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.
59
datasets available to search
ShareScore release 0.9.0
Dataset results
59 results for “Metagenomic analysis”
OMA - Metagenomic analysis datasets
<p><strong>Datasets to test and run LOMA and SOMA metagenomic analysis pipelines. </strong></p> <p><strong>Pipelines:</strong></p> <ul> <li><em><a href="https://github.com/ukhsa-collaboration/LOMA/" target="_blank" rel="noopener">LOMA</a></em> - Long-read (Oxford Nanopore only) metagenomic analysis pipeline. </li> <li><a href="https://github.com/ukhsa-collaboration/SOMA/" target="_blank" rel="noopener"><em>SOMA</em></a> - Short-read metagenomic analysis pipeline.</li> </ul> <p><strong>Files:</strong></p> <div> <ul> <li><em>r220.msh</em> <ul> <li>Mash database created from the Genome Taxonomy Database (GTDB) (Release 220).</li> </ul> </li> </ul> <p> </p> <ul> <li><em>ERR7287988.subset.fastq.gz</em> <ul> <li>Non-randomly subset (~10% original dataset size) of Oxford Nanopore sequencing reads of the ZymoBIOMICS HMW DNA Standard. Derived from a publicly available dataset. The original reads are available <a href="https://www.ebi.ac.uk/ena/browser/view/ERR7287988">here</a> and the relevant publication is available <a href="https://www.nature.com/articles/s41592-022-01539-7">here</a>.</li> </ul> </li> </ul> </div>
Determinants of associations between codon and amino acid usage patterns of microbial communities and the environment inferred based on a cross-biome metagenomic analysis
<p>Raw data set for npj Bioflims and Microbiome article: “Determinants of associations between codon and amino acid usage patterns of microbial communities and the environment inferred based on a cross-biome metagenomic analysis”</p>
Metagenomic analysis of gut microbiome illuminates the mechanisms and evolution of lignocellulose degradation in mangrove herbivorous crabs
Open the record for dataset details and reuse information.
Data for "Analysis of metagenome-assembled viral genomes from the human gut reveals diverse putative CrAss-like phages with unique genomic features"
<p>Data for "Analysis of metagenome-assembled viral genomes from the human gut reveals diverse putative CrAss-like phages with unique genomic features" (submitted to Nature Communications)</p>
Multi-faceted metagenomic analysis of spacecraft associated surfaces reveal planetary protection relevant microbial composition
<p>Supplemental tables and figures for manuscript titled: "Multi-faceted metagenomic analysis of spacecraft associated surfaces reveal planetary protection relevant microbial composition"</p> <p><strong>Abstract</strong></p> <p>NASA has been monitoring the microbial burden of spacecraft since the 1970’s Viking missions. Originally based upon culture-based and then focused 16S sequencing techniques, we have now applied whole metagenomic sequencing of cleanroom samples at the Jet Propulsion Lab (JPL), including the Spacecraft Assembly Facility (SAF) with the goals of taxonomic identification and for functional assignment. Our samples included facility pre-filters, cleanroom vacuum debris, and surface wipes. The taxonomic composition was carried out by three different analysis tools. Hierarchical clustering analysis separated vacuum particles from SAF DNA samples. Vacuum particle samples were the most diverse while DNA samples from the ISO facilities and the SAF were the least diverse; all three were dominated by Proteobacteria. Wipe samples had higher diversity and were predominated by Actinobacteria, including human commensals <em>Cutibacterium acnes</em> and <em>Corynebacterium</em>. Taxa identified by the three methods were not identical, supporting the use of multiple methods for metagenome characterization. Likewise, functional annotation was performed using multiple methods. Vacuum particle and SAF tricarboxylic acid cycle and amino acid biosynthesis suggested that many of the identified microorganisms have the ability to grow in nutrient-limited environments. In total, 18 high quality metagenome assembled genomes were generated and were dominated by <em>Moraxella osloensis</em> or <em>Malassezia restricta</em>. A <em>M. osloensis </em>MAG was assembled into a single circular scaffold and gene annotated. This includes a rigorous quantitative determination of microbial loads, and a qualitative dissection of microbial composition. Genomic assembly led to greater confidence of species identification and their functional roles.</p>
Supplementary material 1 from: Graupner N, Boenigk J, Bock C, Jensen M, Marks S, Rahmann S, Beisser D (2017) Functional and phylogenetic analysis of the core transcriptome of Ochromonadales. Metabarcoding and Metagenomics 1: e19862. https://doi.org/10.3897/mbmg.1.19862
KEGG orthologous genes of the core trancriptome of the herein investigated Ochromonadales (Poteriospumella lacustris strains JBC07, JBM10, JBNZ41; Poterioochromonas malhamensis DS; Spumella vulgaris 199hm; Pedospumella encystans JBMS11) used for phylogenetic analyses.
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.
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>
Metagenomic Analysis of Gut Microbiome in Preterm
ClinicalTrials.gov study NCT03235635. IPD Sharing: YES. Countries: 1. Publications: 8.
Data from: Microbial life in a fjord: metagenomic analysis of a microbial mat in Chilean Patagonia
Open the record for dataset details and reuse information.
Data from: Comparing the effectiveness of metagenomics and metabarcoding for diet analysis of a leaf-feeding monkey (Pygathrix nemaeus)
Fecal samples are of great value as a non-invasive means to gather information on the genetics, distribution, demography, diet, and parasite infestation of endangered species. Direct shotgun sequencing of fecal DNA could give information on these simultaneously, but this approach is largely untested. Here we use two fecal samples to characterize the diet of two Red-Shanked Doucs Langurs (Pygathrix nemaeus) that were fed a known combination of foliage, fruits, vegetables and cereals. Illumina HiSeq sequencing produced ~70 million paired reads per sample, of which ~10000 (0.014%) and ~44000 (0.066%) respectively corresponded to chloroplast genomes. Sequences were matched against a database of available chloroplast 'barcodes' for angiosperms. The results were compared with 'metabarcoding' using PCR amplification of the P6 loop of trnL. Shotgun sequencing identified 7 and 9 of the likely 16 diet plants, against 6 and 5 plant species identified by metabarcoding. Metabarcoding produced thousands of reads that were consistent with the known diet, but the barcodes were too short to identify several diet plants to genus. Metagenomics could utilize multiple, longer barcodes that combined had greater power of identification, but rare diet items were not recovered. Read numbers for diet species in metagenomic and metabarcoding data were correlated, indicating that both approaches are useful for determining relative sequence abundance. Metagenomic reads were uniformly distributed across the chloroplast genomes; thus if chloroplast genomes were to be used as reference, the precision of identifications and species recovery would improve further. Metagenomics also recovered the host mitochondrial genome and numerous intestinal parasite sequences in addition to generating data useful for characterizing the microbiome.
Data from: Metagenomic analysis reveals changes of the Drosophila suzukii microbiota in the newly colonised regions
The spotted wing drosophila, Drosophila suzukii (Matsumura) (Diptera: Drosophilidae) is a highly polyphagous pest of a wide variety of wild or cultivated berry and stone fruit. Originating from Southeast Asia, it has recently invaded a wide range of regions in Europe and North-America. It is well known that insect microbiotas may significantly influence several aspects of the host biology and play an important role in invasive species introduction into new areas. However, in spite of the great economic importance of D. suzukii, a limited attention has been given so far to its microbiota. In this study, we present the first in-depth characterization of gut bacterial diversity from field (native and invasive range) and lab-reared populations of this insect. The gut bacterial communities of field insects were dominated, regardless of their origin, by two families of the phylum Proteobacteria: Acetobacteraceae and Enterobacteriaceae, while Firmicutes, mainly represented by the family Staphylococcaceae, prevailed in lab-reared population. Locality was the most significant factor in shaping the microbiota of wild flies. Moreover, a negative correlation between diversity and abundance of Enterobacteriaceae and the time elapsed since the establishment of D. suzukii in a new region was observed. Altogether our results indicate that habitat, food resources as well as the colonization phase of a new region contribute to shape the bacterial communities of the invasive species which, in turn, by evolving more quickly, could influence host adaptation in a new environment.
Data supporting publication: MiFoDB, a workflow for microbial food metagenomic characterization, enables high-resolution analysis of fermented food microbial dynamics
<p>MiFoDB (Microbial Foods Database) is a workflow and primary reference database which includes 675 assembled MAGs and RefSeq bacterial, yeast, fungal, and substrate genomes from fermented foods.</p>
Advanced Metagenomic Analysis of Human Colonic Microbiota in Patients With Chronic GI Disorders
ClinicalTrials.gov study NCT01099111. IPD Sharing: Not stated. Countries: 1. Publications: 0.
Data from: Comparing the effectiveness of metagenomics and metabarcoding for diet analysis of a leaf-feeding monkey (Pygathrix nemaeus)
Open the record for dataset details and reuse information.
Data from: Metagenomic analysis reveals changes of the Drosophila suzukii microbiota in the newly colonised regions
Open the record for dataset details and reuse information.
Integrated Metagenomics and Transcriptomics Analysis Reveals Pathways Associated with Oral Periapical Lesions Formation and Progression
GEO Series GSE299006. Homo sapiens. 16 samples. Type: Expression profiling by high throughput sequencing.
A Metagenomics Analysis of Pandemic 2009 H1N1 Infection in Patients in North America
GEO Series GSE24034. Homo sapiens; Viruses. 29 samples. Type: Expression profiling by array.
Giant panda metagenomic sequencing analysis table
<p>Giant panda metagenomic sequencing function analysis table</p>
Data from: Integrated metabolomics and metagenomics analysis of plasma and urine identified microbial metabolites associated with coronary heart disease
Coronary heart disease (CHD) is top risk factor for health in modern society, causing high mortality rate each year. However, there is no reliable way for early diagnosis and prevention of CHD so far. So study the mechanism of CHD and development of novel biomarkers is urgently needed. In this study, metabolomics and metagenomics technology are applied to discover new biomarkers from plasma and urine of 59 CHD patients and 43 healthy controls and trace their origin. We identify GlcNAc-6-P which has good diagnostic capability and can be used as potential biomarkers for CHD, together with mannitol and 15 plasma cholines. These identified metabolites show significant correlations with clinical biochemical indexes. Meanwhile, GlcNAc-6-P and mannitol are potential metabolites originated from intestinal microbiota. Association analysis on species and function levels between intestinal microbes and metabolites suggest a close correlation between Clostridium sp. HGF2 and GlcNAc-6-P, Clostridium sp. HGF2, Streptococcus sp. M143, Streptococcus sp. M334 and mannitol. These suggest the metabolic abnormality is significant and gut microbiota dysbiosis happens in CHD patients.
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.