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.
36
datasets available to search
ShareScore release 0.7.1
Dataset results
36 results for “Platynereis”
Platynereis dumerilii - Aligned serial sections of the posterior segments
<p>Aligned serial semi-thin sections (1µm) of the posterior most segments of <em>Platynereis dumerilii.</em></p>
Platynereis dumerilii full-length transcriptome of developmental stages
<p>To generate a high-quality full-length transcriptome for the annelid <em>Platynereis dumerilii</em>, we collected samples from representative developmental stages, from unfertilized eggs to 5 days post-fertilization. Each sample consisted of a bulk mix from 1 to 5 batches of embryos fertilized by different parents. We incubated all batches at 18 degrees Celsius until the desired time point, then collected the embryos into a clean tube and snap-froze them in liquid nitrogen with as little seawater as possible. The samples were stored at -80 degrees Celsius until RNA extraction. We extracted total RNA from the samples using a Trizol protocol. After measuring the RNA concentration with NanoDrop, we created a bulk RNA mix by combining 1 µL from each sample into a new tube. We gave the sample to the Sequencing and Genotyping facility of the Max Planck Institute of Molecular Cell Biology and Genetics, who ran aliquots of this bulk mix through a Bioanalyzer and gel electrophoresis. They found no evidence of RNA degradation. From this sample, they prepared PacBio Iso-Seq libraries using the Express Template Prep Kit 2.0 and sequenced full-length transcripts on a SMRT 8M Cell for 30 hours using a PacBio Sequel II System. They processed the raw movie subreads with SMRT Analysis software, following the Iso-Seq v3 workflow to generate representative circular consensus sequences, demultiplex and remove primers, trim poly(A) tails, and remove concatemers. After transcript clustering and merging, the resulting dataset contained 176,122 polished high-quality isoforms. Using Cogent, we removed redundant isoforms and obtained a dataset with 117,524 transcripts. From this, we generated a dataset containing only the longest isoform for each gene, with 70,003 sequences in total. We calculated descriptive metrics using Transrate. To estimate their completeness, we used BUSCO for metazoa and obtained a score of 85%. Finally, we annotated the longest-isoform dataset using EnTAP. About 85% of the transcripts have a coding sequence. We obtained annotations for 67% of the sequences, while 33% have remained unannotated.</p> <h2>Datasets</h2> <table> <tbody> <tr> <td><strong>file name</strong></td> <td><strong>file size (zipped)</strong></td> <td><strong>sequences</strong></td> <td><strong>description</strong></td> </tr> <tr> <td><a href="https://zenodo.org/records/14250773/files/0-Pdum_workflow.zip?download=1">0-Pdum_workflow.zip</a> (folder)</td> <td>3.40 GB</td> <td>-</td> <td>entire pipeline with notebook entries and analyses</td> </tr> <tr> <td><a href="https://zenodo.org/records/14250773/files/1-Pdum_hq_isoforms.zip?download=1">1-Pdum_hq_isoforms.zip</a> (fasta)</td> <td>180.30 MB</td> <td>176,122</td> <td>polished high-quality isoforms from CCS</td> </tr> <tr> <td><a href="https://zenodo.org/records/14250773/files/2-Pdum_co_isoforms.zip?download=1">2-Pdum_co_isoforms.zip</a> (fasta)</td> <td>70.68 MB</td> <td>117,524</td> <td>non-redundant polished high-quality isoforms</td> </tr> <tr> <td><a href="https://zenodo.org/records/14250773/files/3-Pdum_co_longest.zip?download=1">3-Pdum_co_longest.zip</a> (fasta)</td> <td>54.85 MB</td> <td>70,003</td> <td>longest of non-redundant polished high-quality isoforms</td> </tr> <tr> <td><a href="https://zenodo.org/records/14250773/files/4-Pdum_co_longest_annotations.zip?download=1">4-Pdum_co_longest_annotations.zip</a> (tsv)</td> <td>34.37 MB</td> <td>70,003 (46,635 annotated)</td> <td>annotations for longest-isoform dataset</td> </tr> </tbody> </table> <p> </p>
Platynereis dumerilii - Aligned serial sections of the parapodium used for the 3D Model
<p>Aligned serial semi-thin sections (1µm) of a parapodium of <em>Platynereis dumerillii. </em></p>
Refractive index tomography of chitin-containing bristles (chaetae) from Platynereis dumerilii
<p>This dataset is a supplementary material including refractive index tomograms of an article </p> <p>Ikeda, K., Belevich, I., Zelaya-Lainez, L., Orel, L., Füssl, J., Gumulec, J., Hellmich, C., Jokitalo, E., Raible, F.: Dynamic microvilli sculpt bristles at nanometric scale. Nature Communications 2024.</p> <p><strong>Biochemical isolation of bristles and imaging</strong></p> <p>Larvae were washed twice using artificial sea water. The larvae were washed in artificial seawater supplemented with 25mM EGTA, then lysed for 1 hour in Triton X-100 1% in the same buffer on ice. We could observe the appearance of a gel containing bristles. The gel was washed twice in 10 mM Tris-HCl, 2.5 mM MgCl2, 0.5 mM, CaCl2pH 7.6. 50 μL were left inthe sample at the last wash and the gel was digested with 5 U of DNase I (Thermo Fischer Scientific) for 2.5 hours at 37°C with 360 rpm agitation. Next,the digest was supplemented with 100 μL of artificial sea water and digested with 200 μL of 2.5 μg/μL Liberase Enzyme Blend (Sigma-Aldrich) for 1 hour at 50°C. The bristles were washed 3 times in artificial seawater. The isolated bristles were mounted onμ Slide I Luer (Ibidi). The refractive index tomograms of isolated bristles were obtained by Nanolive 3D Cell Explorer with 60X magnification.</p> <p>The accompanied TIFF is 32-bit, where pixel values correspond to refractive index (e.g. pixel value in image 1.335 = refractive index <em>n</em>). The pixel size is 0.182um, the Z step is 0.372 um.</p>
FIGURE 5. Platynereis juvenile dorsal pigmentation pattern, A–C, P. australis, P in Taxonomy of sympatric New Zealand species of Platynereis, with description of three new species additional to P. australis (Schmarda) (Annelida: Polychaeta: Nereididae)
FIGURE 5. Platynereis juvenile dorsal pigmentation pattern, A–C, P. australis, P. mahanga sp. nov., P. k a u sp. nov. respectively. Scale bar 0.5 mm.
FIGURE 3 in Taxonomy of sympatric New Zealand species of Platynereis, with description of three new species additional to P. australis (Schmarda) (Annelida: Polychaeta: Nereididae)
FIGURE 3. Platynereis kau sp. nov., composite anterior dorsal body of heteronereid, male parapodia on left, female on right, tentacular cirri and chaetae omitted for clarity. Scale bar 1 mm.
FIGURE 6. A in Taxonomy of sympatric New Zealand species of Platynereis, with description of three new species additional to P. australis (Schmarda) (Annelida: Polychaeta: Nereididae)
FIGURE 6. A, Platynereis australis female anterior dorsal; B, P. australis male anterior lateral; C, P. australis juvenile distal tip of homogomph falciger; D, P. mahanga sp. nov. female anterior dorsal; E, P. k a u sp. nov. female anterior dorso-lateral; F, P. k a u sp. nov. male dorsal pygidium; G, P. australis male pygidium in left lateral view; H, P. karaka sp. nov. male anterior lateral; I, P. karaka sp. nov. male dorsal midline papillae (anterior to top). Images A, B, D–I are photographs of live heteronereid specimens captured at night. Scale bar: 1 mm A, B, D, E, G; 0.5 mm F, H; 0.2 mm I; 5 μm C.
Platynereis dumerilii germ cell development diagrams
<p>These are cartoons depicting Platynereis dumerilii germ cell development. </p>
Metadata for the characterization of Platynereis dumerilii cephalic and non-cephalic sensory cell types
<p>Rhabdomeric Opsins (r-Opsins) serve as light-sensory molecules in cephalic eye photoreceptors of many invertebrates, but also play roles in additional sensory organs. This has prompted questions on the evolutionary relationship of the cell types, specifically if ancient r-Opsins cells possessed non-photosensory functions. By extracting and profiling cephalic and non-cephalic <i>r-opsin1</i>-expressing cell types of the marine bristleworm <i>Platynereis dumerilii</i>, we find evidence for shared and distinct identities between these two cell types. We establish that non-cephalic cells possess a mechanosensory signature, but also a full set of phototransduction components. Using cell-culture-based second messenger assays, we determine that <i>Platynereis</i> r-Opsin1 is a Gα<sub>q</sub>-coupled blue-light receptor. Profiling of cells in <i>r-opsin1</i> mutant animals, and comparing cells under dim and bright light conditions reveals that in the non-cephalic cell type, light – mediated by r-Opsin1 – adjusts the expression level of a calcium transporter relevant for auditory mechanosensation in vertebrates. We finally establish a supervised, deep learning-based quantitative behavioral analysis pipeline to assess animal trunk movements. We identify light-dependent differences in the fine-tuning of the worms' undulatory movements in mutant <i>vs.</i> wildtype headless trunks, which are known to require mechanosensory feedback. Altogether, our results provide support for an evolutionary concept in which r-Opsins act as ancient, light-dependent modulators of mechanosensation. Our findings refine the reconstruction of sensory cell type evolution, and suggest that light-independent mechanosensory roles of r-Opsins likely result from secondary evolutionary processes.</p>
FIGURE 18. Ceratonereis singularis Treadwell, 1929. Non-type A–I in Revision of Ceratonereis Kinberg, 1865 recorded from the Caribbean Sea, with description of two new Ceratonereis species and a new combination of Platynereis Kinberg, 1865
FIGURE 18. Ceratonereis singularis Treadwell, 1929. Non-type A–I (AMNH 1950). A, chaetiger 7, right parapodium. B, chaetiger 14, right parapodium. C, chaetiger 17, right parapodium. D, chaetiger 30, right parapodium. E, chaetiger 48, right parapodium. F, chaetiger 63, right parapodium. G, left jaw, dorsal view. H, supra-acicular long-bossed heterogomph falciger, chaetiger 14. I, sub-acicular long-bossed heterogomph falciger, chaetiger 14. Scale bars: A–E, 0.2 mm; F, 0.1 mm; G, 0.5 mm; H, I, 10 µm.
FIGURE 14. Ceratonereis nancyae n in Revision of Ceratonereis Kinberg, 1865 recorded from the Caribbean Sea, with description of two new Ceratonereis species and a new combination of Platynereis Kinberg, 1865
FIGURE 14. Ceratonereis nancyae n. sp. Holotype A–E, K–O (ECOSUR 0248); paratype F–J, P, Q (ECOSUR 0249). A, chaetiger 2, left parapodium. B, chaetiger 8, left parapodium. C, chaetiger 17, left parapodium. D, chaetiger 39, left parapodium. E, chaetiger 57, left parapodium. F, chaetiger 2, right parapodium. G, chaetiger 3, right parapodium. H, chaetiger 10, right parapodium. I, chaetiger 25, right parapodium. J, chaetiger 44, right parapodium. K, notopodial short-bossed heterogomph falciger, chaetiger 39. L, notopodial short-bossed heterogomph falciger, chaetiger 60. M, sub-acicular long-bossed heterogomph falciger, chaetiger 2. N, supra-acicular long-bossed heterogomph falciger, chaetiger 39. O, sub-acicular long-bossed heterogomph falciger, chaetiger 39. P, sub-acicular long-bossed heterogomph falciger, chaetiger 57. Q, left jaw, dorsal view. Scale bars: A–E, 0.2 mm; F–J, 0.3 mm; K–P, 20 µm; Q, 0.2 mm.
FIGURE 8 in Revision of Ceratonereis Kinberg, 1865 recorded from the Caribbean Sea, with description of two new Ceratonereis species and a new combination of Platynereis Kinberg, 1865
FIGURE 8. Ceratonereis gracilis (Webster, 1884) reinst. Non-type female A (AMNH 556); non-type male B–J (AMNH 2538). A, whole specimen, dorsal view. B, whole specimen, dorsal view. C, anterior end, dorsal view. D, posterior end, dorsal view. E, chaetiger 2, right parapodium. F, chaetiger 7, right parapodium. G, chaetiger 17, right parapodium. H, chaetiger 32, right parapodium. I, chaetiger 41, right parapodium. J, chaetiger 66, right parapodium. Scale bars: A, B, 2 mm; C, D, 0.5 mm; E–H, 0.2 mm; I, J, 0.1 mm.
FIGURE 21 in Revision of Ceratonereis Kinberg, 1865 recorded from the Caribbean Sea, with description of two new Ceratonereis species and a new combination of Platynereis Kinberg, 1865
FIGURE 21. Epitoky in Ceratonereis species. A, epitokal patterns recorded for Ceratonereis species: (1) Horst (1924), male with threadlike caudal region, female unknown; (2) Gravier & Dantan (1934), male with short, crowded chaetigers in caudal region, female with threadlike caudal region; (3) Fauvel (1939) and (4) Pamungkas & Glasby (2015), both male and female with threadlike caudal region; (5) Perkins (1980), both male and female with short, crowded chaetigers in caudal region. B, Hypotheses about the epitokal patterns recorded for Ceratonereis australis.
FIGURE 4. Ceratonereis mirabilis Kinberg, 1865. Non-types A–M in Revision of Ceratonereis Kinberg, 1865 recorded from the Caribbean Sea, with description of two new Ceratonereis species and a new combination of Platynereis Kinberg, 1865
FIGURE 4. Ceratonereis mirabilis Kinberg, 1865. Non-types A–M (MNHN A886). A, notopodial short-bossed heterogomph spiniger, chaetiger 23. B, notopodial heterogomph short-bossed falciger, chaetiger 23. C, notopodial short-bossed heterogomph falcigers, chaetiger 33. D, supra-acicular long-bossed heterogomph falciger, chaetiger 23. E, sub-acicular long-bossed heterogomph falciger, chaetiger 23. F, supra-acicular long-bossed heterogomph falciger, chaetiger 33. G, sub-acicular longbossed heterogomph falciger, chaetiger 33. H, left jaw, dorsal view. I, chaetiger 2, right parapodium. J, chaetiger 7, right parapodium. K, chaetiger 13, left parapodium. L, chaetiger 23, left parapodium. M, chaetiger 33, left parapodium (ventral cirrus incomplete). Scale bars: A–G, 10 µm; H–M, 0.1 mm.
FIGURE 5 in Revision of Ceratonereis Kinberg, 1865 recorded from the Caribbean Sea, with description of two new Ceratonereis species and a new combination of Platynereis Kinberg, 1865
FIGURE 5. Ceratonereis gracilis (Webster, 1884) reinst. Syntypes of Nereis gracilis Webster, 1884 A, B (USNM 4787); non-type C, D (USNM 1490820), E–G (USNM 1490818), H (USNM 1490819). A, whole fragments, dorsal view. B, anterior end, dorsal view. C, pharynx, dorsal view (arrow tips point slightly lamelliform papillae in areas VI). D, pharynx, ventral view. E, anterior end, dorsal view. F, posterior end, dorsal view. G, whole specimen, dorsal view. H, anterior end, dorsal view. Scale bars: A, E, 1 mm; G, 2 mm; B–D, F, H, 0.5 mm.
FIGURE 2 in Revision of Ceratonereis Kinberg, 1865 recorded from the Caribbean Sea, with description of two new Ceratonereis species and a new combination of Platynereis Kinberg, 1865
FIGURE 2. Morphology of Ceratonereis species. A, anterior end, lateral view from an epitoke male specimen of C. singularis (AMNH 1950). B, distal view of chaetiger 12 from an atoke specimen of C. nancyae n. sp. (ECOSUR P3194). C, notopodium (upper) and neuropodium (lower) of a middle chaetiger of natatory region from an epitoke specimen of C. singularis (AMNH 1950). D, anterior (right) and posterior (left) view of chaetiger 6 from an atoke specimen of C. nancyae n. sp. (ECOSUR P3194). Scale bars: A, 1 mm; B, 0.2 mm; C, D, 0.1 mm. Abbreviations: (An) antenna, (Cp) cirrophores, (Cr) cirrostyle, (Dc) dorsal cirrus, (DoL) dorsal ligule, (Inf) infra-acicular neurochaetae, (InL) neuropodial inferior lobe, (LVc) lower lamella of ventral cirrus, (MeL) median ligule, (NeL) neuroacicular ligule, (Not) notochaetae, (PoL) neuropodial postchaetal lobe, (Pp) palpophores, (Pr) prostomium, (PreL) notopodial prechaetal lobe, (Ps) palpostyle, (Sup) supra-acicular neurochaetae, (UDc) upper lamella of dorsal cirrus, (UVc) upper lamella of ventral cirrus, (Vc) ventral cirrus, (VeL) ventral ligule, (VeLa) ventral lamella (postchaetal lobe).
FIGURE 1 in Revision of Ceratonereis Kinberg, 1865 recorded from the Caribbean Sea, with description of two new Ceratonereis species and a new combination of Platynereis Kinberg, 1865
FIGURE 1. Maps with the locations of the examined material. A, Caribbean Sea, Gulf of Mexico, and a section of the Sargasso Sea. B, Mexican Eastern Tropical Pacific. C, Brazilian Western Atlantic.
FIGURE 7 in Revision of Ceratonereis Kinberg, 1865 recorded from the Caribbean Sea, with description of two new Ceratonereis species and a new combination of Platynereis Kinberg, 1865
FIGURE 7. Ceratonereis gracilis (Webster, 1884) reinst. Syntypes of Nereis gracilis Webster, 1884 A–C (USNM 4787); nontype D–J (USNM 1490819). A, chaetiger 3, right parapodium. B, chaetiger 8, right parapodium. C, chaetiger 16, right parapodium. D, notopodial short-bossed heterogomph falciger, chaetiger 23. E, notopodial short-bossed heterogomph falciger, chaetiger 30. F, notopodial sshort-bossed heterogomph falciger, chaetiger 40. G, supra-acicular long-bossed heterogomph falciger, chaetiger 23. H, sub-acicular long-bossed heterogomph falcigers, chaetiger 23. I, sub-acicular long-bossed heterogomph falcigers, chaetiger 40. J, sub-acicular long-bossed heterogomph falcigers, chaetiger 57. Scale bars: A–C, 0.2 mm; D–J, 10 µm.
FIGURE 9. Ceratonereis longicirrata Perkins, 1980. Holotype A–C in Revision of Ceratonereis Kinberg, 1865 recorded from the Caribbean Sea, with description of two new Ceratonereis species and a new combination of Platynereis Kinberg, 1865
FIGURE 9. Ceratonereis longicirrata Perkins, 1980. Holotype A–C (USNM 58740); non-type D, E (ECOSUR P1164); non-type F (ECOSUR P3190). A, anterior end, dorsal view. B, whole specimen, dorsal view. C, posterior end, dorsal view. D, anterior end, dorsal view. E, pharynx, dorsal view. F, pharynx, ventral view (arrow tips point rounded papillae in areas VI). Scale bars: A, C, D, 0.5 mm; B, 1 mm; E, F, 0.5 mm.
FIGURE 16. Ceratonereis nancyae n in Revision of Ceratonereis Kinberg, 1865 recorded from the Caribbean Sea, with description of two new Ceratonereis species and a new combination of Platynereis Kinberg, 1865
FIGURE 16. Ceratonereis nancyae n. sp. Non-types (ECOSUR P1152). A, chaetiger 2, right parapodium. B, chaetiger 3, right parapodium. C, chaetiger 49, right parapodium. D, chaetiger 7, right parapodium. E, chaetiger 30, right parapodium. F, chaetiger 24, right parapodium, anterior (right) and posterior (left) views. Labels: (1) upper lamella of dorsal cirrus, (2) dorsal cirrus, (3) dorsal ligule, (4) notopodial prechaetal lobe, (5) median ligule, (6) neuroacicular ligule, (7) ventral lamella (postchaetal lobe), (8) ventral ligule, (9) upper lamella of ventral cirrus, (10) lower lamella of ventral cirrus. Scale bars: A–E, 0.1 mm; F, 0.2 mm.
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.