A fully factorial design was applied combining three different rearing and test temperatures that allowed us to distinguish acute from acclimated thermal effects. Individual oxygen consumption rates of diploid and triploid larvae across declining levels of oxygen availability were measured. We found that both acute and acclimated thermal effects affected the metabolic response. In comparison to triploids, diploids responded more strongly to acute temperatures, especially when reared at the highest temperature. These observations support the hypothesis that animals composed of smaller cells (i.e. diploids) are less vulnerable to oxygen limitation in warm aquatic habitats. Furthermore, we found slightly improved hypoxia tolerance in diploids. By contrast, warm-reared triploids had higher metabolic rates when they were tested at acute cold temperature, suggesting that being composed of larger cells may provide metabolic advantages in the cold. We offer two mechanisms as a potential explanation of this result, related to homeoviscous adaptation of membrane function and the mitigation of developmental noise. Our results suggest that being composed of larger cells provides metabolic advantages in cold water, while being composed of smaller cells provides metabolic advantages in warm water.
Effects of trabectedin in the zebrafish Danio rerio: from cells to larvae
<p>These archives contain the original data set for the research article "Effects of trabectedin in the zebrafish Danio rerio: from cells to larvae"<br> </p> <p><strong>FACS_ZFL_cells_Trabectedin.rar</strong> </p> <p>Contains the original data regarding cells morphology evaluated by flow cytometry (Becton Dickinson FACScan).</p> <p><strong>Original data set_</strong></p> <p>This archive contains the original data tables for the research article "Effects of trabectedin in the zebrafish Danio rerio: from cells to larvae"</p> <p><strong>Original data set_Spreadsheet Trypan Blue test_in vitro</strong></p> <p>Cells viability on ZFL exposed to trabectedin measured by Trypan blue dye exclusion method</p> <p><strong>Original data set_Spreadsheet MTT test_in vitro</strong></p> <p>Cytotoxicity of trabectedin and doxorubicin (positive control) against ZFL cells as analyzed by the MTT assay</p> <p><strong>Original data set_Spreadsheet Survival_in vivo</strong></p> <p>Percentage of zebrafish embryos under trabectedin exposure</p> <p><strong>Original data set_Spreadsheet Abnormalities_in vivo</strong></p> <p>Percentage of abnormalities (somite alteration, pericardial edema, tail malformations, lack of equilibrium) of zebrafish embryos under trabectedin exposure</p> <p><strong>Original data set_Spreadsheet Swimming behavior_in vivo</strong></p> <p>Total distance covered and mean velocity by zebrafish larvae (120 hpf) after exposure to trabectedin</p> <p> </p> <p> </p>
Larval zebrafish H2B bulk spectral sensitivity
<p class="western">The encoding of light increments and decrements by separate On- and Off- systems is a fundamental ingredient of vision, which supports edge detection and makes efficient use of the limited dynamic range of visual neurons. Theory predicts that the neural representation of On- and Off-signals should be balanced, including across an animals' visible spectrum. Here we find that larval zebrafish violate this textbook expectation: in the zebrafish brain, UV-stimulation near exclusively gives On-responses, blue/green stimulation mostly Off-responses, and red-light alone elicits approximately balanced On- and Off-responses. We link these findings to zebrafish visual ecology, and suggest that the observed spectral tuning boosts the encoding of object "colourfulness", which correlates with object proximity in their underwater world.</p>
From behavior to circuit modeling of light-seeking navigation in zebrafish larvae
<p>Bridging brain-scale circuit dynamics and organism-scale behavior is a central challenge in neuroscience. It requires the concurrent development of minimal behavioral and neural circuit models that can quantitatively capture basic sensorimotor operations. Here we focus on light-seeking navigation in zebrafish larvae. Using a virtual reality assay, we first characterize how motor and visual stimulation sequences govern the selection of discrete swim-bout events that subserve the fish navigation in the presence of a distant light source. These mechanisms are combined into a comprehensive Markov-chain model of navigation that quantitatively predict the stationary distribution of the fish's body orientation under any given illumination profile. We then map this behavioral description onto a neuronal model of the ARTR, a small neural circuit involved in the orientation-selection of swim bouts. We demonstrate that this visually-biased decision-making circuit can similarly capture the statistics of both spontaneous and contrast-driven navigation.</p>
Paternal exposure to a common herbicide alters the behavior and serotonergic system of zebrafish offspring
<p>Increasingly, studies are revealing that endocrine disrupting chemicals (EDCs) can alter animal behavior. Early life exposure to EDCs may permanently alter phenotypes through to adulthood. In addition, the effects of EDCs may not be isolated to a single generation − offspring may indirectly be impacted, via non-genetic processes. <span class="fontstyle01"><span>Here, we analyzed the effects of paternal atrazine exposure on behavioral traits (distance moved, exploration, bottom-dwelling time, latency to enter the top zone, and interaction with a mirror) and whole-brain mRNA of genes involved in the serotonergic system regulation (</span></span><span class="fontstyle01"><span><i>slc6a4a</i></span></span><span class="fontstyle01"><span>, </span></span><span class="fontstyle01"><span><i>slc6a4b</i></span></span><span class="fontstyle01"><span>, </span></span><span class="fontstyle01"><span><i>htr1Aa</i></span></span><span class="fontstyle01"><span>, </span></span><span class="fontstyle01"><span><i>htr1B</i></span></span><span class="fontstyle01"><span>, </span></span><span class="fontstyle01"><span><i>htr2B</i></span></span><span class="fontstyle01"><span>) of zebrafish (</span></span><span class="fontstyle01"><span><i>Danio rerio</i></span></span><span class="fontstyle01"><span>). F0 male zebrafish were exposed to atrazine at 0.3, 3 or 30 part per billion (ppb) during early juvenile development, the behavior of F1 progeny was tested at adulthood, and the effect of 0.3 ppb atrazine treatment on mRNA transcription was quantified. Paternal exposure to atrazine significantly reduced interactions with a mirror (a proxy for aggression) and altered the latency to enter the top zone of a tank in unexposed F1 offspring. Bottom-dwelling time (a proxy for anxiety) also appeared to be somewhat affected, and activity (distance moved) was reduced in the context of aggression. </span></span><span class="fontstyle01"><span><i>slc6a4a </i></span></span><span class="fontstyle01"><span>and </span></span><span class="fontstyle01"><span><i>htr1Aa</i></span></span><span class="fontstyle01"><span> mRNA transcript levels were found to correlate positively with anxiety levels in controls, but we found that this relationship was disrupted in the 0.3 ppb atrazine treatment group. Overall, paternal atrazine exposure resulted in alterations across a variety of behavioral traits and showed signs of serotonergic system dysregulation, demonstrating intergenerational effects. Further research is needed to explore transgenerational effects on behavior and possible mechanisms underpinning behavioral effects. </span></span></p>
Differences in oxidative status explain variation in thermal acclimation capacity between individual zebrafish (Danio rerio)
1. Evolutionary theory predicts that the capacity to acclimate should be favoured in variable environments. However, perfect compensation for thermal variation is rare and the capacity for thermal acclimation can vary considerably between individuals within natural populations. This variation may be explained by costs associated with acclimation, but it is not clear what these costs are. 2. We tested the hypothesis that oxidative stress is a cost of acclimation that could explain the variation between individuals in acclimation capacity. We acclimated individual mosquitofish (Gambusia holbrooki, n = 416) to 18oC and 28oC sequentially, and determined swimming performance at each temperature to evaluate their acclimation capacity. Fish were then acclimated to either cold (18oC) or warm (28oC) conditions, and we increased antioxidant capacities of a subset of fish experimentally by administering N-acetyl cysteine (NAC). We measured H2O2 production, catalase antioxidant activities, and oxidative damage to proteins and membranes. 3. We show that there is significant variation in acclimation capacity between individuals, and that there is a trade-off between acclimation capacity and swimming performance in warm conditions. Mean swimming performance across both acclimation temperatures increased with increasing acclimation capacity, but the increase was small biologically. Hence, greater thermal plasticity (high acclimation capacity) resulted in only minor performance benefits across acclimation conditions. We verified this rather surprising result in replicate populations grown in outdoor mesocosms. 4. ROS production, antioxidant activities, and oxidative damage were higher in cold-acclimated fish, and particularly in those fish with low capacity for acclimation. However, experimentally increasing antioxidant capacities with NAC alleviated these changes to oxidative status, suggesting a causal relationship. Hence, oxidative stress may be a cost that constrains the capacity for acclimation. Together, the performance trade-off and oxidative cost indicate that phenotypic plasticity is not always advantageous in variable environments, and instead bet-hedging may be a more beneficial strategy, particularly in short-lived species.
Dense skeleton reconstructions of neurons in the larval zebrafish olfactory bulb
<p>Large-scale reconstructions of neuronal populations are critical for structural analyses of neuronal cell types and circuits. Dense reconstructions of neurons from image data require ultrastructural resolution throughout large volumes, which can be achieved by automated volumetric electron microscopy (EM) techniques. We used serial block face scanning EM (SBEM) and conductive sample embedding to acquire an image stack from an olfactory bulb (OB) of a zebrafish larva at a voxel resolution of 9.25 × 9.25 × 25 nm<sup>3</sup> (Wanner et al., 2016). Skeletons of 1,022 neurons, ~98% of all neurons in the OB, were reconstructed by manual tracing and efficient error correction procedures. An ergonomic software package, PyKNOSSOS, was created in Python for data browsing, neuron tracing, synapse annotation, and visualization. PyKNOSSOS is available for free download (https://github.com/adwanner/PyKNOSSOS). The reconstructions as provided for download here allow for detailed analyses of morphology, projections and subcellular features of different neuron types. The high density of reconstructions enables geometrical and topological analyses of the OB circuitry. Image data can be accessed and viewed through the neurodata web services (http://www.neurodata.io/wanner16). Raw data and reconstructions can be visualized in PyKNOSSOS.</p> <p> </p> <p>PyKNOSSOS: https://github.com/adwanner/PyKNOSSOS</p> <p>Wanner AA, Genoud C, Masudi T, Siksou L, Friedrich RW (2016) Dense EM-based reconstruction of the interglomerular projectome in the zebrafish olfactory bulb. Nat Neurosci 19:816-825.<br /> http://www.nature.com/neuro/journal/v19/n6/full/nn.4290.html</p>
Disrupted development of sensory systems and the cerebellum in a zebrafish ebf3a mutant
<p>Behavior and imaging data for the ebf3a mutant zebrafish line. Also, Supplementary Data S1, which contains additional RNA-seq analyses and code.</p>
Data for: Feeding frequency does not interact with BPA exposure to influence metabolism of behaviour in zebrafish (Danio rerio)
<p><span>Resource limitation can constrain energy (ATP) production, and thereby affect locomotion and behaviour such as exploration of novel environments and boldness. Consequently, ecological processes such as dispersal and interactions within and between species may be influenced by food availability. Energy metabolism, and behaviour are regulated by endocrine signaling, and may therefore be impacted by endocrine disrupting compounds (EDCs) such as bisphenol A (BPA) derived from plastic manufacture and pollution. It is important to determine the impacts of these novel environmental contexts to understand how human activity alters individual physiology and behaviour and thereby populations. Our aim was to determine whether BPA exposure interacts with feeding frequency to alter metabolism and behaviour. In a fully factorial experiment, we show that low feeding frequency reduced zebrafish (<em>Danio rerio</em>) mass, condition, resting metabolic rates, total distance moved and speed in a novel arena, as well as anxiety indicated by the number of times fish returned to a dark shelter. However, feeding frequency did not significantly affect maximal metabolic rates, aerobic scope, swimming performance, latency to leave a shelter, or metabolic enzyme activities (citrate synthase and lactate dehydrogenase). Natural or anthropogenic fluctuation in food resources can therefore impact energetics and movement of animals with repercussions for ecological processes such as dispersal. BPA exposure reduced LDH activity and body mass, but did not interact with feeding frequency. Hence, behaviour of adult fish is relatively insensitive to disruption by BPA. However, alteration of LDH activity by BPA could disrupt lactate metabolism and signalling and together with reduction in body mass could affect size-dependent reproductive output. BPA released by plastic manufacture and pollution can thereby impact conservation and management of natural resources. </span></p>
Using UV stimuli to evoke prey capture strikes in head-fixed zebrafish larvae
<p>Hunting in larval zebrafish begins with eye convergence and orienting turns, proceeds to approach swims, and ends with the strike, where larvae consume the prey. Here, we describe a protocol to present UV stimuli to zebrafish, which greatly increases the occurrence of hunting initiation and strikes. We also describe how we record and analyze strike behavior in head-fixed larvae. Our goals are to increase the robustness of prey capture, and to allow other labs to implement strike behavioural essay</p>
SI Movies for "Dynamics of dominance: maneuvers, contests, and assessment in the posture-scale movements of interacting zebrafish"
<p>This is a repository of the Supplementary Movies from the paper "Dynamics of dominance: maneuvers, contests, and assessment in the posture-scale movements of interacting zebrafish".</p><h3>SM1</h3><p><br>This movie is a visualization of the tracking pipeline output, namely the 3D bodypoint positions of the two zebrafish over time. In this animation, we show the 3D locations of the head (circle), pec (square) and tail (cross) bodypoints of the winner (red) and loser (blue) throughout an entire experiment, the same experiment shown in Fig3(A) of the paper. The movie is downsampled from the 100fps recordings to 25fps to reduce file size. (1hr 23min 29sec)</p><h3>Notes on SM2-6</h3><p>In these movies we show two panels. The left panel shows an animation of the contestant 3D bodypoint positions. The right panel shows the XZ camera view of the tank with the XZ image coordinates of bodypoints drawn over the fish. The movies run at 100fps and are all 2 minutes long. The movies are each centered at a different time during the FishTank20200130_153857 recording, with one minute before, and one minute after, the chosen centered point.</p><h3>SM2</h3><p>This video is centred at the frame identified as the start of the first fight bout.</p><h3>SM3</h3><p>This video is centered at the frame identified as the middle of the first fight bout.</p><h3>SM4</h3><p>This video is centered at the frame identified as the end of the first fight bout.</p><h3>SM5</h3><p>This video is centered at the frame identified as the start of the second fight bout.</p><h3>SM6</h3><p>This video is centered at the frame identified as the end of the second fight bout.</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.