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34 results for “open oceans”

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dryad32/100

Environmental DNA provides quantitative estimates of Pacific hake abundance and distribution in the open ocean.

<p>All species inevitably leave genetic traces in their environments, and the resulting environmental DNA (eDNA) reflects the species present in a given habitat. It remains unclear whether eDNA signals can provide quantitative metrics of abundance on which human livelihoods or conservation successes depend. Here, we report the results of a large eDNA ocean survey (spanning 86,000 km<sup>2</sup> to depths of 500m) to understand the abundance and distribution of Pacific hake <em>Merluccius </em><em>productus</em>, the target of the largest finfish fishery along the west coast of the United States. We sampled eDNA in parallel with a traditional acoustic-trawl survey to assess the value of eDNA surveys at a scale relevant to fisheries management. Despite local differences, the two methods yield comparable information about the broad-scale spatial distribution and abundance. Furthermore, we find depth and spatial patterns of eDNA closely correspond to acoustic-trawl estimates for hake. We demonstrate the power and efficacy of eDNA sampling for estimating abundance and distribution and move the analysis eDNA data beyond sample-to-sample comparisons to management relevant scales. We posit that eDNA methods are capable of providing general quantitative applications that will prove especially valuable in data- or resource-limited contexts.</p>

opencc-zeroMar 2022View details →
dryad32/100

Data for: Linking vertical movements of large pelagic predators with distribution patterns of biomass in the open ocean

<p>Many predator species make regular excursions from near-surface waters to the twilight (200-1,000 m) and midnight (1,000-3,000 m) zones of the deep pelagic ocean. While the occurrence of significant vertical movements into the deep ocean has evolved independently across taxonomic groups, the functional role(s) and ecological significance of these movements remain poorly understood. Here, we integrate results from satellite tagging efforts with model-predictions of deep prey layers in the North Atlantic Ocean to determine if prey distributions are correlated with vertical habitat use across 12 species of predators. Using 3D movement data for 344 individuals that traversed nearly 1.5 million km of pelagic ocean in &gt;42,000 days, we found that nearly every tagged predator frequented the twilight zone and many made regular trips to the midnight zone. Using a predictive model, we found clear alignment of predator depth use with the expected location of deep pelagic prey for at least half of the predator species. We compared high-resolution predator data with shipboard acoustics and selected representative matches that highlight the opportunities and challenges in the analysis and synthesis of these data. While not all observed behavior was consistent with estimated prey availability at depth, our results suggest that deep pelagic biomass likely has high ecological value for a suite of commercially important predators in the open ocean. Careful consideration of the disruption to ecosystem services provided by pelagic food webs is needed before the potential costs and benefits of proceeding with extractive activities in the deep ocean can be evaluated.</p>

opencc-zeroOct 2023View details →
dryad32/100

Data from: Open-ocean fish reveal an omnidirectional solution to camouflage in polarized environments

Open the record for dataset details and reuse information.

publicNov 2016View details →
dryad32/100

Data from: Evidence of small-scale spatial structuring of phytoplankton alpha- and beta-diversity in the open ocean

Open the record for dataset details and reuse information.

publicJun 2017View details →
dryad32/100

Environmental DNA provides quantitative estimates of Pacific hake abundance and distribution in the open ocean.

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publicMar 2022View details →
dryad32/100

Data and code for: The evolution of siphonophore tentilla for specialized prey capture in the open ocean

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publicMay 2021View details →
dryad32/100

Data for: Linking vertical movements of large pelagic predators with distribution patterns of biomass in the open ocean

Open the record for dataset details and reuse information.

publicOct 2023View details →
dryad32/100

Data from: Capturing open ocean biodiversity: comparing environmental DNA metabarcoding to the continuous plankton recorder

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publicJul 2020View details →
dryad28/100

Data from: Genetic monitoring of open ocean biodiversity: an evaluation of DNA metabarcoding for processing continuous plankton recorder samples

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publicNov 2017View details →
geo24/100

Gene expression response to copper toxicity between coastal and open ocean strains of marine Synechococcus

GEO Series GSE13910. Parasynechococcus marenigrum WH 8102; Synechococcus sp. CC9311. 26 samples. Type: Expression profiling by array.

openGEO-OpenJul 2009View details →
geo24/100

OCEAN-C: mapping hubs of open chromatin interactions across the genome reveals gene regulatory networks

GEO Series GSE100832. Homo sapiens. 8 samples. Type: Genome binding/occupancy profiling by high throughput sequencing; Other.

openGEO-OpenMar 2018View details →
zenodo24/100

Simultaneous acclimation to nitrogen and iron scarcity in open ocean cyanobacteria revealed by sparse tensor decomposition of metatranscriptomes

<h2>Description</h2> <p>This dataset contains all of the supplementary files necessary to reproduce the findings published in the research article entitled&nbsp;<em>Simultaneous acclimation to nitrogen and iron scarcity in open ocean cyanobacteria revealed by sparse tensor decomposition of metatranscriptomes.&nbsp;</em>The scripts necessary for reproducing the published analyses can be found in the <a href="https://github.com/blasks/barnacle-manuscript">GitHub repository associated with the article</a>. Below is the article abstract and a description of the files included in this dataset.</p> <h2>Abstract</h2> <p>Microbes respond to changes in their environment by adapting their physiology through coordinated adjustments to the expression levels of functionally related genes. To detect these shifts in situ, we developed a sparse tensor decomposition method that derives gene co-expression patterns from inherently complex whole community RNA-sequencing data. Application of the method to metatranscriptomes of the abundant marine cyanobacteria <em>Prochlorococcus</em> and <em>Synechococcus</em> identified responses to scarcity of two essential nutrients, nitrogen and iron, including increased transporter expression, restructured photosynthesis and carbon metabolism, and mitigation of oxidative stress. Further, expression profiles of the identified gene clusters suggest that both cyanobacteria populations experience simultaneous nitrogen and iron stresses in a transition zone between North Pacific oceanic gyres. The results demonstrate the power of our approach to infer organism responses to environmental pressures, hypothesize functions of uncharacterized genes, and extrapolate ramifications for biogeochemical cycles in a changing ecosystem.</p> <h2>Legends for data S1 to S11</h2> <h3>Data S1. <em>Prochlorococcus</em> component profiles.</h3> <p>Median weight profiles for each <em>Prochlorococcus</em> component, including list of associated CyCOGs with corresponding gene weight, bootstrap support, and consensus annotation.</p> <h3>Data S2.&nbsp;<em>Synechococcus</em> component profiles.</h3> <p>Median weight profiles for each <em>Synechococcus</em> component, including list of associated CyCOGs with corresponding gene weight, bootstrap support, and consensus annotation.</p> <h3>Data S3. Enrichment analysis.</h3> <p>Significantly enriched KEGG pathways associated with each component, and compiled consensus annotations for each CyCOG.</p> <h3>Data S4. MED4 CyCOGs.</h3> <p>Mapping of <em>Prochlorococcus</em> MED4 genes to associated CyCOGs.</p> <h3>Data S5. Nitrogen and iron acclimation clusters.</h3> <p>CyCOGs, genes, and annotations for clusters associated with acclimation to nitrogen and iron scarcity.</p> <h3>Data S6. Sample metadata.</h3> <p>Metadata file detailing sampling conditions for all metatranscriptomes used in this study.</p> <h3>Data S7. Genome metadata.</h3> <p>Metadata file for CyCOG v6 reference genomes, including updated clade assignments.</p> <h3>Data S8. CyCOG v6 database.</h3> <p>Tarball of CyCOG v6 database, including reference genomes and annotation data.</p> <h3>Data S9. Reference sequence phylogenies.</h3> <p>Tarball of <em>Prochlorococcus</em> and <em>Synechococcus</em> reference genome phylogenies, used to update clade assignments.</p> <h3>Data S10. <em>Prochlorococcus</em> transcript abundance data.</h3> <p>A netCDF file of raw and normalized <em>Prochlorococcus</em> transcript abundance data, aggregated by CyCOG and organized into an `xarray.Dataset' tensor data structure.</p> <h3>Data S11. <em>Synechococcus</em> transcript abundance data.</h3> <p>A netCDF file of raw and normalized <em>Synechococcus</em> transcript abundance data, aggregated by CyCOG and organized into an `xarray.Dataset' tensor data structure.</p>

opencc-by-4.0Jun 2024View details →
geo24/100

Open ocean and coastal strains of the N2-fixing cyanobacterium UCYN-A have distinct transcriptomes

GEO Series GSE206403. Candidatus Atelocyanobacterium thalassae. 16 samples. Type: Expression profiling by array.

openGEO-OpenFeb 2023View details →
geo20/100

Open Ocean and Coastal Strains of Marine Synechococcus display distinctly different Global Responses to DNA Damaging Agents

GEO Series GSE39818. Synechococcus sp. CC9311; Parasynechococcus marenigrum WH 8102. 24 samples. Type: Expression profiling by array.

openGEO-OpenAug 2013View details →

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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.

allen-brain-atlas
neuroscienceopenDocumentation, web resources, and API references are available online.
Last verified 2026-04-30Open record

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.

abode-home-cage
behavioral-neuroscienceopenThe DataShare record exposes download links for annotations, documentation, license text, and the zipped per-snippet data directory.
Last verified 2026-04-30Open record

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.

dandi-nwb
electrophysiologyopenPublished Dandiset metadata and archive endpoints are available through the production DANDI API.
Last verified 2026-04-30Open record

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.

ibl
behavioral-neuroscienceopenPublic sessions can be searched and loaded from the IBL public data server through ONE.
Last verified 2026-04-29Open record

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.

openneuro
neuroscienceopenPublished datasets are available on demand over the internet.
Last verified 2026-04-29Open record