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.
35
datasets available to search
ShareScore release 0.9.0
Dataset results
35 results for “Oikopleura dioica”
Supplemental material for the manuscript "Extreme genome scrambling in marine planktonic Oikopleura dioica cryptic species".
<p><strong>Supplementary material for the manuscript “Extreme genome scrambling in marine planktonic <em>Oikopleura dioica</em> cryptic species”.<br></strong></p> <p><strong><em>BreakpointsData.tar.xz contains:</em></strong></p> <ul> <li>Pairwise genome alignment files for <em>Oikopleura</em>, <em>Ciona</em>, <em>Caenorhabditis</em>, insects and muntjaks in GFF format in `inst/extdata/`.</li> <li>dN / dS computation results in `inst/extdata/dNdS/`.</li> <li>Annotations of gene models and repeat elements in GFF format in `inst/extdata/Annotations/`.</li> <li>OrthoGroups in `inst/extdata/OrthoFinder/`, where N19 represents the _O. dioica_ clade,</li> <li>N3 the tunicates and N20 the _Ciona_ clade.</li> <li>`BreakpointsData_3.11.0.tar.gz`, a R package installing the above files in the R environments where we ran our computations.</li> <li>The files needed to build the `BreakpointsData` package.</li> </ul> <p><em><strong>Oidioi_pairwise_v3.tar.gz contains:</strong></em></p> <ul> <li>The pairwise alignment files between genomes, in MAF format.</li> <li>A copy of the Nextflow pipeline used to generate them.</li> </ul> <p><em><strong>oist-assembler.tar.gz contains:</strong></em></p> <ul> <li>A Singularity image and its definition file for flye version 2.8.3-b1763` Flye-flye.2.8.3-b1763.sif` and `Flye-flye.def`.</li> <li>A copy of the Nextflow pipeline used to assemble the Bar2_p4 genome in `oist-assembler-Bar2_p4`.</li> <li>A copy of the Nextflow pipeline used to assemble the other genome in `oist-assembler-other_genomes`.</li> </ul> <p><em>Please note that these files are provided for reproducibility only and probably can not be used easily for other purposes.</em></p> <p><em><strong>Oidioi_genomes.tar.gz contains:</strong></em></p> <ul> <li>For each genome, one file (`<genome>.fa`) containing the whole genome sequence and one directory (`<genome>`) containing each chromosome, scaffold or contig of the genome as a separate file.</li> <li>For each genome, one R package, its source directory, and the vignette to create it, providing the genome information as a `BSgenome` object.</li> </ul> <p><em><strong>OrthoFinderRun.tar.xz contains:</strong></em></p> <ul> <li>A full copy of the OrthoFinder2 run that we used to compute hierarchical orthogroups.</li> </ul> <p><em><strong>Supplemental_Code.tar.gz contains:</strong></em></p> <ul> <li>A copy of <https://github.com/oist/LuscombeU_OikScrambling>, where the `.git` and `doc` directories were removed to save space.</li> </ul> <p><em><strong>AugustusAnnotation.tar.gz (added July 26th 2024) contains:</strong></em></p> <ul> <li>AUGUSTUS runs to produce the annotations that were input to OrthoFinder2. We provide them for reproducibility, with no guarantee that they are suitable for other purposes. The annotations used in the manuscript are AOM-5-5f.sm.OSKA-CDS, Bar2_p4_Flye.sm, Bsty_SCLE01.1.sm.abi.cionamodel, Fbor_SDII01.1.sm.abi, KUM-M3-7f.sm.OKI-CDS, Mery_SCLF01.1.sm.abi.cionamodel, Oalb_SCLG01.1.sm.abi.cionamodel, OKI2018_I69_annotv2.sm, Olon_SCLD01.1.sm.abi, OSKA2016v1.9.sm and Ovan_SCLH01.1.sm.abi.cionamodel.</li> </ul>
Aligned Cox1 and Cob sequences from Oikopleura dioica and other tunicates.
<p>Supporting data for the manuscript « <em>Widespread use of the “ascidian” mitochondrial genetic code in tunicates</em> » containing a) assemblies of the cytochrome oxidase subunit 1 (Cox1) and cytochrome b (Cob) mitochondrial genes from ESTs downloaded from the Oikobase database and b) protein alignment of these sequences and other tunicate sequences to study which genetic code is used in tunicate mitochondria.</p>
Draft genome assembly of a Japanese Oikopleura dioica male individual (O3), using Nanopore long reads.
<p>This draft assembly was used to validate the chrY scaffolds of the OSKA2016 reference genome in the publication “A genome database for a Japanese population of the larvacean Oikopleura dioica”, Development Growth and Differentiation, Wang and coll., 2020 (in press). It is provided as supplemental data for the reproducibility of this work; please note that no further polishing has been done to correct sequencing errors.</p> <p>Genome sequence reads were produced on a MinION sequencer (Oxford Nanopore Technologies) using high-molecular weight DNA from a male individual of the Oikopleura dioica species of zooplankton. The individual was related to the laboratory strain established from a western Japanese population that was used to produce the OSKA2016 reference genome. The raw reads were basecalled with the Guppy software version 3.3.0 using its dna_r9.4.1_450bps algorithm, and deposited in the European Nucleotide Archive (Study ID: PRJEB38559). The draft assembly was made with the Flye software version 2.7 with the options --genome-size 65m and --min-overlap 3000.</p>
Interactive 3D PDF file for the structures 10 hr juvenile of Oikopleura dioica and supplementary movie S1-20 with high resolution
<p>The larvacean, Oikopleura dioica is a planktonic chordate, which is an emerging model organism with short life cycle of 5 days and belongs to tunicates (urochordates). Organ formation in the trunk proceeds in seven hours form hatching of tailbud larvae at three hours after fertilization (hpf) to completion of organ formation in fully functional juveniles that start feeding at 10 hpf and are just miniature of adult form.</p> <p>The juveniles were fixed at 10.5 hours post fertilization, 30 min after the tail shift (Nishida, H., 2008 Development of the appendicularian Oikopleura dioica: culture, genome, and cell lineages. Dev. Growth Differ. 50, S239–S256.). The data would be used as a basic morphological data of this animal to explore organ structures and cellular composition.</p> <p>This PDF file allows one to view 3D juvenile of O. dioica in any desired directions. One can show or hide the organs and rotate them by mouse. Open this PDF file and activate it as described in Adobe Acrobat User Guide (https://helpx.adobe.com/acrobat/using/displaying-3d-models-pdfs.html). Click Toggle "Model Tree button" with three small rectangulars in the tool bar. Then in the left panel, one can select the organs and nuclei you want to see. Select lighting as "daylight". Select solid or transparency mode.<br> The Juvenile 3D image was reconstructed with Amira software using 1967 serial section images of SBF-SEM (Serial block face scanning electron microscopy) that are available at https://doi.org/10.5061/dryad.d51c5b012.</p> <p>The Zip file also contains supplementary movie S1-20 (avi file) with high resolution and the legends (PDF file).</p> <p>This data is related to the paper, 3D reconstruction of structures of hatched larva and young juvenile of the larvacean Oikopleura dioica using SBF-SEM. (https://www.nature.com/articles/s41598-021-83706-y).</p>
Supplementary material for "Oikopleura dioica, the cosmopolitan appendicularian hides multiple cryptic species around the globe"
<p>18S and ITS sequences used to estimate phylogenetic trees for "Oikopleura dioica, the cosmopolitan appendicularian hides multiple cryptic species around the globe." To identify 18S rDNA genes from genome sequences, we searched genome sequences for the best-hit matches to the Rfam models for the eukaryotic small subunit (SSU; RF01960) and large subunit (LSU; RF02543) using cmsearch of the Infernal package (v.1.1.4). The SSU and LSU models from Rfam were downloaded in April 2021. The internal transcribed spacer (ITS) regions were obtained by extracting the region between SSU and LSU.<strong> </strong>Multiple sequence alignments for the 18S and ITS regions were created with MUSCLE (v5) within Seaview (v.3.2).</p>
Supplemental material to the journal article "Tracing Homopolymers in Oikopleura dioica's mitogenome"
<p>Supplemental material to the journal article “Tracing Homopolymers in <em>Oikopleura dioica</em>’s mitogenome”, consisting of:</p> <ul> <li>The I25 mitochondrial genome (GenBank ID PP146516) and its annotation (not in GenBank)</li> <li>Transcript model sequences used to annotate the genome</li> <li>Nucleotide sequences of<em> cytochrome oxidase I </em>used to compute the tree in Figure 3</li> </ul> <p>Updated on August 6th 2024:</p> <ul> <li>Add raw reads used to assemble the mitogenome.</li> <li>ATP6 gene coordinate corrected (7110 -> 7104) to reach TAA stop codon.</li> </ul>
4D time-lapse images of brain and trunk development in the larvacean Oikopleura dioica
<p>The larvacean, <em>Oikopleura</em> <em>dioica</em> is a planktonic chordate, which is an emerging model organism with a short life cycle of 5 days and belongs to tunicates (urochordates). Organ formation in the trunk proceeds in seven hours from hatching of tailbud larvae at three hours after fertilization (hpf) to completion of organ formation in fully functional juveniles that start feeding at 10 hpf and are just miniature of adult form. Development of <em>O. dioica</em> has been described (Nishida, H., 2008 Development of the appendicularian <em>Oikopleura</em> <em>dioica</em>: culture, genome, and cell lineages. Dev. Growth Differ. 50, S239–S256.). The dataset contains 4D (3D+time) time-lapse images that were acquired during larval development using differential interference contrast optics, and wide-field fluorescent microscope, which visualize cell membrane and nuclei of the entire trunk region. In some cases, animal or vegetal hemisphere blastomeres are labelled to trace the descendants. The dataset would be generally utilized as basic morphological data during the larval development and for tracing cell lineages at a single cell level. This data set is related to the manuscript "Formation of the brain by stem cell divisions of large neuroblasts in <em>Oikopleura</em> <em>dioica</em>, a simple chordate".</p>
4D time-lapse images of brain and trunk development in the larvacean Oikopleura dioica
Open the record for dataset details and reuse information.
Interactive 3D PDF file for the structures 10 hr juvenile of Oikopleura dioica and supplementary movie S1-20 with high resolution
Open the record for dataset details and reuse information.
Serial section images of Oikopleura dioica juvenile using SBF-SEM
<p>The larvacean, <i>Oikopleura dioica</i> is a planktonic chordate, which is an emerging model organism with short life cycle of 5 days and belongs to tunicates (urochordates). Organ formation in the trunk proceeds in seven hours form hatching of tailbud larvae at three hours after fertilization (hpf) to completion of organ formation in fully functional juveniles that start feeding at 10 hpf and are just miniature of adult form. The dataset is serial section images of Oikopleura dioica juvenile that were obtained using SBF-SEM (Serial block face scanning electron microscopy). The 1961 TIFF images were compressed to a zip file.</p> <p>The juveniles were fixed at 10.5 hours post fertilization, 30 min after the tail shift (Nishida, H., 2008 Development of the appendicularian Oikopleura dioica: culture, genome, and cell lineages. Dev. Growth Differ. 50, S239–S256.). The dataset would be used as a basic morphological data of this animal to explore organ structures and cellular composition at electron microscopic level.</p> <p>This data is related to the paper, 3D reconstruction of structures of hatched larva and young juvenile of the larvacean Oikopleura dioica using SBF-SEM. (Scientific Reports, 2021, 11, 4833) (https://www.nature.com/articles/s41598-021-83706-y)</p>
Serial section images of Oikopleura dioica juvenile using SBF-SEM
Open the record for dataset details and reuse information.
Serial section images of Oikopleura dioica larva using SBF-SEM
<p>The larvacean, Oikopleura dioica is a planktonic chordate, which is an emerging model organism with short life cycle of 5 days and belongs to tunicates (urochordates). Organ formation in the trunk proceeds in seven hours form hatching of tailbud larvae at three hours after fertilization (hpf) to completion of organ formation in fully functional juveniles that start feeding at 10 hpf and are just miniature of adult form. The dataset is serial section images of Oikopleura dioica juvenile that were obtained using SBF-SEM (Serial block face scanning electron microscopy). The 1812 TIFF images were compressed to a zip file.</p> <p>The larva were fixed at 3 hours post fertilization, 10 min after hatching (Nishida, H., 2008 Development of the appendicularian Oikopleura dioica: culture, genome, and cell lineages. Dev. Growth Differ. 50, S239–S256.). The dataset would be used as a basic morphological data of this animal to explore organ structures and cellular composition at electron microscopic level.</p> <p>This data is related to the paper, 3D reconstruction of structures of hatched larva and young juvenile of the larvacean Oikopleura dioica using SBF-SEM. (Scientific Reports, 2021, 11, 4833) (https://www.nature.com/articles/s41598-021-83706-y).</p>
Movies of Oikopleura dioica behaving (part of a control dataset)
<p>These are movies of Oikopleura dioica which have been video recorded in the Ciona Tracker 2.0 video acquisition setup. </p>
Movies of Oikopleura dioica behaving (2nd part of a control dataset)
<div> </div> <div>These are movies of Oikopleura dioica which have been video recorded in the Ciona Tracker 2.0 video acquisition setup. </div>
Serial section images of Oikopleura dioica larva using SBF-SEM
Open the record for dataset details and reuse information.
Pax37 gene function in Oikopleura dioica supports a neuroepithelial-like origin for its house-making Fol territory
GEO Series GSE255790. Oikopleura dioica. 14 samples. Type: Expression profiling by high throughput sequencing.
Genome-wide profiling of translation in Oikopleura dioica during growth arrest and recovery
GEO Series GSE115265. Oikopleura dioica. 8 samples. Type: Expression profiling by high throughput sequencing.
Genome-wide map of spliced-leader-led trans-splice sites in Oikopleura dioica
GEO Series GSE50849. Oikopleura dioica. 1 samples. Type: Expression profiling by high throughput sequencing.
Maternal and zygotic transcriptomes in the appendicularian, Oikopleura dioica: Novel protein-coding genes, intra-species sequence variations, and trans-spliced RNA leaders
GEO Series GSE64421. Oikopleura dioica. 2 samples. Type: Expression profiling by high throughput sequencing.
Genome-wide high resolution map of transcription start sites across the life cycle of Oikopleura dioica
GEO Series GSE78794. Oikopleura dioica. 6 samples. Type: Expression profiling by high throughput sequencing.
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.