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.
410
datasets available to search
ShareScore release 0.9.0
Dataset results
410 results for “eukaryotic”
Signal, Uncertainty, and Conflict in Phylogenomic Data for a Diverse Lineage of Microbial Eukaryotes (Diatoms, Bacillariophyta)
<p>This data depository contains analysis results from Parks, Wickett, and Alverson 2017 (Signal, Uncertainty, and Conflict in Phylogenomic Data for a Diverse Lineage of Microbial Eukaryotes (Diatoms, Bacillariophyta) (Mol. Biol. Evol. doi:10.1093/molbev/msx268)), and is made freely available to the research community.</p> <p>The file and subfolders here are as follows:</p> <p>gene_alignments<br> - contains compressed (tarred and gzipped) folders with all gene alignments at 0.2, 0.5 and 0.8 alignment column occupancy cutoffs. In each folder, there are also text files listing which gene alignments fall under which taxon occupancy subsetting strategy (i.e., 10-20% taxon occupancy, 40-60% taxon occupancy, 80-100% taxon occupancy, etc).</p> <p>gene_trees<br> - contains all (compressed) gene trees (bootstrapped versions, 100 bootstrap pseudo-replicates)) used in Astral analyses for each alignment column occupancy cutoff (0.2, 0.5, 0.8); nodes with less than 33% bootstrap support are collapsed.</p> <p>hmms.mafft_aligned<br> - contains (compressed) hmm specifications for each major diatom morphotype (radial and polar centrics, araphid and raphid pennates) from the 0.2 alignment column occupancy subset of the data. A summary of the sampling scheme and the hmm results/counts are also available in HMM_sampling.docx.</p> <p>mmetsp_nuclear_transcriptome_assemblies<br> - these are the compressed nuclear transcriptome assemblies that were done in-house (i.e., mostly MMETSP samples). Assemblies do not include organellar or rDNA loci.</p> <p>species_trees<br> - contains (compressed) species trees for all phylogenetic strategies and alignment column occupancy cutoff/data subset strategies.</p> <p>Suppl_1.MMETSP_basic_summaries.xlsx<br> - this an identical file to Parks, Wickett and Alverson 2017 supplementary file 1. This file contains taxon, strain and SRA information for all assembled taxa, and a variety of assembly metric information.</p> <p> </p>
Sedimentary DNA of a human‐impacted lake in Western Canada (Cultus Lake) reveals changes in micro‐eukaryotic diversity over the past ~200 years
<p>Although the use of genetic analyses of sedimentary DNA to track changes in biodiversity has increased over the last decade, questions remain as to how well DNA captures past ecological conditions. Even less is known about how extracellular and intracellular DNA are archived in lake sediments and whether the two fractions yield similar information. Here we characterized the changes of micro‐eukaryotic communities over the past ~200 years in Cultus Lake (British Columbia, Canada), for which a rich body of limnological data and a pre‐existing multi‐proxy paleolimnological study exist. We generated and analyzed 18S rRNA gene amplicons and found that extracellular and intracellular DNA provided different insights, with the preservation of extracellular DNA compromised in sediments older than ~30 years. Principal Coordinates and indicator species analyses based on intracellular DNA showed that changes in micro‐eukaryotic diversity occurred at similar time periods as those identified with the classical paleolimnological study. For instance, decreases of Opisthokonta amplicons occurred during years with elevated numbers of sockeye salmon spawners, which might be associated with an increase of herbivory by juvenile sockeye salmon. Furthermore, two diatom species identified morphologically exhibited similar temporal dynamics to two diatom taxa identified genetically, suggesting that sedimentary DNA can track past diatom species changes as well as micro‐eukaryotic community changes. Overall, our study provides insights into the use of extracellular and intracellular DNA in sedimentary records and showed that sedimentary DNA enriches our understanding of micro‐eukaryotic community changes over centennial time scales.</p>
Bacterial homologs of innate eukaryotic antiviral defenses provide phage protection.
<p>Supplementary data regarding the 'Bacterial homologs of innate eukaryotic antiviral defenses provide phage protection' manuscript.</p><p> </p><p><strong>Abstract:</strong><br>Prokaryotes have evolved a multitude of defense systems to protect themselves from bacteriophage predation. Here, we discovered new phage defense systems related to innate antiviral genes from vertebrates and plants. Our search uncovered over 400 candidates from which eleven were selected and six novel phage defense systems validated. We identified a DNA replication helicase/nuclease 2 (Prometheus) which may act on transcription R-loops, an inositol-monophosphatase-like phage defense protein (Pan), and two ATPases from the NACHT family coupled to novel effectors NucS and SfsA (Nyx and Hypnos). In addition, a fused ubiquitin-like E1-E2-JAB protein combined with a putative MBL nuclease (6A-MBL) was found, and a novel member of the Thoeris family that contains four essential TIR domains with a putative effector SLOG domain (Thoeris type III). Collectively, these defense systems support the concept of deep evolutionary links and shared antiviral mechanisms between prokaryotes and eukaryotes.</p>
Taxonomic and functional annotations of transcripts and proteins derived from a Metatranscriptomic study of microbial eukaryotes from Lake Pavin
<p>These data were obtain as part of a metatranscriptomic study (Monjot <em>et al.,</em> 2023, 2024). All scripts to obtain these annotations are available at https://github.com/amonjot/SSN_Monjot_2024. The sequencing data (i.e. metatranscriptomic) used to obtain this taxonomic and functional information are archived at ENA under accession number PRJEB61515.</p> <p>This repository also contains various protein sequence similarity networks (Lagoon_output.zip). As these files are very time-consuming to produce, we have provided them to complete all the steps in Monjot <em>et al,</em> 2024. All procedures to produce them are present on the following github repository : https://github.com/amonjot/SSN_Monjot_2024.</p> <p> </p>
Full-length huntingtin constructs for eukaryotic expression of huntingtin protein with different polyQ lengths 2018/05/01
<p>Huntingtin structure-function open lab notebook project: Full-length huntingtin constructs for eukaryotic expression of huntingtin protein with different polyQ lengths 2018/05/01</p>
Dataset from: Horizontal transfer of BovB and L1 retrotransposons in eukaryotes
<p><strong>Background: </strong>Transposable elements are mobile DNA sequences, colloquially known as jumping genes because of their ability to replicate to new genomic locations. TEs can jump between organisms or species when given a vector of transfer, such as a tick or a virus, in a process known as horizontal transfer. Here, we propose that LINE-1(L1) and Bovine-B (BovB), the two most abundant transposable element families in mammals, were initially introduced as foreign DNA via ancient horizontal transfer events.</p> <p><strong>Results: </strong>Using analyses of over 759 plant, fungal and animal genomes, we identify multiple possible L1 horizontal transfer events in eukaryotic species, primarily involving Tx-like L1s in marine eukaryotes. We also extend the BovB paradigm by increasing the number of estimated transfer events compared to previous studies, finding new parasite vectors of transfer such as bed bug, leech, and locust, and BovB occurrences in new lineages such as bat and frog. Given that these transposable elements have colonized more than half of the genome sequence in today's mammals, our results support a role for horizontal transfer in causing long-term genomic change in new host organisms.</p> <p><strong>Conclusions:</strong> We describe extensive horizontal transfer of BovB retrotransposons and provide the first evidence that L1 elements can also undergo horizontal transfer. With the advancement of genome sequencing technologies and bioinformatics tools, we anticipate our study to be a valuable resource for inferring horizontal transfer from large-scale genomic data.</p> <p><strong>Dataset:</strong> The deposited dataset contains the identified TE sequences (L1 and BovB) from all genomes and the putative horizontal transfer clusters described in the text. See Additional File 1 (Tables S1-6) and Additional File 2 (Figures S1-55) for detailed descriptions of the sequences and clusters.</p> <p> </p>
Trait Spreadsheet to DwCA: Trophic guild data for microbial eukaryotes
<p></p>https://eol-jira.bibalex.org/browse/DATA-1882<p></p>Updated: 2022-05-31 02:59
Trait Spreadsheet to DwCA: Habitat data for microbial eukaryotes
<p></p>https://eol-jira.bibalex.org/browse/DATA-1882<p></p>Updated: 2022-09-28 15:15
Earth BioGenome Project: Authors and author contributions for publication "The Earth BioGenome Project Phase II: Illuminating the Eukaryotic Tree of Life"
<p>The zipped file cntains three tab-separated datasets (worksheets). These worksheets list</p> <p>The contributing authors for the manuscript "The Earth BioGenome Project Phase II: Illuminating the Eukaryotic Tree of Life" and the roles of these authors in the manuscript.</p> <p>The funding sources for these authors</p> <p>A list of the authors contributing to the "EBP Community of Scientists" collective authorship for the same manuscript.</p>
Supplementary Data associated with the article "LukProt: A database of eukaryotic predicted proteins designed for investigations of animal origins"
<p>Supplementary Data associated with the article "LukProt: A database of eukaryotic predicted proteins designed for investigations of animal origins" - BUSCO example.</p> <p> </p> <p>National Science Centre of Poland is acknowledged for funding of the project 2020/36/C/NZ8/00081, "The role of glycosylation in the emergence of animal multicellularity", which enabled the creation of this dataset.</p> <p> </p> <p> </p>
Seasonality of cyanobacteria and eukaryotes in Lake Geneva and the impacts of cyanotoxins on growth of the model ciliate Tetrahymena pyriformis
<p><span>Toxic cyanobacteria are likely to be favored by global warming and other human impacts, posing significant threats to aquatic ecosystems. While cyanobacterial blooms in eutrophic lakes are widely investigated, the dynamics of cyanobacteria and the effects of their toxins and bioactive metabolites on the plankton communities in mesotrophic and oligotrophic lakes are less well understood. Here we investigated seasonal dynamics of cyanobacteria, eukaryotic algae and cyanotoxins in oligo-mesotrophic Lake Geneva—the largest and deepest lake in western Europe. High-throughput sequencing of the 16S rRNA genes in 143 samples along a water column revealed that Lake Geneva hosts diverse, co-dominant cyanobacterial genera, including <em>Planktothrix</em>, <em>Cyanobium</em>, <em>Pseudanabaena</em>, and <em>Aphanizomenon. </em>The abundance of the <em>mcyA</em> gene marker for microcystin production was highly correlated with total cyanobacteria abundance, obtained from qPCR of the 16S rRNA genes. Targeted LC-HRMS/MS analysis demonstrated peak concentrations of cyanotoxins in September and December 2021 at the deep chlorophyll-a maximum layer, reaching up to 1474 ng/l for anabaenopeptins and 144 ng/l for microcystins. The toxin peaks did not correlate with the abundance or variations in the cyanobacteria or eukaryote community, but they were correlated in time with seasonal lows in the abundances of ciliates (18S rRNA analysis). Laboratory exposure tests demonstrated that growth of the model ciliate <em>Tetrahymena pyriformis </em>was inhibited by Microcystin-RR and Anabaenopeptin A at environmentally relevant concentrations in the ng/l-range, in natural lake water, </span><span>synthetic freshwater, and growth media spiked with the cyanotoxins. Our findings suggest that even low concentrations (in the ng/l-range) of microcystins and anabaenopeptins, reduce growth of ciliates such as <em>T. pyriformis</em> and can be expected to have wider impacts on the eukaryote communities. </span></p>
DNA metabarcoding marker choice skews perception of marine eukaryotic biodiversity
<p>DNA metabarcoding is an increasingly popular technique to investigate biodiversity; however, many methodological unknowns remain, especially concerning the biases resulting from marker choice. Regions of the cytochrome <i>c</i> oxidase subunit I (COI) and 18S rDNA (18S) genes are commonly employed "universal" markers for eukaryotes, but the extent of taxonomic biases introduced by these markers and how such biases may impact metabarcoding performance is not well quantified. Here, focusing on macro-eukaryotes, we use standardized sampling from autonomous reef monitoring structures (ARMS) deployed in the world's most biodiverse marine ecosystem, the Coral Triangle, to compare the performance of COI and 18S markers. We then compared metabarcoding data to image-based annotations of ARMS plates. Although both markers provided similar estimates of taxonomic richness and total sequence reads, marker choice skewed estimates of eukaryotic diversity. The COI marker recovered relative abundances of the dominant sessile phyla consistent with image annotations. Both COI and the image annotations provided higher relative abundance estimates of Bryozoa and Porifera and lower estimates of Chordata as compared to 18S, but 18S recovered 25% more phyla than COI. Thus, while COI more reliably reflects the occurrence of dominant sessile phyla, 18S provides a more holistic representation of overall taxonomic diversity. Ideal marker choice is, therefore, contingent on study system and research question, especially in relation to desired taxonomic resolution, and a multi-marker approach provides the greatest application across a broad range of research objectives. As metabarcoding becomes an essential tool to monitor biodiversity in our changing world, it is critical to evaluate biases associated with marker choice.</p>
Truly ubiquitous CRESS DNA viruses scattered across the eukaryotic tree of life
<p>Until recently, most viruses detected and characterized were of economic significance, associated with agricultural and medical diseases. This was certainly true for the eukaryote-infecting circular Rep (replication-associated protein)-encoding single-stranded DNA (CRESS DNA) viruses, which were thought to be a relatively small group of viruses. With the explosion of metagenomic sequencing over the past decade and increasing use of rolling-circle replication for sequence amplification, scientists have identified and annotated copious numbers of novel CRESS DNA viruses – many without known hosts but which have been found in association with eukaryotes. Similar advances in cellular genomics have revealed that many eukaryotes have endogenous sequences homologous to viral Reps, which not only provide "fossil records" to reconstruct the evolutionary history of CRESS DNA viruses but also reveal potential host species for viruses known by their sequences alone. The Rep protein is a conserved protein that all CRESS DNA viruses use to assist rolling circle replication that is known to be endogenized in a few eukaryotic species (notably tobacco and water yam). A systematic search for endogenous Rep-like sequences in GenBank's non-redundant eukaryotic database was performed using tBLASTn. We utilized relaxed search criteria for the capture of integrated Rep sequence within eukaryotic genomes, identifying 93 unique species with an endogenized fragment of Rep in their nuclear (78 species), plasmid (1 species), mitochondrial (6 species) or chloroplast (8 species) genomes. These species come from 19 different phyla, scattered across the eukaryotic tree of life. Exogenous and endogenous CRESS DNA viral Rep tree topology suggested potential hosts for one family of uncharacterized viruses and supports a primarily fungal host range for genomoviruses.</p>
Tara Eukaryote Annotated 18s OTU Counts
<p>"Marine plankton support global biological and geochemical processes. Surveys of their biodiversity have hitherto been geographically restricted and have not accounted for the full range of plankton size. We assessed eukaryotic diversity from 334 size-fractionated photic-zone plankton communities collected across tropical and temperate oceans during the circumglobal Tara Oceans expedition. We analyzed 18S ribosomal DNA sequences across the intermediate plankton-size spectrum from the smallest unicellular eukaryotes (protists, >0.8 micrometers) to small animals of a few millimeters. Eukaryotic ribosomal diversity saturated at ~150,000 operational taxonomic units, about one-third of which could not be assigned to known eukaryotic groups... Most eukaryotic plankton biodiversity belonged to heterotrophic protistan groups."</p> <p>https://www.science.org/doi/10.1126/science.1261605</p>
Truly ubiquitous CRESS DNA viruses scattered across the eukaryotic tree of life
Open the record for dataset details and reuse information.
Data for: Tunable self-cleaving ribozymes for modulating gene expression in eukaryotic systems
Open the record for dataset details and reuse information.
Ice gliding diatoms establish record-low temperature limits for motility in a eukaryotic cell
Open the record for dataset details and reuse information.
Sedimentary DNA of a human‐impacted lake in Western Canada (Cultus Lake) reveals changes in micro‐eukaryotic diversity over the past ~200 years
Open the record for dataset details and reuse information.
Glissandra oviformis n. sp.: A novel predatory flagellate illuminates the character evolution within the eukaryotic clade CRuMs
Open the record for dataset details and reuse information.
Data from: Biodiversity assessment of tropical shelf eukaryotic communities via pelagic eDNA metabarcoding
Open the record for dataset details and reuse information.
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.