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 4 from: Li Y, Evans NT, Renshaw MA, Jerde CL, Olds BP, Shogren AJ, Deiner K, Lodge DM, Lamberti GA, Pfrender ME (2018) Estimating fish alpha- and beta-diversity along a small stream with environmental DNA metabarcoding. Metabarcoding and Metagenomics 2: e24262. https://doi.org/10.3897/mbmg.2.24262
Mantel r and p-values for all the pairwise comparisons between single marker, three markers and longitudinal distance. :
Supplementary material 5 from: Li Y, Evans NT, Renshaw MA, Jerde CL, Olds BP, Shogren AJ, Deiner K, Lodge DM, Lamberti GA, Pfrender ME (2018) Estimating fish alpha- and beta-diversity along a small stream with environmental DNA metabarcoding. Metabarcoding and Metagenomics 2: e24262. https://doi.org/10.3897/mbmg.2.24262
The correlation between environmental variables and β-diversity and longitudinal distance using Mantel test :
Metagenomics 16S data
<p>from Igor Makunin. </p>
Metagenomics binning and annotation dataset of Elkhorn Slough microbial mats
<p>Supplemental sequencing and annotation data for metagenomics binning and annotation dataset of Elkhorn Slough microbial mats. </p> <p>Mats.Combined.Annotations.IP.GN.RS.IMG.PA.SE.KO.zip : Zipped annotation file of MG-RAST annotations from 3 combined metagenomic binning datasets. Annotations are pulled from Interpro, GenBank, RefSeq, IMG, PATRIC, SEED, and KEGG.</p> <p>k63.seq.zip : Scaffold and Prodigal called ORFs of the k63 co-assembly</p> <p>k45.seq.zip : Scaffold and Prodigal called ORFs of the k45 co-assembly</p> <p>k29.seq.zip : Scaffold and Prodigal called ORFs of the k29 co-assembly</p> <p>binning.zip: Scaffold coverage and annotations used for binning</p>
Metagenomic datasets Gutless Oligochetes (2018)
<p>This list contains accession numbers to:</p> <p>-Metatranscriptomic data of gutless oligochaete Olavius algarvensisworms depositied in European Nucleotide Archive ENA</p> <p>-Metaproteomic data of gutless oligochaete Olavius algarvensisworms deposited in proteomics data repositories</p> <p>-Draft genomes of endosymbionts from various gutless oligochaete hosts, in submission process.</p> <p>If you are interested in these datasets, please let us know.</p>
Supplementary material 2 from: Cahoon AB, Huffman AG, Krager MM, Crowell RM (2018) A meta-barcoding census of freshwater planktonic protists in Appalachia – Natural Tunnel State Park, Virginia, USA. Metabarcoding and Metagenomics 2: e26939. https://doi.org/10.3897/mbmg.2.26939
Figure 2. Rarefaction analysis estimates demonstrate that family and genus collections were approaching saturation :
Fueling ab initio folding with oceanic metagenomics enables structure and function predictions of new protein families
<p>Code and protein sequence database to construct multiple sequence alignment from Tara Ocean data.</p>
Dataset for "Metagenome-Assembled Bacterial Genomes from Long Accurate Reads Associated with Capilliphycus salinus ALCB114379"
<p>We present the raw genomic dataset of the marine cyanobacterium Capilliphycus salinus ALCB114379, sequenced using PacBio HiFi long-read technology.</p> <p><strong>ABSTRACT</strong></p> <p><span>We report the complete genome sequences of five bacteria linked to the marine cyanobacterium <em>Capilliphycus salinus</em> ALCB114379 from the phylum Pseudomonadota. This genetic diversity offers new insights into the genetic landscape and potential symbiotic relationships of cyanobacteria-associated microbiota.</span></p>
Benchmarking datasets used in the manuscript "HyLight: Strain aware assembly of low coverage metagenomes"
Open the record for dataset details and reuse information.
Annual dynamics and metagenomics of marine vesicles: a layer of complexity in the dissolved organic fraction
<p>The dataset includes additional data for the same paper, <em>"Annual dynamics and metagenomics of marine vesicles: a layer of complexity in the dissolved organic fraction."</em> The data were uploaded separately due to the 50.00 GB limit on available upload space.</p> <p>The gene sequences contained within EVs were annotated using the DRAM program within the Kbase platform, enabling us to identify the specific types and functions of genes packaged within EV fractions. This annotation process provided a comprehensive overview of the genetic cargo potentially encapsulated in EV fractions 25% and 20%.</p> <p>The provided Excel files represent the output from DRAM annotation and contain the detected genes in EV fractions 25% and 20%. Although the gene names in the files are labeled as 30%, 25%, and 20%, this is a naming error. The file labeled "annotation for EVs 25%" contains genes detected in the 25% EV fraction, while the file labeled "annotation for EVs 20%" corresponds to genes from the 20% EV fraction.</p> <p>There are two replicates for the 20% EV fraction, denoted as rep1 and rep2, and both samples were analyzed. The gene abundance was calculated as the mean percentage of the two replicates, corrected with standard error.</p> <p> </p>
Relative abundance tables for bacterial species, pathways, ARGs, and VFGs in "Gut Microbial Community Structure, Metabolic Signature, and Resistome in Dyslipidemia: Insights from Metagenomic Sequencing"
<p>Dyslipidemia, characterized by abnormal blood lipid levels, is a significant risk factor for cardiovascular disease. Emerging evidence suggests that the gut microbiota plays a role in lipid metabolism, although findings across studies have varied. In this study, we analyzed the gut microbiota, metabolic pathways, predicted gut metabolites, and resistome in 1384 participants (895 with dyslipidemia cases and 489 controls) using shotgun metagenomic sequencing. Our results revealed that Bacteroides caccae was enriched in dyslipidemia cases, potentially contributing to inflammation and altered lipid metabolism, while Coprococcus eutactus and Coprococcus catus, known producers of short-chain fatty acids (SCFAs) in lipid regulation, and Blautia obeum, known to be positively impacted by SCFAs, were more abundant in controls. We also identified an enrichment of the dTDP-beta-D-fucofuranose biosynthesis pathway gene family, which is linked to bacterial pathogenicity, in dyslipidemia cases, with Bacteroides stercoris contributing strongly. Dyslipidemia cases exhibited depleted glycogen and peptidoglycan biosynthesis pathways, potentially impairing energy storage and immune function, alongside distinct metabolic profiles, including decreased pseudouridine, which may affect RNA metabolism. Furthermore, we observed a higher abundance of antibiotic-resistance genes, particularly tetQ, in dyslipidemia cases, suggesting a link between gut resistome and metabolic disorders. These findings provide new insights into how dysbiosis of the gut microbiota may contribute to the pathophysiology of dyslipidemia, offering potential avenues for microbiome-based interventions in personalized medicine.</p>
Large-scale metagenomic analysis of oral microbiomes reveals markers for autism spectrum disorders, MetaPhlAn 3 profiles
Open the record for dataset details and reuse information.
Interactive heatmaps for metagenome assembled genome (MAG) metagenomic potential and metaproteomic peptide recruitment
<p>Interactive heatmaps for supplementary figure 1 and supplementary figure 4 from publication to be submitted titled "<strong>Microbial genome-resolved metaproteomic analyses frame intertwined carbon and nitrogen cycles in river hyporheic sediments". </strong></p>
Supplementary material 7 from: {"en": "Buchner D, Haase P, Leese F (2021) Wet grinding of invertebrate bulk samples – a scalable and cost-efficient protocol for metabarcoding and metagenomics. Metabarcoding and Metagenomics 5: e67533. https://doi.org/10.3897/mbmg.5.67533"}
Figure S2. Baseline-corrected amplification curves (left half) and melting -curves (right half) for A & B) kick-net samples and C & D) malaise trap samples
Sequencing summary files for "Nanopore adaptive sampling: a tool for enrichment of low abundance species in metagenomic samples"
<p>Sequencing summary files for experiments in "Nanopore adaptive sampling: a tool for enrichment of low abundance species in metagenomic samples". </p>
Time-series drinking water metagenomes: Assemblies & MAGs
<p><span><span><span><span><span><span><span><span><span><span><span>Reconstructing microbial genomes from metagenomic short-read data can be challenging due to the unknown and uneven complexity of microbial communities. This complexity encompasses highly diverse populations which often includes strain variants. Reconstructing high-quality genomes is a crucial part of the metagenomic workflow as subsequent ecological and metabolic inferences depend on their accuracy, quality and completeness. In contrast to microbial communities in other ecosystems, there has been no systematic assessment of genome-centric metagenomic workflows for drinking water microbiomes. In this study, we assessed the performance of a combination of assembly and binning strategies for time-series drinking water metagenomes that were collected over 6 months. The goal of this study was to identify the combination of assembly and binning approaches that results in high quality and quantity metagenome-assembled genomes (MAGs), representing most of the sequenced metagenome. Our findings suggest that the metaSPAdes co-assembly strategies had the best performance as they resulted in larger and less fragmented assemblies with at least 85% of the sequence data mapping to contigs greater than 1kbp. Furthermore, a combination of metaSPAdes co-assembly strategies and MetaBAT2 produced the highest number of medium-quality MAGs while capturing at least 70% of the metagenomes based on read recruitment. Utilizing different assembly/binning approaches also assist in the reconstruction of unique MAGs from closely related species that would have otherwise collapsed into a single MAG using a single workflow. Overall, our study suggests that leveraging multiple binning approaches with different metaSPAdes co-assembly strategies may be required to maximize the recovery of good-quality MAGs.</span></span></span></span></span></span></span></span></span></span></span></p>
Metagenomic and metatranscriptomics data for Bathymodiolus mussel and deep-sea sponge associated symbionts deposited in NCBI, IMG and other databases
<p>Metagenomic data for the sulfur- and methane-oxidizing symbionts of <em>Bathymodiolus</em> mussels and different sponge species deposited in the Integrated Microbial Genomes (IMG) database of the DOE Joint Genome Institute (http://img.jgi.doe.gov/) and NCBI until October 2018</p>
Data for: Metagenomics show high spatiotemporal virus diversity and ecological compartmentalisation: virus infections of melon, Cucumis melo, crops and adjacent wild communities
<p>Emergence of viral diseases results from novel transmission dynamics between wild and crop plant communities. The bias of studies towards pathogenic viruses of crops has distracted from knowledge of non-antagonistic symbioses in wild plants. Here we implemented a high throughput approach to compare the viromes of melon (<em>Cucumis melo</em>)<em>, </em>and wild plants of crop (Crop) and adjacent boundaries (Edge). Each of the 41-plant species examined was infected by at least one virus. The interactions of 104 virus operational taxonomic units (OTUs) with these hosts occurred largely within ecological compartments of either Crop or Edge, Edge having traits of a reservoir community. The positive correlation of virus and plant richness at each site, the tendency for increased specialist host use through seasons, and specialist host use by OTUs observed only in Melon, characterised local-scale patterns of infection. In this study of systematically sampled viromes of crop and adjacent wild communities most hosts showed no disease symptoms, suggesting non-antagonistic symbioses are common. The coexistence of viruses within species-rich ecological compartments of agro-systems might promote the evolution of a diversity of virus strategies for survival and transmission. These communities, including those suspected as reservoirs, are subject to sporadic changes in assemblages, and so too are the conditions that favour the emergence of disease.</p>
Metagenomic analysis of paleofeces using metaGEM
<p>Re-analysis using <a href="https://github.com/franciscozorrilla/metaGEM">metaGEM</a> of 8 ancient metagenomes published by Wibowo, M.C., Yang, Z., Borry, M. <em>et al.</em> Reconstruction of ancient microbial genomes from the human gut. <em>Nature</em> <strong>594</strong>, 234–239 (2021). https://doi.org/10.1038. </p> <p>1. metagem_wibowo2021.tar.gz: DNA fasta files for 805 reconstructed MAGs of at least medium quality</p> <p>2. reassembled.checkm: CheckM output for 805 MAGs</p> <p>3. GTDBTk.stats: GTDB-Tk output for 805 MAGs</p>
Supplementary material 4 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
Phylogenetic analyses of the ranked top 50 families identified from Ophiocordyceps nujiangensis based on maximum likelihood (ML). Values at the nodes are ML bootstrap proportions
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.