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.
4,683
datasets available to search
ShareScore release 0.9.0
Dataset results
4,683 results for “embryonic”
Data from: Bacterial community dynamics during embryonic and larval development of three confamilial echinoids
Open the record for dataset details and reuse information.
Data from: Potential for local adaptation in response to an anthropogenic agent of selection: effects of road deicing salts on amphibian embryonic survival and development
Open the record for dataset details and reuse information.
Data from: Post-embryonic development of Dalmanitina, and the evolution of facial suture fusion in Phacopina
Open the record for dataset details and reuse information.
Data from: Young but not defenseless: antifungal activity during embryonic development of a social insect
Open the record for dataset details and reuse information.
Data from: Kin recognition in embryonic damselfishes
Open the record for dataset details and reuse information.
Young but not defenseless: Antifungal activity during embryonic development of a social insect
<p> Termites live in environments heavily colonized by diverse microbial communities, including pathogens. Eggs laid within the nest likely experience similar pathogenic pressures as their older nestmates. Consequently, they may have also been under selective pressures to be immune-competent. Through <i>in vitro</i> experiments, we tested the ontogeny, location and strength of embryos' antifungal activity against the fungus <i>Metarhizium brunneum</i>. Extraembryonic washes and intraembryonic components were incubated with fungal conidia, which was then scored for viability. Fungistatic activity was location- and stage-dependent. Extraembryonic washes had relatively weak antifungal activity. Conversely, intraembryonic contents were highly antifungal, exhibiting increased potency through development. Boiling both embryonic washes and intraembryonic contents rescued conidia viability, indicating the antifungal agent(s) is (are) heat-sensitive, and likely proteinaceous. Embryonic protein profiles shifted from putative vitellogenins in young embryos to multiple proteins in subsequent stages, suggesting that the increase in fungistatic activity may be due to the expression of endogenous proteins during embryogenesis. This study is the first to address embryonic antifungal activity in a hemimetabolous, eusocial taxon. Our results support the hypothesis that microbes have been significant agents of selection, fostering the evolution of antifungal properties in termite eggs, the most immature and supposed, most vulnerable stage of development.</p>
3D models of mouse embryonic development (stl, converted from EMAP)
<p>A collection of readily-usable volumetric models for all tissues and stages of mouse peri-implantation development as extracted from the eMouse Atlas Project (E5.0 to E9.0), as well as custom-made models of all pre-implantation stages (E0 to E4.0). These models have been converted to a commonly used 3D format (.stl), and are provided in ready-made files for digital exploration and illustration.</p> <p>Specifically:</p> <ol> <li>individual .stl models of embryonic subcomponents for each developmental stage (e.g. epiblast, visceral endoderm; 1 folder per EMAP embryonic stage)</li> <li>ready-made .blend files where such components have been reassembled as a full embryo model, and in a scene with pre-prepared light sources and aligned camera (1 file per embryonic stage)</li> <li>a .blend file with all embryonic models provided arranged in a temporal lineup; and a .blend file with a "starter-pack" of pre-made materials to use for easy illustration.</li> </ol> <p>Also included are two data tables:</p> <ol> <li>"EMAP_key.xlsx" indicating the source of its model, and the embryonic stage corresponding to each Theiler Stage</li> <li> "EMAP_partslist.xlsx" containing the original name of each embryonic component provided (as used in <a href="https://www.emouseatlas.org/emap/ema/home.php">EMAP</a>), and the corresponding name used in this dataset.</li> </ol>
Data from: Dynamic changes in DNA methylation during embryonic and postnatal development of an altricial wild bird
DNA methylation could shape phenotypic responses to environmental cues and underlie developmental plasticity. Environmentally induced changes in DNA methylation during development can give rise to stable phenotypic traits and thus affect fitness. In the laboratory, it has been shown that the vertebrate methylome undergoes dynamic reprogramming during development, creating a critical window for environmentally induced epigenetic modifications. Studies of DNA methylation in the wild are lacking, yet are essential for understanding how genes and the environment interact to affect phenotypic development and ultimately fitness. Furthermore, our knowledge of the establishment of methylation patterns during development in birds is limited. We quantified genome-wide DNA methylation at various stages of embryonic and postnatal development in an altricial passerine bird, the great tit Parus major. While there was no change in global DNA methylation in embryonic tissue during the second half of embryonic development, a two-fold increase in DNA methylation in blood occurred between 6 and 15 d posthatch. Though not directly comparable, DNA methylation levels were higher in the blood of nestlings compared with embryonic tissue at any stage of prenatal development. This provides the first evidence that DNA methylation undergoes global change during development in a wild bird, supporting the hypothesis that methylation mediates phenotypic development. Furthermore, the plasticity of DNA methylation demonstrated during late postnatal development, in the present study, suggests a wide window during which DNA methylation could be sensitive to environmental influences. This is particularly important for our understanding of the mechanisms by which early-life conditions influence later-life performance. While we found no evidence for differences in genome-wide methylation in relation to habitat of origin, environmental variation is likely to be an important driver of variation in methylation at specific loci.
Data from: The evolutionary economics of embryonic-sac fluids in squamate reptiles
The parchment-shelled eggs of squamate reptiles take up substantial water from the nest environment, enabling the conversion of yolk into neonatal tissue and buffering the embryo against the possibility of subsequent dry weather. During development, increasing amounts of water are stored in the embryonic sacs (i.e., membranes around the embryo: amnion, allantois, and chorion). The evolution of viviparity (prolonged uterine retention of developing embryos) means that embryonic-sac fluid storage now imposes a cost (increased maternal burdening), confers less benefit (because the mother buffers fetal water balance), and introduces a potential conflict among uterine siblings (for access to finite water supplies). Our data on nine species of squamate reptiles and published information on three species show that the embryonic-sac fluids comprise around 33% of neonatal mass in viviparous species versus 94% in full-term eggs of oviparous squamates. Data on parturition in 149 vipers (Vipera aspis, a viviparous species) show that larger offspring store more fluids in their fetal sacs and that an increase in litter size is associated with a decrease in fluid-sac mass per offspring. Overall, the evolutionary transition from oviparity to viviparity may have substantially altered selective forces on offspring packaging and created competition among offspring for access to water reserves during embryonic development.
Data from: Genome reannotation of the lizard Anolis carolinensis based on 14 adult and embryonic deep transcriptomes
Background: The green anole lizard, Anolis carolinensis, is a key species for both laboratory and field-based studies of evolutionary genetics, development, neurobiology, physiology, behavior, and ecology. As the first non-avian reptilian genome sequenced, A. carolinesis is also a prime reptilian model for comparison with other vertebrate genomes. The public databases of Ensembl and NCBI have provided a first generation gene annotation of the anole genome that relies primarily on sequence conservation with related species. A second generation annotation based on tissue-specific transcriptomes would provide a valuable resource for molecular studies. Results: Here we provide an annotation of the A. carolinensis genome based on de novo assembly of deep transcriptomes of 14 adult and embryonic tissues. This revised annotation describes 59,373 transcripts, compared to 16,533 and 18,939 currently for Ensembl and NCBI, and 22,962 predicted protein-coding genes. A key improvement in this revised annotation is coverage of untranslated region (UTR) sequences, with 79% and 59% of transcripts containing 5' and 3' UTRs, respectively. Gaps in genome sequence from the current A. carolinensis build (Anocar2.0) are highlighted by our identification of 16,542 unmapped transcripts, representing 6,695 orthologues, with less than 70% genomic coverage. Conclusions: Incorporation of tissue-specific transcriptome sequence into the A. carolinensis genome annotation has markedly improved its utility for comparative and functional studies. Increased UTR coverage allows for more accurate predicted protein sequence and regulatory analysis. This revised annotation also provides an atlas of gene expression specific to adult and embryonic tissues.
Data from: Chemical suppression of embryonic cane toads Rhinella marina by larval conspecifics
1. Mechanisms that evolved to suppress the development of potential competitors may offer novel methods for species-specific control of invasive organisms. The tadpoles of cane toads Rhinella marina compete for limited food resources in small ponds, and older tadpoles eliminate competitors not only by eating newly-laid eggs, but also by releasing a chemical that suppresses development of conspecific eggs. 2. We conducted laboratory trials to assess the magnitude and generality of this suppression effect, and to identify the developmental stages capable of producing the suppressor cue and those that are vulnerable to its presence. 3. In all clutches that we tested, the suppressor cue reduced larval growth, development and survival (>95% mortality vs. <50% in controls). The suppressor exerts a general effect on larval development, rather than causing malformations of specific organ systems. 4. Free-swimming tadpoles of all developmental stages produce the cue (but are not affected by it), whereas embryos do not produce the cue, but are vulnerable to it. Tadpoles produce the cue consistently rather than facultatively (e.g. in response to detecting eggs). 5. A preliminary trial shows that the cue is effective in natural spawning ponds as well as in the laboratory. 6. Synthesis and applications. Our data have strong implications for current methods of toad control (culling tadpoles will remove suppression effects on the next generation, so it may be better to maintain live toad tadpoles in secure containers rather than removing them from the pond). Longer-term, understanding the chemical basis of this powerful mechanism for intraspecific competition may facilitate invader control.
PAAQ-Heart : Beating Embryonic Zebrafish Heart Imaged by Paired Alternating Acquisitions (PAAQ) Microscopy
<p><strong>Description</strong></p><p>This dataset contains images of the beating heart of live embryonic zebrafish acquired using Paired Alternating AcQuisitions (PAAQ) microscopy.</p><p>The dataset was collected to illustrate a multichannel video reconstruction method, which virtually increases the framerate of a repeating process (e.g., cardiac heartbeat) as compared to what would be achievable through direct imaging with a single-channel fluorescence setup and a low-framerate camera.</p><p>The imaged embryos were obtained by crossing transgenic Tg(<i>fli1a:GFP</i>)<i>y1Tg</i> and Tg(<i>myl7:mRFP</i>)<i>ko08Tg</i> zebrafish and selecting homozygous embryos. The embryos were were imaged at 4dpf on an implementation of the OpenSPIM microscope equiped with and the illumination controller available as part of the CBI-MMTools microscopy controltools package for micromanager (https://github.com/idiap/CBI-MMTools) to generate alternating illumination patterns in even and odd frames. The odd frames correspond to illumination by a brightfield with intensity that increases as a ramp over the duration of the frame exposure (reference modality) and even frames are either the result of laser illumination (fluorescence imaging) or a short brightfield illumination burst.</p><p> </p><p><strong>Reference</strong></p><p>If you use this dataset, please cite the following publication:</p><p><i>Marelli, F., Ernst, A., Mercader, N., Liebling, M. (2023). PAAQ: Paired Alternating AcQuisitions for Virtual High Frame Rate Multichannel Cardiac Fluorescence Microscopy. Biological Imaging, 3, E20.</i><br><a href="https://doi.org/10.1017/S2633903X23000223 ">10.1017/S2633903X23000223</a></p>
Fig 3 from: Srygley RB, Senior LB (2024) Illustrated review of Mormon cricket Anabrus simplex (Tettigoniidae, Tettigoniinae) embryonic development. Journal of Orthoptera Research 33(1): 87-93. https://doi.org/10.3897/jor.33.98763
Fig 3 Phase III: Mesentrepsis. Images left to right showing the posterior end of the egg: A. Stage 12; B. Stage 13; C. Stage 14; D. Lateral view of same stage 14 embryo. Scale bars: 2 mm.
Fig 2 from: Srygley RB, Senior LB (2024) Illustrated review of Mormon cricket Anabrus simplex (Tettigoniidae, Tettigoniinae) embryonic development. Journal of Orthoptera Research 33(1): 87-93. https://doi.org/10.3897/jor.33.98763
Fig 2 Phase II: Anatrepsis. Images show the posterior end of the egg: A. Stage 7 to 8; B. Stage 9; C. Stage 10; D. Stage 11 with micropyles clearly visible. Scale bars: 2 mm.
Fig 5 from: Srygley RB, Senior LB (2024) Illustrated review of Mormon cricket Anabrus simplex (Tettigoniidae, Tettigoniinae) embryonic development. Journal of Orthoptera Research 33(1): 87-93. https://doi.org/10.3897/jor.33.98763
Fig 5 Phase V: Dorsal closure A. Stage 19, ventral view; B. Stage 20, ventral view; C. Stage 21, lateral view; D. Stage 21 to 22, ventral view; Phase VI: Completion E. Stage 23, ventral view; F. Stage 23, lateral view; G. Stage 24, ventral view. Scale bars: 2 mm.
Fig 1 from: Srygley RB, Senior LB (2024) Illustrated review of Mormon cricket Anabrus simplex (Tettigoniidae, Tettigoniinae) embryonic development. Journal of Orthoptera Research 33(1): 87-93. https://doi.org/10.3897/jor.33.98763
Fig 1 Phase I: Formation and differentiation of the embryonic primordium. Images show the posterior end of the egg only: A. Stage 4; B. Stage 5; C. Stage 6; and D. Stage 6 transitioning to Stage 7. Scale bars: 2 mm.
Fig 6 from: Srygley RB, Senior LB (2024) Illustrated review of Mormon cricket Anabrus simplex (Tettigoniidae, Tettigoniinae) embryonic development. Journal of Orthoptera Research 33(1): 87-93. https://doi.org/10.3897/jor.33.98763
Fig 6 The minimum age of each embryo from day of oviposition (maximum age indicated by error bar). Embryos that were between two stages (e.g., Stage 6 to 7) were given a value half-way between the two stages (e.g., 6.5). Closed circles: embryos incubated at a daily 12:12 h cycle of 30:15°C; open circles: embryos incubated at 30:15°C for the initial 35 days and then the daily maximum and minimum temperatures were varied each week thereafter. Inset: embryos in various stages of development in week 8.
Fig 4 from: Srygley RB, Senior LB (2024) Illustrated review of Mormon cricket Anabrus simplex (Tettigoniidae, Tettigoniinae) embryonic development. Journal of Orthoptera Research 33(1): 87-93. https://doi.org/10.3897/jor.33.98763
Fig 4 Phase IV: Katatrepsis. A. Stage 15, lateral view with anterior end of embryo to the left; B. Stage 15, dorso-lateral view with chorion removed; C. Stage 16, lateral view with anterior end of embryo to the right; D. Stage 17, lateral view; E. Stage 18, ventral view showing its length relative to the whole egg. Scale bars: 2 mm.
Embryonic muscle splitting patterns reveal homologies of amniote forelimb muscles
<p class="MsoCommentText">Limb muscles are remarkably complex and evolutionarily labile; although their anatomy is of great interest for studies of the evolution of form and function, their homologies among major amniote clades have remained obscure. Studies of adult musculature are inconclusive owing to the highly derived morphology of modern amniote limbs, but correspondences become increasingly evident earlier in ontogeny. Amniote forelimb muscles derive from early embryonic muscle masses of somitic origin, which grow and cleave into recognizable divisions that split into the individualized muscles. We followed the embryonic development of forelimb musculature in representatives of six major amniote clades and found, contrary to current consensus, that these early splitting patterns are highly conserved across Amniota. Muscle mass cleavage patterns and topology are highly conserved in reptiles including birds, irrespective of their skeletal modifications: the avian flight apparatus results from slight early topological modifications that are exaggerated during ontogeny. Therian mammals, while conservative in their cleavage patterns, depart drastically from the ancestral amniote musculoskeletal organization in terms of topology. These topological changes occur through extension, translocation, and displacement of muscle groups later in development. Overall, the simplicity underlying the apparent complexity of forelimb muscle development allows us to resolve conflicting hypotheses about homology and to trace the history of each individual forelimb muscle throughout the amniote radiations. </p>
Plastic adjustments of biparental care behaviour across embryonic development under elevated temperature in a marine ectotherm
<p>Phenotypic plasticity in parental care investment allows organisms to promptly respond to rapid environmental changes by potentially benefiting offspring survival and thus parental fitness. To date, a knowledge gap exists on whether plasticity in parental care behaviours can mediate responses to climate change in marine ectotherms. Here, we assessed the plasticity of parental care investment under elevated temperatures in a gonochoric marine annelid with bi-parental care, Ophryotrocha labronica, and investigated its role in maintaining the reproductive success of this species in a warming ocean. We measured the time individuals spent carrying out parental care activities across three phases of embryonic development, as well as the hatching success of the offspring as a proxy for reproductive success, at control (24°C) and elevated (27°C) temperature conditions. Under elevated temperature we observed: (i) a significant decrease in total parental care activity, underpinned by a decreased in male and simultaneous parental care activity, in the late stage of embryonic development; and ii) a reduction of hatching success, that was however not significantly related to changes in parental-care activity levels. These findings, along with the observed unaltered somatic growth of parents and decreased brood size, suggest that potential cost-benefit trade-offs between offspring survival (i.e. immediate fitness) and parents somatic condition (i.e. longer-term fitness potential) may occur under ongoing ocean warming. Finally, our results suggest that plasticity in parental care behaviour is a mechanism able to partially mitigate the negative effects of temperature-dependent impacts.</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.