The general objective of the study was to determine modulation of gene expression by environmental factors with a special emphasis on bone formation. For this reason the specific period of treatment was chosen between 5-6 days post-fertilization (dpf) when bone formation and calcification are taking place. This experiment was designed as a new type of gravitational experiment which we like to call relative microgravity referring to the fact that the larvae first grow in hyper gravity for 5 days and are then returned to 1g normal gravity for 1 day. Zebrafish embryos were placed on a Large Diameter Centrifuge at 3 hpf brought to a gravitational force of 3 g until 5 dpf. Reference embryos were kept in parallel at 1g (Inc). At 5dpf one batch was left at 3g (3g) one batch was returned to 1g (3g>1g) while a third batch was returned to 1g but left on the axis of the centrifuge (Axe; 3g>Axe). The experiment was repeated 4 times each time with 4 batches of 60 larvae.

Multi-angle OCT data for 3D OCRT reconstruction of zebrafish larva

ZFIN serves as the zebrafish model organism database. It aims to: a) be the community database resource for the laboratory use of zebrafish, b) develop and support integrated zebrafish genetic, genomic and developmental information, c) maintain the definitive reference data sets of zebrafish research information, d) to link this information extensively to corresponding data in other model organism and human databases, e) facilitate the use of zebrafish as a model for human biology, and f) serve the needs of the research community.

This zebrafish motion dataset contains

Model organism database that serves as central repository and web-based resource for zebrafish genetic, genomic, phenotypic and developmental data. Data represented are derived from three primary sources: curation of zebrafish publications, individual research laboratories and collaborations with bioinformatics organizations. Data formats include text, images and graphical representations.Serves as primary community database resource for laboratory use of zebrafish. Developed and supports integrated zebrafish genetic, genomic, developmental and physiological information and link this information extensively to corresponding data in other model organism and human databases.

Zebrafish Market Outlook

In 2023, the global zebrafish market size is estimated to be valued at approximately USD 215 million, and it is anticipated to reach USD 462 million by 2032, driven by a robust Compound Annual Growth Rate (CAGR) of 8.8%. This impressive growth is primarily propelled by the increasing adoption of zebrafish in biomedical research and drug discovery, due to their genetic similarities to humans and the cost-effectiveness of zebrafish-based studies compared to traditional mammalian models.

One of the key growth factors in the zebrafish market is the rising demand for efficient and cost-effective models in drug discovery and toxicology testing. Zebrafish have gained traction in these fields due to their rapid development, transparent embryos, and the ease with which their genetic makeup can be manipulated. This has made them an invaluable resource for high-throughput screening in pharmaceutical research, significantly accelerating the drug development process while reducing costs. Moreover, advancements in zebrafish husbandry and genetic engineering techniques have further cemented their role as a versatile model organism in various scientific domains.

Another critical driver for market growth is the increasing prevalence of chronic diseases and the corresponding need for innovative therapeutic strategies. Zebrafish are extensively used in disease modeling for conditions such as cancer, cardiovascular diseases, and neurodegenerative disorders. Their genetic and physiological similarities to humans enable researchers to gain deep insights into disease mechanisms and explore potential treatment avenues. Additionally, the regenerative capabilities of zebrafish have sparked significant interest in regenerative medicine, providing a valuable platform for studying tissue regeneration and developing regenerative therapies.

The growing emphasis on personalized medicine and precision healthcare is also contributing to the expansion of the zebrafish market. Zebrafish offer a unique opportunity for personalized drug screening and toxicity testing, allowing for the identification of patient-specific therapeutic responses. This is particularly beneficial in the context of rare diseases and conditions where traditional models may fall short. The integration of zebrafish models into personalized healthcare paradigms is expected to drive further market growth as researchers and clinicians seek to tailor treatments to individual patient profiles, enhancing therapeutic efficacy and safety.

Regionally, North America holds a dominant position in the zebrafish market, driven by substantial investments in biomedical research and the presence of leading pharmaceutical and biotechnology companies. The region's well-established research infrastructure and favorable regulatory environment further support the adoption of zebrafish models. However, the Asia Pacific region is anticipated to exhibit the highest growth rate during the forecast period. This can be attributed to the increasing focus on research and development activities, expanding pharmaceutical industry, and rising government initiatives to promote scientific research in countries like China and India.

Product Type Analysis

The zebrafish market is segmented by product type into Live Zebrafish, Zebrafish Embryos, Zebrafish Larvae, and Zebrafish Adults. Live zebrafish represent a significant segment due to their widespread use in various research applications. They offer the advantage of being an intact organism that can be studied in real-time, making them highly valuable for understanding developmental processes, disease progression, and drug effects. Researchers can observe phenotypic changes and conduct longitudinal studies, which are critical for comprehensive biomedical research.

Zebrafish embryos also hold a prominent place in the market due to their transparency and rapid development. These characteristics make embryos ideal for high-throughput screening and genetic studies. Scientists can easily manipulate and observe genetic modifications, which aids in studying gene functions and interactions. The use of zebrafish embryos in toxicology testing is particularly notable, as it allows for the assessment of chemical toxicity and environmental pollutants in a cost-effective and ethical manner.

The segment of zebrafish larvae is gaining traction, especially in behavioral and neurological studies. Larvae are small, transparent, and exhibit a range of behaviors that can be quantitatively analyzed. This makes them suitable for studies related to neurodevelopmental

This dataset contains recordings of larval zebrafish behavior. The full details are described in the paper "A lexical approach for identifying behavioral action sequences".Â

The experiment investigates zebrafish larvae behavior in free swimming and aversive chemotaxis conditions. In each experiment, 12 larvae (7 dpf) are placed in 12 rectangular wells. Ten min-long videos were recorded at 160 Hz with an exposure time of 1 ms, and a pixel size of 70 µm using a ViewWorks camera (Basler acA2040-180km) controlled by the Hiris software (R&D Vision, Nogent sur Marne, http://www.rd-vision.com/r-d-vision-eng).

The fish are tracked using a custom-made software, Zebrazoom (https://zebrazoom.org/). The algorithm begins by locating all the wells and by extracting the background of the video. ZebraZoom first applies a series of actions to detect the animal in each well: i) contours of head and entire body are detected using active contours, ii) the center of the head is identified as the c...

This dataset contains raw data of gene expression levels, cell size, cell number, growth, development and swimming performance of diploid and triploid larval zebrafish, used for analyses and figures of the PLOS ONE paper: Triploidy in zebrafish larvae: effects on gene expression, cell size and cell number, growth, development and swimming performance. (2020) by van de Pol, Flik and Verberk. In this paper we investigated the use of triploid zebrafish as a model to study cell size consequences. Details about the experimental procedures can be found in the Materials and Methods section of the paper. We have also included the R scripts for data analyses in this dataset. A brief description of the data files and column descriptions can be found below.The data files include:- Gene_expression_hkgenes.csvColumns:gene: abbreviated name of housekeeping gene.ploidy: ploidy level of larvae.sample: number of sample; each sample contained 3 larvae.dpf: days post fertilisation; indicates the sampling time.expr: relative quantity of housekeeping genes normalised for the other five housekeeping genes.- qpcr_series.rR script for analysing gene expression data.- cellnumber.csvColumns:ploidy: ploidy level of larva.cell number: cell number calculated as the sum of cells in G1, G2 and G3 (6n or 9n) phase.sample: sample number; these are paired data.- cell_number_analysis.rR script for analysing cell numbers.- ratioG2G1.csvColumns:ploidy: ploidy level of larva.ratioG2G1: calculated as G2/G1*100.- ratio_g1g2.rR script for analysing G2/G1 ratios.- Cell_size.csvColumns:ploidy: ploidy levelarea: cell area in μm2vol: cell volume in μm3code: factor 1 = 3n, factor 0 = 2n.- cell_area.rR script for analysing cell area and cell volume.- devstages26.5ref.csvColumns:cycle: refers to the week/batch in which the larvae were sampled.id: identifier number of larvae.ploidy: ploidy level of larva.rt: rearing temperature in degrees Celsius.hpf: hours post fertilisation; indicates the sampling time (as factor).devst: developmental stage in which the larvae were categorised.devh: corresponding hours post fertilisation.ref: "real" hours post fertilisation (as integer).- development_data.rR script for analysing development rate.- length.csvColumns:ind: individual identifier.batch: refers to the week/batch in which the larvae were sampled.rearT: rearing temperature in degrees Celsius.Length: length in mm.ploidy: ploidy level of larva.- length_data.rR script for analysing length of diploid and triploid larval zebrafish.- Swimming_performance.csvColumns:rtemp: rearing temperature in degrees Celsius.mtemp: measuring temperature in degrees Celsius.individual: individual identifier.trial: swimming performance trial.rankstim: rank number of startle.speed: velocity measured in mm/s. note that for startle = 0, this represents the average spontaneous velocity over 19 seconds after the startle stimulus.lgspeed: 10 log of speed.startle: startle = 1 means a startle stimulus was presented. startle stimulus = 0 means there was no startle stimulus, representing inter-startle-interval.cs: cs = 1 means this larva received a cold shock to induce triploidy. cs = 0 means no cold shock was applied.ploidy: ploidy level of larva.responder: responder = 1 is defined as a larva that at least once showed a velocity higher than 15 mm/s. responder = 0 if a larva never showed a velocity higher than 15 mm/s.- daniovision_data.rR script for analysing swimming performance.- assessing_ploidy_levels.rR script for analyzing ploidy levels on .LMD files.- description data files.docxA description of all before mentioned data files.- Materials and methods.docxMaterials and methods section of the paper: Triploidy in zebrafish larvae: effects on gene expression, cell size and cell number, growth, development and swimming performance. (2020) by van de Pol, Flik and Verberk.

These are three datasets of videos and annotated frames of zebrafish larvae poses. The datasets are named "Main", "Benchmarking" and "Additional". The main dataset contains 1641 annotated frames, from 28 videos and their metadata. The benchmarking datasets are two sets of data. Finally, the additional dataset has 512 frames selected from 12 different videos. The annotations were done using DeepLabCut/napari annotator and are in the DLC project format.

['To reveal the potential mechanisms involved in the dysfunction of antiviral immune responses under simulated microgravity conditions, we investigated the transcriptional changes related to the status of innate immune responses by RNA-seq with poly I:C or mock PBS treatment under Normal gravity or simulated microgravity conditions. Our results indicate that the retinoic acid inducible gene (RIG)-I-like receptor (RLR) and Toll-like receptor (TLR) signal pathways, which are both involved in the type-I interferon induction, are significantly inhibited by simulated microgravity effects.']

Anatomical entities only, file with advanced columns.

The 3D datasets included in the zebrafish anatomical resources ZFAP and referred to in Salgado D, Marcelle C, Currie PD, Bryson-Richardson RJ 2012. The Zebrafish Anatomy Portal A novel integrated resource to facilitate zebrafish research. Developmental Biology 372:1–4. doi:10.1016/j.ydbio.2012.08.031.

The global zebrafish services market, valued at $115 million in 2025, is projected to experience robust growth, driven by a 15.4% Compound Annual Growth Rate (CAGR) from 2025 to 2033. This expansion is fueled by the increasing adoption of zebrafish as a model organism in drug discovery and development, particularly in areas like oncology, neuroscience, and cardiovascular research. Zebrafish offer significant advantages, including their genetic tractability, rapid development, and optical transparency, making them cost-effective and efficient tools for high-throughput screening and in vivo studies. Furthermore, the growing demand for personalized medicine and the increasing prevalence of chronic diseases are bolstering the market's growth trajectory. The market is segmented by service type (e.g., transgenic zebrafish creation, high-throughput screening services, customized assay development, and data analysis) and application (e.g., drug discovery, toxicology testing, and disease modeling). Key players like Shanghai Model Organisms Center, Inc., Biobide, and Charles River Laboratories are driving innovation and expanding service offerings to cater to the rising market demand. Despite the positive outlook, the market faces certain challenges. High initial investment costs for establishing zebrafish facilities and the need for specialized expertise can hinder market penetration, especially among smaller research organizations. Regulatory hurdles related to the use of animals in research also pose a constraint. However, ongoing advancements in zebrafish technology, increasing collaborations between academia and industry, and the development of more standardized protocols are expected to mitigate these restraints, further stimulating market growth. The presence of numerous companies in the space signals competitiveness and implies further market segmentation based on specialized offerings, a trend that should be considered in future market analyses. The historical period of 2019-2024 provides a solid foundation for the projected growth, assuming consistent trends in research investment and technological advancement.

The spontaneous tail coiling (STC) of zebrafish embryos represents the earliest observable motor activity in the developing neural network. We present here the STC data for single substances (singlechemicaldata) used for the concentration response curves which are published in the paper: "Optimization of the spontaneous tail coiling test for fast assessment of neurotoxic effects in the zebrafish embryo using an automated workflow in KNIME by Ogungbemi et al. 2020. In addition, we present STC data for chemical mixtures (mixturedata) which were used to generate the concentration response curves in the paper manuscript: "Assessing combined effects for mixtures of similar and dissimilar acting neuroactive substances on zebrafish embryo movement by Ogungbemi et al. 2021 For more details on the data, please see the papers.

The general objective of the study was to determine modulation of gene expression by environmental factors, with a special emphasis on bone formation. For this reason, the specific period of treatment was chosen between 5-6 days post-fertilization (dpf), when bone formation and calcification are taking place. Zebrafish larvae were placed at 5 dpf into a Large Diameter Centrifuge and brought to a gravitational force of 3g or 5g for 24 hours. We show that this treatment causes a clear increase of bone formation, as illustrated by cranial skeleton staining of the bone matrix by Alizarin Red, by morphometric analysis of the resulting images and by gene expression studies of selected genes. Thus, a whole genome micro-array experiment was conducted to identify genes that may be involved in the observed effect on bone formation.

Figure S1: BMC curves. Table S1: Fish assessments. Table S2: Data to make visualization of toxicity (Figure 3). Table S3: Data to make BMC curves. This dataset is associated with the following publication: Britton, K., R. Judson, B. Hill, K. Jarema, J. Olin, B. Knapp, M. Lowery, M. Feshuk, J. Brown, and S. Padilla. Using Zebrafish to Screen Developmental Toxicity of Per- and Polyfluoroalkyl Substances (PFAS). Toxics. MDPI, Basel, SWITZERLAND, 12(7): 501, (2024).

Many animals, including humans, have evolved to live and move in groups. In humans, disrupted social interactions are a fundamental feature of many psychiatric disorders. However, we know little about how genes regulate social behavior. Zebrafish may serve as a powerful model to explore this question. By comparing the behavior of wild-type fish to 90 genetic lines, we show that mutations of genes associated with human psychiatric disorders can alter the collective behavior of adult zebrafish. We identify three categories of behavioral variation across mutants: "scattered", in which fish show reduced cohesion; "coordinated", in which fish swim more in aligned schools; and "huddled", in which fish form dense but disordered groups. Changes in individual interaction rules can explain these differences. This work demonstrates how emergent patterns in animal groups can be altered by genetic changes in individuals, and establishes a framework for understandin...

This dataset contains zebrafish (Danio rerio) raw RNA and ChIP (paired-end) sequencing data:

RNA-seq

lane1_BSwt5dpf*: 3 biological replicates of RNA-seq data from 5dpf wild-type (AB background) pooled intestines

lane1_BSwt7dpf*: 3 biological replicates of RNA-seq data from 7dpf wild-type (AB background) pooled intestines

lane1_BSwt9dpf*: 3 biological replicates of RNA-seq data from 9dpf wild-type (AB background) pooled intestines

ChIP-seq

Cldn-wt-int-5dpf-H3K27me3*: 2 biological replicates of H3K27me3 ChIP-seq data from 5dpf wild-type (AB background) pooled intestines

Cldn-wt-int-5dpf-H3K4me3*: 2 biological replicates of H3K4me3 ChIP-seq data from 5dpf wild-type (AB background) pooled intestines

Cldn-wt-int-5dpf-input-12727_R[12].fastq.gz: 1 sample of input ChIP-seq data from 5dpf wild-type (AB background) pooled intestines

Cldn-wt-int-7dpf-H3K27me3*: 2 biological replicates of H3K27me3 ChIP-seq data from 7dpf wild-type (AB background) pooled intestines

Cldn-wt-int-7dpf-H3K4me3*: 2 biological replicates of H3K4me3 ChIP-seq data from 7dpf wild-type (AB background) pooled intestines

Cldn-wt-int-7dpf-input-12727_R[12].fastq.gz: 1 sample of input ChIP-seq data from 7dpf wild-type (AB background) pooled intestines

Cldn-wt-int-9dpf-H3K27me3*: 2 biological replicates of H3K27me3 ChIP-seq data from 9dpf wild-type (AB background) pooled intestines

Cldn-wt-int-9dpf-H3K4me3*: 2 biological replicates of H3K4me3 ChIP-seq data from 9dpf wild-type (AB background) pooled intestines

Cldn-wt-int-9dpf-input-12727_R[12].fastq.gz: 1 sample of input ChIP-seq data from 9dpf wild-type (AB background) pooled intestines

Zebrafish is increasingly used to assess biological properties of chemical substances and thus is becoming a specific tool for toxicological and pharmacological studies. The effects of chemical substances on embryo survival and development are generally evaluated manually through microscopic observation by an expert and documented by several typical photographs. Here, we present a methodology to automatically classify brightfield images of wildtype zebrafish embryos according to their defects by using an image analysis approach based on supervised machine learning. We show that, compared to manual classification, automatic classification results in 90 to 100% agreement with consensus voting of biological experts in nine out of eleven considered defects in 3 days old zebrafish larvae. Automation of the analysis and classification of zebrafish embryo pictures reduces the workload and time required for the biological expert and increases the reproducibility and objectivity of this classification.

Zebrafish embryos/larvae are a choice model system for studying early stages of vertebrate development and how these stages can be perturbed by environmental stressors. Petrochemical combustion products elicit developmental toxicity that is associated with transcriptome changes in zebrafish embryos (ZFE). We used microarrays to characterize transcriptome changes in ZFE that had been exposed in the laboratory to oil emulsions collected from the GoM shoreline, ~9 weeks after the Deepwater Horizon blowout. ZFE were exposed to oil emulsions collected (July 1-4, 2010) at the shoreline in Gulfport, MS, Fort Morgan, AL and Perdido Key, FL. ZFE were exposed to emulsions, consisting of varying amounts of alkanes, polynuclear aromatic hydrocarbons (PAHs), sand and seawater that had been “buttered†on the bottom of cups, in which ZFE were suspended in zebrafish medium. ZFE development was monitored by light microscopy. Control ZFE were suspended in zebrafish medium without emulsions. Gross developmental abnormalities, including axial changes, altered swimming patterns and yolk sac and pericardial sac swelling were noted and photographed. ZFE were collected at 48-hr intervals, after exposures had begun, and either placed in clean medium for up to 48 hours more, or, were collected immediately for RNA extraction. and hybridization on Affymetrix zebrafish microarrays, each containing 14,900 probe sets. We extracted RNA from all 30 ZFE in each cup for microarray analysis.