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372 results for “MAG”
27 MAGs from the Family of Endozoicomonadaceae derived from Tara Pacific Metagenomes
<p>This dataset contains 27 MAGs from the family of Endozoicomonadaceae generated from a subset of Tara Pacific metagenomes.</p> <p>Contextual information of the MAGs can be found in the associated publication: <strong>Ecology of Endozoicomonadaceae in three coral species across the Pacific Ocean</strong>, Hochart et al, submitted</p> <p> </p>
Field Administration of Stroke Therapy - Magnesium (FAST-MAG) Trial
ClinicalTrials.gov study NCT00059332. IPD Sharing: Not stated. Countries: 1. Publications: 14.
gapseq reconstructions for representative MAGs from the Diet-Microbiome-Study, Kiel, Germany
<p>The archive contains the gapseq (<a href="https://doi.org/10.1186/s13059-021-02295-1">https://doi.org/10.1186/s13059-021-02295-1</a>) output files from the reconstruction of genome-scale metabolic network models for 182 representative (species-level) metagenome-assembled genomes from the manuscript:</p> <p>A Troci, P Rausch, s Waschina, W Lieb, C Bang, A Franke (in preparation) "Long-term dietary effects on human gut microbiota composition employing shotgun metagenomics data analysis"</p> <p> </p>
MAGs from hypersaline swamp in Karpathos island (Greece)
<p>Descriptions of the MAGs derived from a hypersaline swamp in Karpathos island (Greece) using the Protologger software. </p>
Prokaryotic gene catalog, prokaryotic Metagenome-Assembled Genomes (MAGs) and taxonomic profiling of metagenomic data of NEREA Augmented Observatory
<p>The NEREA_metaG directory is dedicated to the in-depth analysis of NEREA microbial communities using metagenomic sequencing data. </p> <p><strong>Gene catalog:</strong> This directory contains the gene catalog compiled from metagenomic data, which includes: Protein and nucleotide sequence files for genes; Cluster files grouping similar genes; Annotation files mapping genes to KEGG pathways; Normalized gene abundance profiles.</p> <div><strong>MAGs:</strong> Directory for Metagenome-Assembled Genomes (MAGs). It contains comprehensive annotation files for the MAGs, providing insights into gene functions, metabolic pathways, and other genomic features. It also contains the individual MAGs categorized by sample origin. Each MAG is stored in a compressed FASTA format.</div> <p><strong>mOTUs</strong>: Contains files related to microbial taxonomic units identified and quantified using the mOTUs profiler. </p>
Supplementary MAGs: SSA Experiments
<p>These are the supplementary MAG fasta files for the manuscript titled for the SSA manuscript. These data will be released alongside a full PNNL DataHub entry upon publication, but are provided here so that reviewers can have access to the files if needed.</p>
MAGs from Glacier-Fed Streams
<p>The biofilm mode of life contributes to the success of microorganisms in extreme environments. Glacier-fed streams feature among Earth’s most extreme aquatic ecosystems because of marked oligotrophy and environmental fluctuations. Here, leveraging 156 metagenomes from the Vanishing Glaciers project, we report thousands of assembled genomes (MAGs) encompassing prokaryotes, algae, fungi, and viruses, and which are involved in biotic interactions within glacier-fed stream biofilms. Bacterial community composition varied regionally and was partially driven by environmental conditions. Bacterial MAGs were characterized by various strategies to exploit inorganic and organic energy sources, functional redundancy and mixotrophy, altogether possible adaptive responses to the glacier-fed stream environment. Our findings suggest that biofilms become more complex and switch from chemoautotrophy to heterotrophy as algal biomass increases in glacier-fed streams owing to glacier shrinkage. Our MAG compendium sheds light on the success of microbial life in glacier-fed streams and provides a resource for future research on a microbiome potentially imperiled by climate change.</p>
Annotation files of 206 MAGs from three different hydrothermal environments
<p>It contains genome annotation files (for 206 genomes). The MAG genomic sequences are deposited to NCBI Genome database under the BioProject ID of PRJNA488180.</p>
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>
20 MAG FoS and the publications and related FoS
<p>Dataset used for the topic evolution experiments</p>
MAGs from Lindstrom et al
<p>Fasta files and information file for 243 microbial metagenome assembled genomes (MAGs) from publication to be submitted titled "<strong>Crop genotypic variation in root exudate composition influences soil microbiome membership and functional potential". </strong></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>
MAGs generated in "Global scale phylogeography of functional traits and microdiversity in Prochlorococcus"
<p>High quality metagenomic assemblies from the manuscript "Global scale phylogeography of functional traits and microdiversity in <em>Prochlorococcus</em>". Pre-print available at: https://doi.org/10.1101/2023.01.24.525399</p>
Genes associated with plant growth-promoting traits (PGPTs) in acidobacteriota MAGs
<p>The prevalence and abundance of Acidobacteriota raise concerns about their ecological function and metabolic activity in the environment. Studies have reported the potential of some members of Acidobacteriota to interact with plants and play a significant role in biogeochemical cycles. However, their role in this context has not been extensively studied. Here, we performed a comprehensive genomic analysis of 758 metagenome-assembled genomes (MAGs) of Acidobacteriota, revealing a high frequency of plant growth-promoting traits (PGPTs) genes.</p>
Large-scale attributed hypergraph datasets: Amazon & MAG-PM
<p>Amazon and MAG-PM are two large-scale datasets of real-world attributed hypergraphs. The ScaNN indices for fast K-nearest neighbor searching are also included.</p><p>For further details, please refer to our publication "Efficient and Effective Attributed Hypergraph Clustering via K-Nearest Neighbor Augmentation" on SIGMOD 2023, and the <a href="https://github.com/CyanideCentral/AHCKA">GitHub repository</a>.</p>
Rituximab to Treat Neuropathy With Anti-MAG Antibodies
ClinicalTrials.gov study NCT00050245. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Anti-MAG First Administration to Human
ClinicalTrials.gov study NCT00622609. IPD Sharing: YES. Countries: 2. Publications: 1.
Pro-resolving Effect of MAG-DHA in Cystic Fibrosis (PREMDIC)
ClinicalTrials.gov study NCT02518672. IPD Sharing: Not stated. Countries: 1. Publications: 14.
Evaluating the Safety of and Immune Response to HIV-MAG DNA Vaccine With or Without Plasmid IL-12 Adjuvant Delivered Intramuscularly Via Electroporation Followed by VSV-gag HIV Vaccine Boost in Health
ClinicalTrials.gov study NCT01578889. IPD Sharing: Not stated. Countries: 1. Publications: 6.
RIMAG Study: Trial of Rituximab Versus Placebo in Polyneuropathy Associated With Anti-MAG IgM Monoclonal Gammopathy
ClinicalTrials.gov study NCT00259974. IPD Sharing: Not stated. Countries: 1. Publications: 1.
ScienceDex guides
Understand access before you commit
These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
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International Brain Laboratory public data
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OpenNeuro
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