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.
915
datasets available to search
ShareScore release 0.7.1
Dataset results
915 results for “metagenomics”
Supplementary material 2 from: Baricevic A, Chardon C, Kahlert M, Karjalainen SM, Pfannkuchen DM, Pfannkuchen M, Rimet F, Tankovic MS, Trobajo R, Vasselon V, Zimmermann J, Bouchez A (2022) Recommendations for the preservation of environmental samples in diatom metabarcoding studies. Metabarcoding and Metagenomics 6: e85844. https://doi.org/10.3897/mbmg.6.85844
Data 2
Supplementary material 3 from: Baricevic A, Chardon C, Kahlert M, Karjalainen SM, Pfannkuchen DM, Pfannkuchen M, Rimet F, Tankovic MS, Trobajo R, Vasselon V, Zimmermann J, Bouchez A (2022) Recommendations for the preservation of environmental samples in diatom metabarcoding studies. Metabarcoding and Metagenomics 6: e85844. https://doi.org/10.3897/mbmg.6.85844
Data 3
Supplementary material 1 from: Baricevic A, Chardon C, Kahlert M, Karjalainen SM, Pfannkuchen DM, Pfannkuchen M, Rimet F, Tankovic MS, Trobajo R, Vasselon V, Zimmermann J, Bouchez A (2022) Recommendations for the preservation of environmental samples in diatom metabarcoding studies. Metabarcoding and Metagenomics 6: e85844. https://doi.org/10.3897/mbmg.6.85844
Data 1
Zoo elephant metagenomic Kraken2 reports
<p>Non-invasive biological samples benefit studies that investigate rare, elusive, endangered, and/or dangerous species. Integrating genomic techniques that use non-invasive biological sampling with advances in computational approaches can benefit and inform wildlife conservation and management. We use non-invasive fecal DNA samples to generate low- to medium-coverage genomes (e.g., >90% of the complete nuclear genome at 6 X-fold coverage) and metagenomic sequences, combining widely available and accessible DNA collection cards with commonly used DNA extraction and library-building approaches. DNA preservation cards are easy to transport and can be stored non-refrigerated, avoiding cumbersome and/or costly sample methods. The genomic library construction and shotgun sequencing approach did not require enrichment or targeted DNA amplification. The utility and potential of the generated data generated were demonstrated through genome-scale analysis and metagenomics of zoo and free-ranging African savanna elephants (<em>Loxodonta</em> <em>africana</em>). Fecal samples collected from free-ranging individuals contained an average of 12.41% (5.54–21.65%) endogenous elephant DNA. Clustering of these elephants with others from the same geographic region was demonstrated by principal component analysis of genetic variation using nuclear genome-wide SNPs. Metagenomic analyses generated compositional taxon classifications that included Loxodonta, green plants, fungi, arthropods, bacteria, viruses, and archaea, showcasing the utility of this approach for addressing complementary questions based on host-associated DNA, e.g., pathogen and parasite identification. The molecular and bioinformatic analyses presented here contribute towards the expansion and application of genomic techniques to conservation science and practice.</p>
Supplementary material 1 from: Sun T, Zou W, Dong Q, Huang O, Tang D, Yu H (2022) Morphology, phylogeny, mitogenomics and metagenomics reveal a new entomopathogenic fungus Ophiocordyceps nujiangensis (Hypocreales, Ophiocordycipitaceae) from Southwestern China. MycoKeys 94: 91-108. https://doi.org/10.3897/mycokeys.94.89425
Relevant species information and GeneBank accession numbers for phylogenetic research in this study
Metagenomics Dataset From Chemocline of Lake Cadagno
<p>The metagenomics dataset was collected from the persistent microbial bloom from the chemocline (oxic-anoxic boundary) of Lake Cadagno. The location of the chemocline was between 13-15.5 m in depth on the day of sampling (29 August 2017). There are a total of 4 metagenomics samples collected between 13-15.5m depth labeled as 13m, 15mm, 15mw (without mesh), and 15_5m.</p> <h3><strong>If you use this dataset, please cite both the article and Zenodo source</strong></h3> <p>1) Saini, J.S., Manni, M., Hassler, C. <em>et al.</em> Genomic insights into the coupling of a <em>Chlorella</em>-like microeukaryote and sulfur bacteria in the chemocline of permanently stratified Lake Cadagno. <em>ISME J</em> <strong>17</strong>, 903–915 (2023). <a href="https://doi.org/10.1038/s41396-023-01396-y">https://doi.org/10.1038/s41396-023-01396-y</a></p> <p>2) Jaspreet Singh Saini, Mosè Manni, Christel Hassler, Rachel Cable, Melissa B. Duhaime, & Evgeny M. Zdobnov. (2023). Metagenomics Dataset From Chemocline of Lake Cadagno [Data set]. Zenodo. <a href="https://doi.org/10.5281/zenodo.7505505">https://doi.org/10.5281/zenodo.7505505 </a></p>
Supplementary material 2 from: Osman OA, Andersson J, Martin-Sanchez PM, Eiler A (2022) National eDNA-based monitoring of Batrachochytrium dendrobatidis and amphibian species in Norway. Metabarcoding and Metagenomics 6: e85199. https://doi.org/10.3897/mbmg.6.85199
Table S2
Supplementary material 7 from: Bíró T, Duleba M, Földi A, Kiss KT, Orgoványi P, Trábert Z, Vadkerti E, Wetzel CE, Ács É (2022) Metabarcoding as an effective complement of microscopic studies in revealing the composition of the diatom community – a case study of an oxbow lake of Tisza River (Hungary) with the description of a new Mayamaea species. Metabarcoding and Metagenomics 6: e87497. https://doi.org/10.3897/mbmg.6.87497
Alignment S1
Supplementary material 6 from: Bíró T, Duleba M, Földi A, Kiss KT, Orgoványi P, Trábert Z, Vadkerti E, Wetzel CE, Ács É (2022) Metabarcoding as an effective complement of microscopic studies in revealing the composition of the diatom community – a case study of an oxbow lake of Tisza River (Hungary) with the description of a new Mayamaea species. Metabarcoding and Metagenomics 6: e87497. https://doi.org/10.3897/mbmg.6.87497
Figure S1
Supplementary material 3 from: Osman OA, Andersson J, Martin-Sanchez PM, Eiler A (2022) National eDNA-based monitoring of Batrachochytrium dendrobatidis and amphibian species in Norway. Metabarcoding and Metagenomics 6: e85199. https://doi.org/10.3897/mbmg.6.85199
Table S3, Figures S1, S2
Supplementary material 9 from: Bíró T, Duleba M, Földi A, Kiss KT, Orgoványi P, Trábert Z, Vadkerti E, Wetzel CE, Ács É (2022) Metabarcoding as an effective complement of microscopic studies in revealing the composition of the diatom community – a case study of an oxbow lake of Tisza River (Hungary) with the description of a new Mayamaea species. Metabarcoding and Metagenomics 6: e87497. https://doi.org/10.3897/mbmg.6.87497
Alignment S3
Supplementary material 5 from: Bíró T, Duleba M, Földi A, Kiss KT, Orgoványi P, Trábert Z, Vadkerti E, Wetzel CE, Ács É (2022) Metabarcoding as an effective complement of microscopic studies in revealing the composition of the diatom community – a case study of an oxbow lake of Tisza River (Hungary) with the description of a new Mayamaea species. Metabarcoding and Metagenomics 6: e87497. https://doi.org/10.3897/mbmg.6.87497
Table S5
Supplementary material 4 from: Bíró T, Duleba M, Földi A, Kiss KT, Orgoványi P, Trábert Z, Vadkerti E, Wetzel CE, Ács É (2022) Metabarcoding as an effective complement of microscopic studies in revealing the composition of the diatom community – a case study of an oxbow lake of Tisza River (Hungary) with the description of a new Mayamaea species. Metabarcoding and Metagenomics 6: e87497. https://doi.org/10.3897/mbmg.6.87497
Table S4
Supplementary material 1 from: Martoni F, Smith RL, Piper AM, Nancarrow N, Aftab M, Trebicki P, Kimber RBE, Rodoni BC, Blacket MJ (2023) Non-destructive insect metabarcoding as a surveillance tool for the Australian grains industry: a first trial for the iMapPESTS smart trap. Metabarcoding and Metagenomics 7: e95650. https://doi.org/10.3897/mbmg.7.95650
All the taxa (ASVs) recorded in this study
Supplementary material 2 from: Martoni F, Smith RL, Piper AM, Nancarrow N, Aftab M, Trebicki P, Kimber RBE, Rodoni BC, Blacket MJ (2023) Non-destructive insect metabarcoding as a surveillance tool for the Australian grains industry: a first trial for the iMapPESTS smart trap. Metabarcoding and Metagenomics 7: e95650. https://doi.org/10.3897/mbmg.7.95650
Species accumulation curve
Supplementary material 1 from: Dou H, Wang M, Yin X, Feng L, Yang H (2023) Can the Eurasian otter (Lutra lutra) be used as an effective sampler of fish diversity? Using molecular assessment of otter diet to survey fish communities. Metabarcoding and Metagenomics 7: e96733. https://doi.org/10.3897/mbmg.7.96733
Bioinformatic processing
Supplementary material 2 from: Dou H, Wang M, Yin X, Feng L, Yang H (2023) Can the Eurasian otter (Lutra lutra) be used as an effective sampler of fish diversity? Using molecular assessment of otter diet to survey fish communities. Metabarcoding and Metagenomics 7: e96733. https://doi.org/10.3897/mbmg.7.96733
appendices S1–S4.2
Supplementary material 3 from: Okanishi M, Kohtsuka H, Wu Q, Shinji J, Shibata N, Tamada T, Nakano T, Minamoto T (2023) Development of two new sets of PCR primers for eDNA metabarcoding of brittle stars (Echinodermata, Ophiuroidea). Metabarcoding and Metagenomics 7: e94298. https://doi.org/10.3897/mbmg.7.94298
A specimen list of brittle star species collected from Sagami Bay in the last 10 years
Supplementary material 4 from: Okanishi M, Kohtsuka H, Wu Q, Shinji J, Shibata N, Tamada T, Nakano T, Minamoto T (2023) Development of two new sets of PCR primers for eDNA metabarcoding of brittle stars (Echinodermata, Ophiuroidea). Metabarcoding and Metagenomics 7: e94298. https://doi.org/10.3897/mbmg.7.94298
Supplementary images S1–S16
Supplementary material 2 from: Okanishi M, Kohtsuka H, Wu Q, Shinji J, Shibata N, Tamada T, Nakano T, Minamoto T (2023) Development of two new sets of PCR primers for eDNA metabarcoding of brittle stars (Echinodermata, Ophiuroidea). Metabarcoding and Metagenomics 7: e94298. https://doi.org/10.3897/mbmg.7.94298
Taxonomic notes for detected taxa
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.