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1,676 results for “C elegans”
C. elegans data sample for Pergola documentation
<p>C. elegans data sample for Pergola documentation (<a href="http://cbcrg.github.io/pergola/quick_start.html">http://cbcrg.github.io/pergola/quick_start.html</a>). The sample data set consists in two folders: One named "worm_speeds" containing a CSV file for each of the tracked worms. From the several measures that can be found in the individual files, in this example we will use mid-body speed. The "mapping" folder contains the "worm_speed2pergola.txt", which sets the mappings between the information represented in the worm_speed files and the pergola ontology.</p>
Per-gene per-strain data: expression divergence between strains and alleles in F1s in wild C. elegans
<p>This dataset comprises p<span>er-gene per-strain data (used to perform all analyses and generate all figures), including regulatory pattern and inheritance mode classifications and underlying statistical differential expression results</span>.</p> <p>This is supplemental data for the linked preprint/publication describing insights derived from comparing gene expression (RNA-seq) between seven wild <em>C. elegans</em> strains and the laboratory reference strain N2, as well as the allelic expression of the wild and N2 alleles in F1s of crosses between all these wild strains and the reference strain.</p> <p>The PDF file <code>column_names_descriptions_worm_ase_data_pergene_perstrain.pdf</code> and excel spreadsheet <code>column_names_descriptions_worm_ase_data_pergene_perstrain.xlsx</code> serve as READMEs for the data file by providing details of the data held in each column of the data file <code>worm_ase_data_pergene_perstrain.txt.gz</code></p> <p>If you use this dataset (we hope someone does!), please cite the latest version of the accompanying preprint/publication.</p> <p>To query each gene in a user-friendly, visual format, see our shiny app <a href="https://wildworm.biosci.gatech.edu/ase/" target="_blank" rel="noopener">https://wildworm.biosci.gatech.edu/ase/</a></p>
Text-fig. 3. Scanning electron micrographs (a, b) and synchrotron radiation X-ray tomographic microscopy orthoslices (c–e) of flower of Lambertiflora elegans gen. et sp. nov. from the Early Cretaceous Puddledock locality, Virginia, USA (holotype, PP53796, Puddledock sample 082). a) Flower in lateral view showing long pedicel and overlapping elongated tepals; b) Detail of flower showing overlapping elongated tepals; note the numerous holes indicating the position of probable secretory cells; c) Flower in longitudinal section showing overlapping elongated tepals, remains of probable poorly developed stamens or staminodes and probable poorly developed carpels on the central conical gynoecial region of the receptacle (cut between orthoslices xz0510 and 0570); d) Flower in longitudinal section (comparable to c) showing overlapping tepals, poorly developed stamens or staminodes, and probable poorly developed carpels on the central conical gynoecial region of the receptacle; note the prominent cavities from secretory cells scattered through the tissues (cut between orthoslice xz0560 and 0575); e) Flower in transverse section showing overlapping tepals, poorly developed stamens or staminodes, and remains of probable poorly developed carpels (cut between orthoslices xy1160 and 1180). Scale bars = 1 mm (a), 500 µm (b–e). in Multiparted, Apocarpous Flowers From The Early Cretaceous Of Eastern North America And Portugal
Text-fig. 3. Scanning electron micrographs (a, b) and synchrotron radiation X-ray tomographic microscopy orthoslices (c–e) of flower of Lambertiflora elegans gen. et sp. nov. from the Early Cretaceous Puddledock locality, Virginia, USA (holotype, PP53796, Puddledock sample 082). a) Flower in lateral view showing long pedicel and overlapping elongated tepals; b) Detail of flower showing overlapping elongated tepals; note the numerous holes indicating the position of probable secretory cells; c) Flower in longitudinal section showing overlapping elongated tepals, remains of probable poorly developed stamens or staminodes and probable poorly developed carpels on the central conical gynoecial region of the receptacle (cut between orthoslices xz0510 and 0570); d) Flower in longitudinal section (comparable to c) showing overlapping tepals, poorly developed stamens or staminodes, and probable poorly developed carpels on the central conical gynoecial region of the receptacle; note the prominent cavities from secretory cells scattered through the tissues (cut between orthoslice xz0560 and 0575); e) Flower in transverse section showing overlapping tepals, poorly developed stamens or staminodes, and remains of probable poorly developed carpels (cut between orthoslices xy1160 and 1180). Scale bars = 1 mm (a), 500 µm (b–e).
Text-fig. 8. Plant fossils from Primorye, Partizansk coal basin, Frentsevka Formation, Bolshoy Kuvshin locality, early – middle Albian. a – undetermined species, spec. IBSS 320-137; b, c – Asiatifolium elegans G.SUN, S.X.GUO et SHAO L.ZHENG: b – spec. IBSS 320-86, c – spec. IBSS 320-8. Scale bar 0.5 cm. in An Angiosperm Dominated Herbaceous Community From The Early - Middle Albian Of Primorye, Far East Of Russia
Text-fig. 8. Plant fossils from Primorye, Partizansk coal basin, Frentsevka Formation, Bolshoy Kuvshin locality, early – middle Albian. a – undetermined species, spec. IBSS 320-137; b, c – Asiatifolium elegans G.SUN, S.X.GUO et SHAO L.ZHENG: b – spec. IBSS 320-86, c – spec. IBSS 320-8. Scale bar 0.5 cm.
Text-fig. 7. Plant fossils from Primorye, Partizansk coal basin, Frentsevka Formation, Bolshoy Kuvshin locality, early – middle Albian. a, c, e – Achaenocarpites capitellatus KRASSILOV et VOLYNETS: a – spec. IBSS 320-132, c – spec. IBSS 320-132, e – spec. IBSS 320-120; b – Onychiopsis psilotoides (STOKES et WEBB) WARD, spec. – IBSS 320-165; d, g – branching infructescence with several follicular fruits: d – spec. IBSS 320-145, g – IBSS 320-145; f – Asiatifolium elegans G.SUN, S.X.GUO et SHAO L.ZHENG, spec. IBSS 320-75. Scale bar 0.5 cm. in An Angiosperm Dominated Herbaceous Community From The Early - Middle Albian Of Primorye, Far East Of Russia
Text-fig. 7. Plant fossils from Primorye, Partizansk coal basin, Frentsevka Formation, Bolshoy Kuvshin locality, early – middle Albian. a, c, e – Achaenocarpites capitellatus KRASSILOV et VOLYNETS: a – spec. IBSS 320-132, c – spec. IBSS 320-132, e – spec. IBSS 320-120; b – Onychiopsis psilotoides (STOKES et WEBB) WARD, spec. – IBSS 320-165; d, g – branching infructescence with several follicular fruits: d – spec. IBSS 320-145, g – IBSS 320-145; f – Asiatifolium elegans G.SUN, S.X.GUO et SHAO L.ZHENG, spec. IBSS 320-75. Scale bar 0.5 cm.
Biogenesis of C. elegans spermatogenesis small RNAs is initiated by a zc3h12a like ribonuclease
<p><span>Small RNAs regulate spermatogenesis in many species, ranging from <em>Caenorhabditis elegans</em> to mammals. In <em>C. elegans</em>, two Argonaute proteins, ALG-3 and ALG-4, and their associated <em>alg-3/4</em> 26G-small RNAs are essential for spermatogenesis at 25°C and for imprinting paternal memory of germline gene expression in offspring. The <em>alg-3/4</em> 26G-small RNAs are antisense to their target mRNAs and are known to be produced by </span><span>the</span><span> RNA-dependent RNA polymerase, RRF-3. However, it remains unclear how the RNA templates for RRF-3 are generated and which cellular processes are affected by </span><em><span>alg-3/4</span></em><span> 26G-small RNAs</span><span>. Here, we demonstrate a key role for the conserved zc3h12a-ribonuclease-like NYN-domain-containing protein, NYN-3, in spermatogenesis at 25°C. Expression of NYN-3 was temporally coordinated with ALG-3, and our sequencing of both total and 2xFLAG::ALG-3-immunoprecipitated small RNAs revealed that NYN-3 is required for the biogenesis of <em>alg-3/4</em> 26G small RNAs. We further used ePAR-CLIP sequencing to identify NYN-3 binding sites on <em>alg-3/4</em>-targeted mature mRNAs; the NYN-3 binding sites were downstream of the binding sites for <em>alg-3/4</em> 26G-small RNAs. Additionally, 3'-RACE results placed the NYN-3 mRNA recognition upstream of RRF-3 binding and further revealed NYN-3 cleavage sites in <em>alg-3/4</em>-targeted mRNAs. Finally, a bioinformatics analysis was performed to parse the 26G small RNA-targeted genes into functional subclasses (e.g., signaling, chromatin defects). Collectively, these findings reveal NYN-3 as an initiator of small RNA generation that is central to the coordination of 26G small RNA-mediated gene regulation during spermatogenesis.</span></p>
Dataset for Extensive programmed centriole elimination unveiled in C. elegans embryos
<p>Spreadsheets, confocal and wide field microscopy images and related scripts. Related to the publication "Extensive programmed centriole elimination unveiled in C. elegans embryos." For the complete dataset, please refer to https://doi.org/10.5075/epfl-upgon-305930 </p>
WormSwin: C. elegans Video Datasets
<p>Data used for our paper "WormSwin: Instance Segmentation of C. elegans using Vision Transformer".<br>This publication is divided into three parts:</p> <ol> <li>CSB-1 Dataset</li> <li>Synthetic Images Dataset</li> <li>MD Dataset</li> </ol> <p>The CSB-1 Dataset consists of frames extracted from videos of Caenorhabditis elegans (C. elegans) annotated with binary masks. Each C. elegans is separately annotated, providing accurate annotations even for overlapping instances. All annotations are provided in binary mask format and as COCO Annotation JSON files (see <a href="https://cocodataset.org/#format-data">COCO website</a>).</p> <p>The videos are named after the following pattern:</p> <pre><code><"worm age in hours"_"mutation"_"irradiated (binary)"_"video index (zero based)"></code></pre> <p>For mutation the following values are possible: </p> <ol> <li>wild type</li> <li>csb-1 mutant</li> <li>csb-1 with rescue mutation</li> </ol> <p>An example video name would be <em>24_1_1_2</em> meaning it shows C. elegans with csb-1 mutation, being 24h old which got irradiated.</p> <p>Video data was provided by M. Rieckher; Instance Segmentation Annotations were created under supervision of K. Bozek and M. Deserno.<br><br>The Synthetic Images Dataset was created by cutting out C. elegans (foreground objects) from the CSB-1 Dataset and placing them randomly on background images also taken from the CSB-1 Dataset. Foreground objects were flipped, rotated and slightly blurred before placed on the background images.<br>The same was done with the binary mask annotations taken from CSB-1 Dataset so that they match the foreground objects in the synthetic images. Additionally, we added rings of random color, size, thickness and position to the background images to simulate petri-dish edges.</p> <p>This synthetic dataset was generated by M. Deserno.<br><br>The Mating Dataset (MD) consists of 450 grayscale image patches of 1,012 x 1,012 px showing C. elegans with high overlap, crawling on a petri-dish.<br>We took the patches from a 10 min. long video of size 3,036 x 3,036 px. The video was downsampled from 25 fps to 5 fps before selecting 50 random frames for annotating and patching.<br>Like the other datasets, worms were annotated with binary masks and annotations are provided as COCO Annotation JSON files.</p> <p>The video data was provided by X.-L. Chu; Instance Segmentation Annotations were created under supervision of K. Bozek and M. Deserno.</p> <p><br>Further details about the datasets can be found in our <a href="https://doi.org/10.1038/s41598-023-38213-7" target="_blank" rel="noopener">paper</a>.</p>
A single neuron in C. elegans orchestrates multiple motor outputs through parallel modes of transmission
<p class="MsoNormal"><span>Animals generate a wide range of highly coordinated motor outputs, which allows them to execute purposeful behaviors. Individual neurons in the circuits that generate behaviors have a remarkable capacity for flexibility, as they exhibit multiple axonal projections, transmitter systems, and modes of neural activity. How these multi-functional properties of neurons enable the generation of adaptive behaviors remains unknown. Here we show that the HSN neuron in <em>C. elegans</em> evokes multiple motor programs over different timescales to enable a suite of behavioral changes during egg-laying. Using HSN activity perturbations and in vivo calcium imaging, we show that HSN acutely increases egg-laying and locomotion while also biasing the animals towards low-speed dwelling behavior over minutes. The acute effects of HSN on egg-laying and high-speed locomotion are mediated by separate sets of HSN transmitters and different HSN axonal projections. The long-lasting effects on dwelling are mediated by HSN release of serotonin that is taken up and re-released by NSM, another serotonergic neuron class that directly evokes dwelling. Our results show how the multi-functional properties of a single neuron allow it to induce a coordinated suite of behaviors and also reveal that neurons can borrow serotonin from one another to control behavior.</span></p>
Image stacks for full-body transcription factor expression atlas with completely resolved cell identities in C. elegans
<p>Each image stack presented as zip file. Once decompressed, each folder contain '.ano' linker file, straightening C. elegans L1 images file, the segmentation mask image file and the cell annotation file. The image files are stored in Peng Hanchuan RAW/TIFF format, and the cell annotation file is stored in simple comma separated values format. To visualize the image stack data, drag the '.ano' linker file to VANO interface. </p> <p>vano_win32_1.741.zip contains VANO for worm visualization.</p>
Lineage-resolved analysis of embryonic gene expression evolution in C. elegans and C. briggsae
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A single neuron in C. elegans orchestrates multiple motor outputs through parallel modes of transmission
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Data from: A proprioceptive feedback circuit drives C. elegans locomotor adaptation through dopamine signaling
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Population dynamics of C. elegans and C. briggsae dormancy mutants
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Biogenesis of C. elegans spermatogenesis small RNAs is initiated by a zc3h12a like ribonuclease
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Data from: Whole-organism behavioral profiling reveals a role for dopamine in state-dependent motor program coupling in C. elegans.
<p>Animal behaviors are commonly organized into long-lasting states that coordinately impact the generation of diverse motor outputs such as feeding, locomotion, and grooming. However, the neural mechanisms that coordinate these diverse motor programs remain poorly understood. Here, we examine how the distinct motor programs of the nematode <i>C. elegans </i>are coupled together across behavioral states. We describe a new imaging platform that permits automated, simultaneous quantification of each of the main <i>C. elegans</i> motor programs over hours or days. Analysis of these whole-organism behavioral profiles shows that the motor programs coordinately change as animals switch behavioral states. Utilizing genetics, optogenetics, and calcium imaging, we identify a new role for dopamine in coupling locomotion and egg-laying together across states. These results provide new insights into how the diverse motor programs throughout an organism are coordinated and suggest that neuromodulators like dopamine can couple motor circuits together in a state-dependent manner. </p>
[Dataset and Code] Axis convergence in C. elegans embryos
<p>Embryos develop in a surrounding that guides key aspects of their development. For example, the anteroposterior (AP) body axis is always aligned with the geometric long axis of the surrounding eggshell in fruit flies and worms. The mechanisms that ensure convergence of the AP axis with the long axis of the eggshell remain unresolved. We investigate axis convergence in early C. elegans development, where the nascent AP axis, when misaligned, actively re-aligns to converge with the long axis of the egg. Here, we identify two physical mechanisms that underlie axis convergence. First, bulk cytoplasmic flows, driven by actomyosin cortical flows, can directly reposition the AP axis. Second, active forces generated within the pseudocleavage furrow, a transient actomyosin structure similar to a contractile ring, can drive a mechanical re-orientation such that it becomes positioned perpendicular to the long axis of the egg. This in turn ensures AP axis convergence. Numerical simulations, together with experiments that either abolish the pseudocleavage furrow or change the shape of the egg, demonstrate that the pseudocleavage furrow-dependent mechanism is the major driver of axis convergence. We conclude that active force generation within the actomyosin cortical layer drives axis convergence in the early nematode.</p>
Data for: Neuroendocrine gene expression coupling of interoceptive bacterial food cues to foraging behavior of C. elegans
<p>Animal internal state is modulated by nutrient intake, resulting in behavioral responses to changing food conditions. The neural mechanisms by which internal states are generated and maintained are not well understood. Here, we show that in the nematode <em>Caenorhabditis elegans, </em>distinct cues from bacterial food – interoceptive signals from the ingestion of bacteria and gustatory molecules sensed from nearby bacteria – act antagonistically on the expression of the neuroendocrine TGF-beta ligand DAF-7 from the ASJ pair of sensory neurons to modulate foraging behavior. A positive-feedback loop dependent on the expression of <em>daf-7 </em>from the ASJ neurons acts to promote transitions between roaming and dwelling foraging states and influence the persistence of roaming states. SCD-2, the <em>C. elegans </em>ortholog of mammalian Anaplastic Lymphoma Kinase (ALK), which has been implicated in the central control of metabolism of mammals, functions in the AIA interneurons to regulate foraging behavior and cell-non-autonomously control the expression of DAF-7 from the ASJ neurons. Our data establish how a dynamic neuroendocrine <em>daf-7 </em>expression feedback loop regulated by SCD-2 functions to couple sensing and ingestion of bacterial food to foraging behavior. We further suggest that this neuroendocrine feedback loop underlies previously characterized exploratory behaviors in <em>C. elegans</em>. Our data suggest that the expression of <em>daf-7</em> from the ASJ neurons contributes to and is correlated with an internal state of "unmet need" that regulates exploratory foraging behavior in response to bacterial cues in diverse physiological contexts.</p>
Data from: Dimensionality of locomotor behaviors in developing C. elegans
<p>Adult animals display robust locomotion, yet the timeline and mechanisms of how juvenile animals acquire coordinated movements and how these movements evolve during development are not well understood. Recent advances in quantitative behavioral analyses have paved the way for investigating complex natural behaviors like locomotion. In this study, we tracked the swimming and crawling behaviors of the nematode <em>Caenorhabditis elegans</em> from postembryonic development through to adulthood. Our principal component analyses revealed that adult <em>C. elegans </em>swimming is low dimensional, suggesting that a small number of distinct postures, or eigenworms, account for most of the variance in the body shapes that constitute swimming behavior. Additionally, we found that crawling behavior in adult <em>C. elegans</em> is similarly low dimensional, corroborating previous studies. Further, our analysis revealed that swimming and crawling are distinguishable within the eigenworm space. Remarkably, young L1 larvae are capable of producing the postural shapes for swimming and crawling seen in adults, despite frequent instances of uncoordinated body movements. In contrast, late L1 larvae exhibit robust coordination of locomotion, while many neurons crucial for adult locomotion are still under development. In conclusion, this study establishes a comprehensive quantitative behavioral framework for understanding the neural basis of locomotor development, including distinct gaits such as swimming and crawling in <em>C. elegans</em>.</p>
Cryo soft X-ray tomography of 5 microns thick slab extracted from C. elegans midbody region
<p>Samples of C. elegans <span>larvae of strain DM8005 </span>were high pressure frozen using the waffle method. Multiple <span>roughly </span>5 micron thick slabs spanning <span>an L2 larva</span> were extracted using <span>the Serial Lift-Out</span> technique, and placed on rectangular <span>mesh </span>grids. Soft X-ray tomography was performed on individual slabs using the SXT-100 soft x-ray microscope at SiriusXT. The data reveals label free internal structure of fully hydrated C. elegans tissue, annotating the worm volume and adding context to cryo electron tomography data. </p> <p>SXT data was acquired from -50° to +53° in 1° steps and reconstructed using Weighted Back Projection. A 32 nm objective zone plate was used. Data pixel size is 29 nm. </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.