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82 results for “Ciona”
Confocal stacks of Cii_beta gamma crystalin_hM4D(Gi)_mCherry transgenic Ciona Larvae
<p>Confocal stacks of Cii_beta gamma crystalin_hM4D(Gi)_mCherry transgenic Ciona Larvae used to generate the panels of Hoyer et al.</p>
Neural crest lineage in the proto-vertebrate model Ciona
<p>Larva single cell data (SRA accession number: SRR9051005, SRR9051006 and SRR9051007) from Cao and colleagues (GEO accession number: GSE131155; Cao et al, 2019) were remapped on the <em>Ciona</em> KY21 gene models released in 2022 (Satou et al, 2019; Satou et al, 2022) using CellRanger v7.0.0. The expression matrices were analyzed with the package Seurat v4.3.0 (Butler et al, 2019) in R version 4.2.3 (R, 2022). The different tissue types were first identified (Table1_tissueTypes-wholeLarvae) before the nervous system was subsetted and the neural cell types identified (Table2_cellTypes-nervousSystem). The significantly differentially expressed genes between the <em>Hh2</em><sup>+</sup> ependymal cells (Table3_DEGs) and the rest of the nervous system were identified with Seurat using Wilcoxon rank-sum test with Bonferroni correction (Butler et al, 2019).</p>
Data from: Distinguishing contemporary hybridization from past introgression with postgenomic ancestry-informative SNPs in strongly differentiated Ciona species
Biological introductions bring into contact species that can still hybridize. The evolutionary outcomes of such secondary contacts may be diverse (e.g. adaptive introgression from or into the introduced species) but are not yet well examined in the wild. The recent secondary contact between the non-native sea squirt Ciona robusta (formerly known as C. intestinalis type A) and its native congener C. intestinalis (formerly known as C. intestinalis type B), in the Western English Channel, provides an excellent case study to examine. To examine contemporary hybridization between the two species, we developed a panel of 310 ancestry-informative SNPs from a population transcriptomic study. Hybridization rates were examined on 449 individuals sampled in eight sites from the sympatric range and five sites from allopatric ranges. The results clearly showed an almost complete absence of contemporary hybridization between the two species in syntopic localities, with only one-first-generation hybrid and no other genotype compatible with recent backcrosses. Despite the almost lack of contemporary hybridization, shared polymorphisms were observed in sympatric and allopatric populations of both species. Furthermore, one allopatric population from SE Pacific exhibited a higher rate of shared polymorphisms compared to all other C. robusta populations. Altogether, these results indicate that the observed level of shared polymorphism is more probably the outcome of ancient gene flow spread afterwards at a worldwide scale. They also emphasize efficient reproductive barriers preventing hybridization between introduced and native species, which suggests hybridization should not impede too much the expansion and the establishment of the non-native species in its introduction range.
Confocal stacks of Cii_PC2_hM4D(Gi)_mCherry transgenic Ciona Larvae
<p>Data related to Supplementary Figure 5 of the manuscript titled: <strong>Polymodal sensory perception drives robust attachment and metamorphosis of a pre-vertebrate zooplanktonic larva. </strong></p>
Data related to Ciona spp. and ascidians as bioindicator organisms for evaluating effects of endocrine disrupting chemicals: A discussion paper
<p>This dataset is related to "Ciona spp. and ascidians as bioindicator organisms for evaluating effects of endocrine disrupting chemicals: A discussion paper" PMID: <strong>37708617</strong> doi: 10.1016/j.marenvres.2023.106170. Epub 2023 Sep 9.</p>
Interactive 3D peptide atlas of Ciona cerebral ganglion
<p>Interactive 3D peptide atlas of Ciona cerebral ganglion. File format is power point and blender. </p>
Imaging MS data of Ciona brain No. 4
<p>Imaging MS data of the Ciona brain. 10 um sections. Apparatus: Bruker rapifleX.</p>
Imaging MS data of Ciona brain No. 3
<p>Imaging MS data of the Ciona brain. 10 um sections. Apparatus: Bruker rapifleX.</p>
Imaging MS data of Ciona brain No. 2
<p>Imaging MS data of the Ciona brain. 10 um sections. Apparatus: Bruker rapifleX.</p>
FIGURE 1. Ciona pomponiae. A in Poorly known Ascidiacea collected in the vicinity of the Commander Islands and East Kamchatka, NW Pacific
FIGURE 1. Ciona pomponiae. A, internal view of antero-dorsal midline (branchial tentacles, prepharyngeal groove, dorsal tubercle, ganglion and anterior part of dorsal lamina); B, rectum and genital papilla; C, gut loop, pharyngeo-epicardiac openings in retropharyngeal groove, dorsal languets; D, body removed from the test.
Data from: Distinguishing contemporary hybridization from past introgression with postgenomic ancestry-informative SNPs in strongly differentiated Ciona species
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Data from: Constrasting global genetic patterns in two biologically similar, widespread and invasive Ciona species (Tunicata, Ascidiacea)
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Data from: The role of metalloproteases in fertilisation in the ascidian Ciona robusta
In the ascidian Ciona robusta (formerly C. intestinalis type A), the mechanism underlying sperm penetration through the egg investment remains unknown. We previously reported that proteins containing both an astacin metalloprotease domain and thrombospondin type 1 repeats are abundant in the sperm surface protein-enriched fraction of C. robusta. Here we investigated the involvement of those proteins in fertilisation. We refined the sequences of astacin metalloproteases, confirmed that five of them are present in the sperm, and labelled them as tunicate astacin and thrombospondin type 1 repeat-containing (Tast) proteins. Fertilisation of C. robusta eggs was potently inhibited by a metalloprotease inhibitor GM6001. The eggs cleaved normally when they were vitelline coat-free or the inhibitor was added after insemination. Furthermore, vitelline coat proteins were degraded after incubation with intact sperm. These results suggest that sperm metalloproteases are indispensable for fertilisation, probably owing to direct or indirect mediation of vitelline-coat digestion during sperm penetration. TALEN-mediated knockout of Tast genes and the presence of GM6001 impaired larval development at the metamorphic stage, suggesting that Tast gene products play a key role in late development.
Data from: Genome-wide gene-associated microsatellite markers for the model invasive ascidian, Ciona intestinalis species complex
The vase tunicate, Ciona intestinalis species complex, has become a good model for ecological and evolutionary studies, especially those focusing on microevolution associated with rapidly changing environments. However, genome-wide genetic markers are still lacking. Here we characterized a large set of genome-wide gene-associated microsatellite markers for C. intestinalis spA (= C. robusta). Bioinformatic analysis identified 4654 microsatellites from expressed sequence tags (ESTs), 2126 of which successfully assigned to chromosomes were selected for further analysis. Based on the distribution evenness on chromosomes, function annotation and suitability for primer design, we chose 545 candidate microsatellites for further characterization. After amplification validation and variation assessment, 218 loci were polymorphic in at least one of the two populations collected from the coast of Arenys de Mar, Spain (N = 24 - 48) and Cape Town, South Africa (N = 24 - 33). The number of alleles, observed heterozygosity and expected heterozygosity ranged from two to 11, 0 to 0.833 and 0.021 to 0.818, and from two to 10, 0 to 0.879 and 0.031 to 0.845 for the Spanish and African populations, respectively. When all microsatellites were tested for cross-species utility, only 60 loci (25.8%) could be successfully amplified and all loci were polymorphic in C. intestinalis spB. A high level of genome-wide polymorphism is likely responsible for the low transferability. The large set of microsatellite markers characterized here is expected to provide a useful genome-wide resource for ecological and evolutionary studies using C. intestinalis as a model.
Peptide mapping images of Ciona brain
<p>Peptide mapping images of the Ciona cerebral ganglion. GIMP format. </p>
Ciona intestinalis Tierpsy tracked skeletons as of 2022-06-23
<p>This dataset contains the data that currently (2022-06-23) corresponds to swimming <em>Ciona intestinalis</em> larvae (controls and drug treated animals) that were recorded in our behavioural setups and were subsequently segmented, tracked and analyzed using the Tierpsy Tracker (developed by Andre Brown's lab, MRC LMS).</p> <p> </p>
Comprehensive analysis of locomotion dynamics in the protochordate Ciona intestinalis reveals how neuromodulators flexibly shape its behavioral repertoire.
<p>This record contains (as of 2022-06-27) datasets corresponding to the study of behavior in swimming <em>Ciona intestinalis</em> larvae (controls and drug treated animals) that were recorded in our behavioural setups. In particular, it contains:</p> <ol> <li>multi-point tracking data of the larvae obtained using the Tierpsy Tracker (developed by Andre Brown's lab, MRC LMS).</li> <li>features like curvature, speed etc calculated from the tracking data</li> <li>results of time-series analyses (matrix-profiling, hidden markov modelling, spatio-temporal clustering) performed on the feature dataset</li> <li>Hidden Markov Models trained for inferences</li> </ol>
Dataset associated with "Quantitative analysis reveals the basic behavioural repertoire of the urochordate Ciona intestinalis."
<p>This dataset contains the data used in the publication “Quantitative analysis reveals the basic behavioural repertoire of the early branching chordate Ciona intestinalis.”. It is available in .hdf format which can be opened with the pandas library in python.</p> <p>The dataframe is structured as one row of descriptive parameters per tracked trace, but one entry in the row is an entire dataframe containing all data for observations per tracked point for the respective trace. </p> <p>Parameter descriptions:</p> <p>chor: Wether an animal is with chorion ("C") or dechorionated ("D")<br> age: Age of animal expressed in hours post hatching<br> video: Name of video file associated with trace<br> light: Which light stimulus was used.<br> fps: framerate of video<br> temp: temperature the experiment was performed at<br> crowdsize: number of animals in well<br> modafinil: concentration of modafinil used<br> lazy: boolean. True if an animal did not move more than a threshold value. Lazy/Dead/Immobile/Stuck animals were discarded from analysis.<br> tto: Thigmotaxis defined in percentage of time spent in thigmotactic area.<br> tdo: Thigmotaxis defined in percentage of distance covered in thigmotactic area.<br> ac: activity coeffiecient. Fraction of video where the animal had a speed of a threshold or higher.<br> complexity: Path complexity expressed in bits of entropy<br> dfs: Dataframes decribing the trace coordinate by coordinate.</p>
Data from: The role of metalloproteases in fertilisation in the ascidian Ciona robusta
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Data from: Genome-wide gene-associated microsatellite markers for the model invasive ascidian, Ciona intestinalis species complex
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DANDI Archive for NWB datasets
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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.