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.
278
datasets available to search
ShareScore release 0.9.0
Dataset results
278 results for “water samples”
PIE LTER, Year 2017-2018, locations, date, sediment concentration and spectral reflectance measurement methods of 40 water samples at Plum Island Sound and deep ocean, Massachusetts.
PIE LTER, Year 2017-2018, locations, date, sediment concentration and spectral reflectance measurement methods of 40 water samples at Plum Island Sound and deep ocean, Massachusetts
Genome-scale target capture of mitochondrial and nuclear environmental DNA from water samples
<p>Environmental DNA (eDNA) provides a promising supplement to traditional sampling methods for population genetic inferences, but current studies have almost entirely focused on short mitochondrial markers. Here, we develop one mitochondrial and one nuclear set of target capture probes for the whale shark (<i>Rhincodon typus</i>) and test them on seawater samples collected in Qatar to investigate the potential of target capture for eDNA-based population studies. The mitochondrial target capture successfully retrieved ~235x (90x-352x per base position) coverage of the whale shark mitogenome. Using a minor allele frequency of 5%, we find 29 variable sites throughout the mitogenome, indicative of at least five contributing individuals. We also retrieved numerous mitochondrial reads from an abundant non-target species mackerel tuna<i> </i>(<i>Euthynnus affinis</i>), showing a clear relation between sequence similarity to the capture probes and the number of captured reads. The nuclear target capture probes retrieved only few reads and polymorphic variants from the whale shark, but we successfully obtained millions of reads and thousands of polymorphic variants with different allele frequencies from <i>E</i>. <i>affinis</i>. We demonstrate that target capture of complete mitochondrial genomes and thousands of nuclear loci is possible from aquatic eDNA samples. Our results highlight that careful probe design, taking into account the range of divergence between target and non-target sequences as well as presence of non-target species at the sampling site, is crucial to consider. Environmental DNA sampling coupled with target capture approaches provide an efficient means with which to retrieve population genomic data from aggregating and spawning aquatic species.</p>
Grain size distribution of Amazon river sediment samples collected over the period 2005-2008; and ADCP water velocity profiles collected on the major tributaries of the Amazon in Bolivia and Peru, 2007-2008
<p>This dataset contains two items:</p> <p>- The grain size distribution of river sediment samples collected along the Amazon River and its tributaries during four sampling campaigns performed in June 2005 (lower Amazon, Brazil), March 2006 (lower Amazon, Brazil), May 2007 (Upper Madeira, Bolivia), and April 2008 (Upper Solimões-Amazonas, Peru). [spreadsheet "Grain_size_distribution_dataset_Amazon_2005-2008_Bouchez_data.xlsx"].</p> <p>- River water velocity profiles derived from Acoustic Doppler Current Profiler (ADCP) measurements performed on the major tributaries of the Amazon in May 2007 (Upper Madeira, Bolivia) and April 2008 (Upper Solimões-Amazonas, Peru) [folder "ADCP_dataset_Amazon_2007-2008_Bouchez_data"].</p> <p>The dataset description and the relevant references are provided in the text files "Grain_size_distribution_dataset_Amazon_2005-2008_Bouchez_description.docx" and "ADCP_dataset_Amazon_2007-2008_Bouchez_description.docx" .</p> <p>These data were acquired thanks to the support of the French National Service for Observation "HYBAM" ("Hydrogeochemistry of the Amazon Basin"), part of the CNRS National Infrastructure "OZCAR" ("Critical Zone Observatories: Applications and Research").</p>
FIG. 25 in Triphoridae (Gastropoda) from Martinique sampled by the MADIBENTHOS expedition, with notes on shallow-water species from Guadeloupe
FIG. 25. — Depth range of triphorid species in Martinique, sampled by MADIBENTHOS.
FIG. 10 in Triphoridae (Gastropoda) from Martinique sampled by the MADIBENTHOS expedition, with notes on shallow-water species from Guadeloupe
FIG. 10. — Metaxia sp. MNHN, sta. AB181, 2.6 mm. Scale bars: A, B, 1 mm; C, 200 μm; D, 100 μm.
Figure. Sampling stations (BS: beach seine, BT: beam trawl). in Length-weight relationships of forty-nine fish species from shallow waters of Gökçeada Island, northern Aegean Sea
Figure. Sampling stations (BS: beach seine, BT: beam trawl).
Data from: Detection of the endangered European weather loach (Misgurnus fossilis) via water and sediment samples: testing multiple eDNA workflows.
<p>The European weather loach (<i>Misgurnus fossilis</i>) is classified as highly endangered in several countries of Central Europe. Populations of <i>M. fossilis</i> are predominantly found in ditches with low water levels and thick sludge layers and are thus hard to detect using conventional fishing methods. Therefore, environmental DNA (eDNA) monitoring appears particularly relevant for this species. In previous studies, <i>M. fossilis</i> was surveyed following eDNA water sampling protocols, which were not optimized for this species. Therefore, we created two full factorial study designs to test six different eDNA workflows for sediment samples and twelve different workflows for water samples. We used qPCR to compare the Threshold cycle (Ct) values of the different workflows, which indicate the target DNA amount in the sample, and spectrophotometry to quantify and compare the total DNA amount inside the samples. We analyzed 96 water samples and 48 sediment samples from a pond with a known population of <i>M. fossilis</i>. We tested several method combinations for long-term sample preservation, DNA capture and DNA extraction. Additionally, we analyzed the DNA yield of samples from a ditch with a natural <i>M. fossilis</i> population monthly over one year to determine the optimal sampling period. Our results showed that the long-term water preservation method commonly used for eDNA surveys of <i>M. fossilis </i>did not lead to optimal DNA yields, and we present a valid long-term sample preservation alternative. A cost-efficient high salt DNA extraction led to the highest target DNA yields and can be used for sediment and water samples. Furthermore, we were able to show that in a natural habitat of <i>M. fossilis</i>, total and target eDNA were higher between June and September, which implies that this period is favorable for eDNA sampling. Our results will help to improve the reliability of future eDNA surveys of <i>M. fossilis</i>.</p>
Data from: Detection of vertebrates from natural and artificial inland water bodies in a semi-arid habitat using eDNA from filtered, swept and sediment samples
<p>Climate warming will impact the sustainability of arid and semi-arid zone environments so we need to understand the influence of changes in arid lands on vertebrate populations. However, biomonitoring and biodiversity assessment in arid environments can be prohibitively time-consuming, expensive, and logistically challenging due to their often remote and inhospitable nature. Sampling of environmental DNA (eDNA) coupled with high-throughput sequencing is an emerging biodiversity assessment method. Here we explore the application of eDNA metabarcoding and various sampling approaches to estimate vertebrate richness and assemblage at human-constructed and natural water sources in a semi-arid region of Western Australia. Three sampling methods: sediment samples, filtering through a membrane with a pump, and membrane sweeping in the water body, were compared using two eDNA metabarcoding assays, 12S-V5 and 16smam, for 120 eDNA samples collected from four gnammas (gnamma: Australian Indigenous Noongar language term – granite rock pools) and four cattle troughs in the Great Western Woodlands, Western Australia. We detected higher vertebrate richness in samples from cattle troughs and found differences between assemblages detected in gnammas (more birds and amphibians) and cattle troughs (more mammals, including feral taxa). Total vertebrate richness was not different between swept and filtered samples, but all sampling methods yielded different assemblages. Our findings indicate that eDNA surveys in arid lands will benefit from collecting multiple samples at multiple water sources to avoid underestimating vertebrate richness. The high concentration of eDNA in small, isolated water bodies permits the use of sweep sampling which simplifies sample collection, processing, and storage, particularly when assessing vertebrate biodiversity across large spatial scales.</p>
Data from: Refining sampling efforts for fish diversity assessment in subtropical urban estuarine and oceanic waters using environmental DNA with multiple primers
Open the record for dataset details and reuse information.
Bony fish 12S rRNA sequencing data from coastal water samples in gulf of Maine
Open the record for dataset details and reuse information.
Genome-scale target capture of mitochondrial and nuclear environmental DNA from water samples
Open the record for dataset details and reuse information.
Data from: Detection of the endangered European weather loach (Misgurnus fossilis) via water and sediment samples: testing multiple eDNA workflows.
Open the record for dataset details and reuse information.
Deep eutectic solvent-based emulsification liquid-liquid microextraction coupled with HPLC-UV for the analysis of phenoxy acid herbicides in paddy field water samples
Open the record for dataset details and reuse information.
Data from: Detection of vertebrates from natural and artificial inland water bodies in a semi-arid habitat using eDNA from filtered, swept and sediment samples
Open the record for dataset details and reuse information.
Marine biomonitoring with eDNA: can metabarcoding of water samples cut it as a tool for surveying benthic communities?
<p>In the marine realm, biomonitoring using eDNA of benthic communities requires destructive direct sampling or the setting-up of settlement structures. Comparatively much less effort is required to sample the water column, which can be accessed remotely. In this study we assess the feasibility of obtaining information from the eukaryotic benthic communities by sampling the adjacent water layer. We studied two different rocky-substrate benthic communities with a technique based on quadrat sampling. We also took replicate water samples at distances from a few centimetres to 20 m from the benthic habitat. Using as marker a fragment of the Cytochrome c oxidase subunit I gene with universal primers, we obtained a total of 3,543 molecular operational taxonomic units (MOTUs) from the samples. The structure obtained in the two environments was markedly different, with Metazoa, Archaeplastida Rhodophyta and Stramenopiles being the most diverse group in benthic samples, and HacrobiaAlveolata, Metazoa and Alveolata Rhizaria in the water. Only 265 MOTUs (7.5%) were shared between benthos and water samples, and of these 180 MOTUs (5.1%) were identified as benthic MOTUs that left their DNA in the water. Most of them were found immediately adjacent to the benthos, and their number decreased and The distribution of these benthic shared MOTUs showed a decrease both in number of MOTUs and in number of reads as we moved apart from the benthic habitat. It was concluded that water eDNA, even in the close vicinity of the benthos, was a poor proxy for the analysis of benthic structure, and that direct sampling methods are required for monitoring these complex benthic communities via metabarcoding.</p>
Data from: Detection of invasive mosquito vectors using environmental DNA (eDNA) from water samples
Repeated introductions and spread of invasive mosquito species (IMS) have been recorded on a large scale these last decades worldwide. In this context, members of the mosquito genus Aedes can present serious risks to public health as they have or may develop vector competence for various viral diseases. While the Tiger mosquito (Aedes albopictus) is a well-known vector for e.g. dengue and chikungunya viruses, the Asian bush mosquito (Ae. j. japonicus) and Ae. koreicus have shown vector competence in the field and the laboratory for a number of viruses including dengue, West Nile fever and Japanese encephalitis. Early detection and identification is therefore crucial for successful eradication or control strategies. Traditional specific identification and monitoring of different and/or cryptic life stages of the invasive Aedes species based on morphological grounds may lead to misidentifications, and are problematic when extensive surveillance is needed. In this study, we developed, tested and applied an environmental DNA (eDNA) approach for the detection of three IMS, based on water samples collected in the field in several European countries. We compared real-time quantitative PCR (qPCR) assays specific for these three species and an eDNA metabarcoding approach with traditional sampling, and discussed the advantages and limitations of these methods. Detection probabilities for eDNA-based approaches were in most of the specific comparisons higher than for traditional survey and the results were congruent between both molecular methods, confirming the reliability and efficiency of alternative eDNA-based techniques for the early and unambiguous detection and surveillance of invasive mosquito vectors. The ease of water sampling procedures in the eDNA approach tested here allows the development of large-scale monitoring and surveillance programs of IMS, especially using citizen science projects.
FIGURE 17 in Morphological features of larvae of Pandalus eous, P. goniurus, and P. tridents (Decapoda, Pandalidae) from planktonic samples taken in marine waters near Kamchatka Peninsula
FIGURE 17. Morphology features of Pandalus tridens. First zoeal stage. Abbreviations above in Materials and methods. Scale: 1 mm.
FIGURE 16 in Morphological features of larvae of Pandalus eous, P. goniurus, and P. tridents (Decapoda, Pandalidae) from planktonic samples taken in marine waters near Kamchatka Peninsula
FIGURE 16. Morphology features of Pandalus goniurus. Decapodid stage. Abbreviations above in Materials and methods. Scale: 1 mm.
FIGURE 11 in Morphological features of larvae of Pandalus eous, P. goniurus, and P. tridents (Decapoda, Pandalidae) from planktonic samples taken in marine waters near Kamchatka Peninsula
FIGURE 11. Morphology features of Pandalus goniurus. Second zoeal stage. Abbreviations above in Materials and methods. Scale: 1 mm.
FIGURE 9 in Morphological features of larvae of Pandalus eous, P. goniurus, and P. tridents (Decapoda, Pandalidae) from planktonic samples taken in marine waters near Kamchatka Peninsula
FIGURE 9. Morphology features of Pandalus eous. Decapodid stage. Abbreviations above in Materials and methods. Scale: 1 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.