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opencc-by-4.0Jun 2024View details →

One-cell-stage to 21-somite-stage development of a zebrafish embryo

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. 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. 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).

Microscopy data: interaction of the gene ripply1 with RNA polymerase II clusters during early zebrafish embryo development

Microscopy image data containing fluorescently labeled gene loci, recruited RNA polymerase II, and elongating RNA polymerase II. This data set is for the gene ripply1 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). The image data are in the ND2 format (Nikon proprietary) and can be imported using the BioFormats importer (Open Microscopy Environment).

Microscopy data: interaction of the gene klf2b with RNA polymerase II clusters during early zebrafish embryo development

Microscopy image data containing fluorescently labeled gene loci, recruited RNA polymerase II, and elongating RNA polymerase II. This data set is for the gene klf2b 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). The image data are in the ND2 format (Nikon proprietary) and can be imported using the BioFormats importer (Open Microscopy Environment).

Microscopy data: interaction of the gene foxd5 with RNA polymerase II clusters during early zebrafish embryo development

Microscopy image data containing fluorescently labeled gene loci, recruited RNA polymerase II, and elongating RNA polymerase II. This data set is for the gene foxd5 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). The image data are in the ND2 format (Nikon proprietary) and can be imported using the BioFormats importer (Open Microscopy Environment).

Microscopy data: interaction of the gene gadd45ga with RNA polymerase II clusters during early zebrafish embryo development

Microscopy image data containing fluorescently labeled gene loci, recruited RNA polymerase II, and elongating RNA polymerase II. This data set is for the gene gadd45ga 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). The image data are in the ND2 format (Nikon proprietary) and can be imported using the BioFormats importer (Open Microscopy Environment).

Microscopy data: interaction of the gene drll2 with RNA polymerase II clusters during early zebrafish embryo development

Microscopy image data containing fluorescently labeled gene loci, recruited RNA polymerase II, and elongating RNA polymerase II. This data set is for the gene drll2 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). The image data are in the ND2 format (Nikon proprietary) and can be imported using the BioFormats importer (Open Microscopy Environment).

Microscopy data: interaction of the gene iscub with RNA polymerase II clusters during early zebrafish embryo development

Microscopy image data containing fluorescently labeled gene loci, recruited RNA polymerase II, and elongating RNA polymerase II. This data set is for the gene iscub 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). The image data are in the ND2 format (Nikon proprietary) and can be imported using the BioFormats importer (Open Microscopy Environment).

opencc-by-4.0Jun 2023View details →

Crosstalk assessment for multi-colour immunofluorescence of Histone 3 and Polymerase II post-translational modifications in pluripotent zebrafish embryos

Microscopy images recorded to assess the extent of crosstalk from the detection channels of H3K27ac and recruited RNA polymerase II (Serine 5 phosphorylation of the C-terminal domain heptad repeat of subunit 1) to the detection channel of elongating RNA polymerase II (Serine 5 phosphorylation of the C-terminal domain heptad repeat of subunit 1). Sample preparation and image recording was carried out jointly by Süheyla Eroğlu-Kayikci, Elisa Kämmer, and Lennart Hilbert.

opencc-by-4.0Aug 2023View details →

TBT exposure dataset of the manuscript "Assessment of endocrine disruptors effects on zebrafish (Danio rerio) embryos by untargeted LC-HRMS metabolomic analysis"

Raw LC-HRMS data of the TBT exposure of zebrafish embryos (for more details see https://doi.org/10.1016/j.scitotenv.2018.03.369) The exposure protocol involved zebrafish embryos exposed in groups of 20 to various concentrations of chemical compounds, with five replicates per treatment. The concentrations ranged from the lowest observed effect concentrations (LOECs) to control levels. After exposure, embryos were collected, washed, frozen, and stored. Metabolites were extracted from individual embryo pools using methanol and methionine sulfone. The extraction process included vortexing, sonication, and centrifugation, followed by addition of water and chloroform. The aqueous fraction was dried and reconstituted using acetonitrile-water solution. Liquid chromatography coupled with high-resolution mass spectrometry (LC-HRMS) was used for analysis. Chromatographic separations were carried out on a hydrophilic interaction liquid chromatography (HILIC) column. Mass spectrometry was performed using an Orbitrap mass spectrometer with electrospray ionization in positive and negative modes. The mass spectra were acquired at high resolution, and fragmentation scans were used for metabolite identification. The overall process aimed to analyze the metabolomic profile of zebrafish embryos exposed to different chemical concentrations. Data files <blockquote> TBT ESI+ (tbt_pos.rar) - CDF files - QC (4 replicates) - Control (5 replicates) - TBT 3 nM (5 replicates) - TBT 10 nM (5 replicates) - TBT 30 nM (5 replicates) - TBT 100 nM (5 replicates) </blockquote>   <blockquote> TBT ESI- (tbt_neg.rar) - CDF files - QC (6 replicates) - Control (5 replicates) - TBT 3 nM (5 replicates) - TBT 10 nM (5 replicates) - TBT 30 nM (5 replicates) - TBT 100 nM (5 replicates) </blockquote>

dryad36/100

Raw Sanger sequences of the tyr fragment from crispant and control zebrafish embryos

Open the record for dataset details and reuse information.

publicDec 2022View details →

opencc-zeroAug 2020View details →

Vape flavorants dull sensory perception and cause hyperactivity in developing zebrafish embryos

E-cigarette use (vaping) during pregnancy has been increasing, and the potential exists for the developing brain in utero to be exposed to chemical constituents in the vape. Vapes come in over 7,000 unique flavors with and without nicotine, and while nicotine is a known neurotoxicant, the effects of vape flavoring alone, in the absence of nicotine, on brain function are not well understood. Here we performed a screen of vape aerosol extracts (VAEs) to determine the potential for prenatal neurotoxicity using the zebrafish embryo photomotor response (PMR) – a translational biosensor of neurobehavioral effects. We screened three commonly used aerosolized vape liquids (flavored and flavorless) either with or without nicotine. No neurobehavioral effects were detected in flavorless, nicotine-free VAEs, while the addition of nicotine to this VAE dulled sensory perception. Flavored nicotine-free VAEs also dulled sensory perception and caused hyperactivity in zebrafish embryos. The combination of flavor and nicotine produced largely additive effects. Flavored VAEs without nicotine had similar neuroactive potency as nicotine. Similar effects were also seen in embryos exposed to the pure flavoring compound, cinnamaldehyde. Together, using zebrafish PMR as a high throughput translational behavioral model for prenatal exposure, our results demonstrate that e-cigarette flavorants that we screened elicit neurobehavioral effects worthy of further investigation for long-term neurotoxic potential, and also have the potential to modulate nicotine impact on the developing brain.

Microscopy of RNA Polymerase II clusters in live zebrafish embryos

This data set contains raw image data and derived images illustrating clusters of RNA polymerase II as observed in zebrafish embryos. The clusters are labelled by fluorescently marked antibody fragments (Fab) that detect phosphorylation of the C-terminal roman of RNA polymerase II. Antibody fragments were provided by the laboratory of Hiroshi Kimura.

Observation of RNA polymerase clusters in a live zebrafish embryo

Data showing the distribution of RNA polymerase II with serine 5 phosphorylation in the C-terminal domain (CTD) of the subunit 1 (Pol II Ser5P) in a live zebrafish embryo. Images were acquired by instant-SIM microscopy, Pol II Ser5P was marked by fluorescently labeled antibody fragments (Fab) provided by the laboratory of Hiroshi Kimura, Tokyo Institute of Technology. Data were processed using FIJI.

Time-lapse recordings of RNA polymerase in a live zebrafish embryo

Raw data and derived data showing the distribution of RNA polymerase II with serine 5 phosphorylation in the C-terminal domain (CTD) of the subunit 1 (Pol II Ser5P) in a live zebrafish embryo. Images were acquired by instant-SIM microscopy, with a time step of 40 second between consecutive time points. Pol II Ser5P was marked by fluorescently labeled antibody fragments (Fab) provided by the laboratory of Hiroshi Kimura, Tokyo Institute of Technology. Data were processed using FIJI.

Effect of hexanediol treatment on clusters of RNA polymerase II in zebrafish embryo primary cell culture

This data set assesses changes in RNA polymerase II clusters upon treatment with 3% 1,6-hexanediol in zebrafish embryos. RNA polymerase was labeled by immunofluorescence, microscopy images were acquired by instant-SIM microscopy and analyzed using MatLab scripts and the bioformats importer. This data set contains the raw image data as well as all further analysis scripts.

Scripts and raw data for comparing 2D vs 3D image analysis of zebrafish embryo microscopic data

Raw data and MatLab scripts used for image analysis of RNA polymerase II with serine 5 phosphorylation in the C-terminal domain (CTD) of the subunit 1 (Pol II Ser5P) in a fixed zebrafish embryo, comparing a 2D vs 3D approach to segment out the Pol II Ser5P clusters. Pol II Ser5P was labeled by immunofluorescence, microscopy images were acquired by instant-SIM microscopy and analyzed using MatLab scripts and the bioformats importer.

opencc-zeroApr 2020View details →

In-plate toxicometabolomics of single zebrafish embryos

Toxicometabolomic studies involving zebrafish embryos have become increasingly popular for linking apical endpoints to biochemical perturbations as part of adverse outcome pathway determination. These experiments involve pooling embryos to generate sufficient biomass for metabolomic measurement, which adds both time and cost. To address this limitation, we developed a high-throughput toxicometabolomic assay involving single zebrafish embryos. Incubation, microscopy, embryo extraction, and instrumental metabolomic analysis were all performed in the same 96-well plate, following acquisition of conventional toxicological endpoints. The total time for the assay (including testing of 6 doses/n = 12 embryos per dose plus positive and negative controls, assessing conventional endpoints, instrumental analysis, data processing and multivariate statistics) is <14 days. Metabolomic perturbations at low dose were linked statistically to those observed at high dose and in the presence of an adverse effect, thereby contextualizing omic data amongst apical endpoints. Overall, this assay enables collection of high resolution metabolomic data in a high throughput manner, suitable for mode of action hypothesis generation in the context of pharmaceutical or toxicological screening.

opencc-zeroSep 2022View details →

Single-molecule tracking of Nodal and Lefty in live zebrafish embryos supports hindered diffusion model

The hindered diffusion model postulates that the movement of a signaling molecule through an embryo is affected by tissue geometry and binding-mediated hindrance, but these effects have not been directly demonstrated in vivo. Here, we visualize extracellular movement and binding of individual molecules of the activator-inhibitor signaling pair Nodal and Lefty in live developing zebrafish embryos using reflected light-sheet microscopy. We observe that diffusion coefficients of molecules are high in extracellular cavities, whereas mobility is reduced and bound fractions are high within cell-cell interfaces. Counterintuitively, molecules nevertheless accumulate in cavities, which we attribute to the geometry of the extracellular space by agent-based simulations. We further find that Nodal has a larger bound fraction than Lefty and shows a binding time of tens of seconds. Together, our measurements and simulations provide direct support for the hindered diffusion model and yield insights into the nanometer-to-micrometer-scale mechanisms that lead to macroscopic signal dispersal.

opencc-zeroOct 2022View details →

Wisenden zebrafish embryo early hatching

Plasticity in hatching time allows embryos to maximize fitness by balancing benefits and costs of remaining bound within the chorion against the benefits and costs of emerging as a free-swimming larva. In our first experiment, we exposed zebrafish (Danio rerio) embryos to either chemical cues from crushed embryos (simulating egg predation) or to blank water control. Embryos exposed to alarm cues hatched sooner with shorter body lengths and underdeveloped fins relative to larvae from the water treatment. Burst swimming speed was significantly slower for larvae that hatched from the alarm cue treatment. In a second 2 x 2 experiment, we exposed zebrafish embryos to either chemical alarm cues from conspecific embryos, mechanical disturbance (magnetic stir bar) to simulate a predator probing the substrate for developing embryos, both chemical and mechanical indicators of risk, or neither (control). We found similar effects in terms of earlier time to hatch at an earlier stage of development and poorer swimming performance of hatchling larvae. In the second experiment these effects occurred in response to mechanical disturbance with or without the presence of chemical alarm cues. Alarm cues alone produced no effects in the second experiment. Taken together, these data indicate that zebrafish embryos demonstrate a facultative tradeoff between risk of predation acting on two stages of their life history.