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372 results for “MAGs”
Venusian bow shock crossings manually identified from measurements by the ASPERA-4 and MAG instruments onboard Venus Express
<p>Bow shock crossings at Venus identified manually from the ASPERA-4 and MAG instruments onboard Venus Express for the full mission from 2006 to 2014.</p> <p>A detailed description of the dataset can be found in the paper "Influence of solar wind variations on the shapes of Venus’ plasma boundaries based on Venus Express observations" by Signoles et al.</p> <p>The boundary crossings by Venus Express are determined from combining the measurements of both ion, electron and magnetic field measurements. The bow shock is identified from the sharp increase in the magnetic field magnitude, and the increase in electron and ion temperature. The ion composition boundary is identified from the decrease in magnetosheath protons and electrons, and the appearance of planetary heavy ions.</p> <p>The dataset contains 5193 identified bow shock crossings and 2679 identified ion composition boundary crossings.</p> <p>For more information on the dataset contact: M. Persson, moaperssonphd at gmail.com</p>
MAG Collection - Rühlemann et al.: Comparative metagenomics reveals host-specific functional adaptation of intestinal microbiota across hominids
<p>This tar-Archives hold the complete collection of n=7,506 metagenome-assembled genomes presented in the preprint "Comparative metagenomics reveals host-specific functional adaptation of intestinal microbiota across hominids" by Rühlemann <em>et al., <a href="https://www.biorxiv.org/content/10.1101/2023.03.01.530589v1">bioRxiv</a>, </em>2023.</p> <p>Article Summary</p> <p>Characterizing trajectories of the composition and function of hominid gut microbiota across diverse environments and host species can help reveal specific properties of the human microbiota, with possible implications for host evolution and health. Using shotgun metagenomic sequencing, we investigated taxonomic and functional diversity in the gut microbiota of wild-living great apes, including two gorilla subspecies (<em>Gorilla gorilla gorilla, Gorilla beringei beringei</em>), three chimpanzee subspecies (<em>Pan troglodytes verus, P.t. troglodytes, P.t. schweinfurthii</em>), and bonobos (<em>Pan paniscus</em>), together with human samples from Africa and Europe. We identified microbial taxonomic and functional adaptations convergent with host phylogeny at both the community and microbial genomic levels. We could show that repeated horizontal gene transfer and gene loss are processes involved in these adaptations. We hypothesize, that these adaptation processes and changes in the microbiome predispose the host to chronic inflammatory disorders, such as type 2 diabetes via altered histidine metabolism and inflammatory bowel disease indicated by adaptation of microbes to aerobic conditions. Additionally, we find multiple lines of evidence suggesting a widespread loss of microbial diversity and evolutionary conserved clades in the human microbiota, especially in the European population. Lastly, we observed patterns consistent with codivergence of hosts and microbes, particularly for the bacterial family <em>Dialisteraceae</em>, though we find that overall, co-phylogeny patterns are frequently disrupted in humans.</p>
Novel metagenome assembled genomes (MAGs) that best represent novel species level taxa within the phylum Chloroflexota
<p>1280 Chloroflexita MAGs from the study "Taxonomic re-classification and expansion of the phylum Chloroflexota based on over 5000 genomes and metagenome-assembled genomes". Only MAGs that improved the representation of a species-level genome cluster within the phylum <em>Chloroflexota</em> were included in this deposition.</p> <p>Most of these MAGs were assembled from publicly availabe metagenome sequence data obtained from the NCBI sra database.</p> <p>An overview of the here deposited MAGs can be found in <a href="https://zenodo.org/api/files/2a6a7fa1-489c-426d-8e05-ada23038dfdf/Zenodo_deposited_MAGS_overview.xlsx?versionId=9cde1488-8388-4fdb-a45e-2d48dc066f9a"> Zenodo_deposited_MAGS_overview.xlsx</a>, for more details please refer to the abive mentioned publication.</p> <p>MAG assemblies are deposited as gzip compressed tar.archive. Three tar.gz archives have been deposited, containing the same MAG assemblies but sorted by different criteria:</p> <ol> <li>All MAGs sorted by category of the source environment</li> <li>All MAGs sorted by class designation</li> <li>All MAGs sorted by MIMAG quality (high or moderate)</li> </ol>
Metagenome-assembled genomes(MAGs) generated by MetaCC binning
<p>MAGs generated by MetaCC binning from the human gut short-read, the wastewater (WW) short-read, the cow rumen long-read, and the sheep gut long-read metaHi-C datasets</p>
MAGs from papers: doi:10.1186/s40168-017-0253-y and doi:10.1038/ismej.2015.185
<p>Metagenome Assembled Genomes (MAGs) assembled and binned from publications doi:10.1186/s40168-017-0253-y and doi:10.1038/ismej.2015.185, where microbial communities from deep biosphere environments sampled from Äspö aquifers (Sweden) are taxonomically and functionally described.</p>
Rhizopus_stolonifer_40x_mag_Volatile_exposure
<p>This set of images show 9-10 examples of various volatile-exposed hyphae of R. stolonifer, NRRL 66455. Included is a spreadsheet of vacuole count data.</p>
Supplementary Material - Table 1: MAG summary
<p><strong>Supplementary Table 1. Details on taxonomic classification, genes of interest, completeness, redundancy, and abundance of MAGs obtained in this study. </strong>This file relates to the preprint https://www.biorxiv.org/content/10.1101/2020.09.22.307553v1, "Enrichment of novel <em>Verrucomicrobia, Bacteroidetes</em> and <em>Krumholzibacteria</em> in an oxygen-limited, methane- and iron-fed bioreactor inoculated with Bothnian Sea sediments".</p>
BepiColombo/Mio MSA, MIA and MPO MAG Data During the second Venus Flyby
<p>This data set includes the DDEF of MSA and MIA data, and MPO-MAG data during the 2nd BepiColombo Mio's Venus flyby. The format of the files and the "one file per figure" was required by Nature Astronomy. To properly use these data, contacting the PI of the instruments and MSA team is highly recommended.</p>
VESPA mercury_mag_boundaries sample
<p>This dataset is based on the original MESSENGER mission magnetometer and coordinate data as made available at PDS PPI. It introduces a number of improvements upon the original [1 sec temporal resolution]:</p> <ol> <li>Magnetometer calibration signals have been removed.</li> <li>Coordinates and magnetic field measurements have been merged together.</li> <li>Additional fields, such as model dipole magnetic field and planetary position in a heliocentric coordinate system have been added.</li> <li>The dataset has been split up into files by orbit numbers, with each file centered on the periapsis.</li> <li>Data for a number of partially recorded orbits has been removed.</li> </ol>
Metagenome-assembled genomes(MAGs) generated from soil dataset.
<p>MAGs generated from soil dataset with Maxbin2, VAMB, Metabat2, SemiBin(single-sample binning) and VAMB, SemiBin(multi-sample binning).</p> <p>Single-sample binning: Maxbin2.tar.gz, Metabat2.tar.gz, VAMB.tar.gz and SemiBin(pretrain).tar.gz. </p> <p>Multi-sample binning: VAMB_multi.tar.gz and SemiBin_multi.tar.gz.</p>
Dereplicated Metagenome assembled genomes (MAGs) from Columbia River hyporheic sediments
<p>Fasta file containing 55 metagenome assembled genomes (MAGs) from publication to be submitted titled "<strong>Microbial genome-resolved metaproteomic analyses frame intertwined carbon and nitrogen cycles in river hyporheic sediments". </strong></p>
GTDB-Tk Phylogenetic Information for 102 MAGs from Columbia River hyporheic sediments
<p>These are the phylogenetic analyses output for the GTDB-Tk that was run on the 102 MAGs from the Columbia River Hyporheic Zone. They form part of supplementary material from publication titled "<strong>Microbial genome-resolved metaproteomic analyses frame intertwined carbon and nitrogen cycles in river hyporheic sediments". </strong></p>
Metagenome-assembled genomes (MAGs), colorectal cancer (CRC)
<p>This archive contains (i) Metagenome assemblies of short-term enrichment cultures of CRC mucosal tissue microbiota, and (ii) Reconstructed metagenome-assembled genomes (MAGs) generated through binning of metagenome contigs.</p>
Wolbachia MAGs from Culex pipiens midgut and ovary metagenomes
<p><em>Wolbachia</em> MAGs (fasta files) from <em>Culex pipiens</em> midgut and ovary samples. </p>
Fathi Camel Microbiome Project (FCMP) Fecal Metagenome-assembled Genomes (MAGs)
<p>The Fathi Camel Microbiome Project (FCMP) aims to characterize the diversity and phenotypic associations of the dromedary camel microbiome. The gut microbiome of N = 55 camels was deeply sequenced via dropped stool. The raw reads, after QC, were assembled and binned into metagenome-assembled genomes (MAGs). We include here a collection of 3165 medium-quality or higher prokaryotic MAGs by MiMAG-like criteria (completeness >= 50%, contamination <= 5%). </p>
Metagenome Assembled Genomes (MAGs) from faecal microbiomes of great tits and blue tits
<h2><span>Overview:</span></h2> <p><span>The vertebrate gut microbiome plays crucial roles in host health and disease. However, there is limited data on the microbiomes of wild birds, most of which is restricted to barcode sequences. We therefore explored the use of shotgun metagenomics on the faecal microbiomes of two wild bird species widely used as model organisms in ecological studies: the great tit (<em>Parus major</em>) and the Eurasian blue tit (<em>Cyanistes caeruleus</em>). High and Medium quality Metagenome Assembled Genomes (MAGs) were assembled from these metagenomes and are made available as a catalogue in this archive.</span></p> <h2><span>Methods:</span></h2> <p><span><span>Metagenomic reads were trimmed, and quality controlled using FastP configured to a minimum phred score of 20 and minimum length of 50 bp</span><span>. In order to avoid contamination of the bins by eukaryotic sequences, Tiara v1.0.3 was used to classify contigs longer than 3.000 kb into their high-level kingdoms, allowing to exclude sequences of a eukaryotic or of an organelle origin, and only retaining all unclassified contigs and prokaryotic contigs for the binning step. <br>Contigs were binned using MaxBin2 v2.2.7 , SemiBin2 v2.1.0 and Metabat2 v 2.15 independently. The bins were refined using DasTool v 1.1.7 using a min score threshold of 0.3. The quality of the refined bins was obtained using CheckM2 v 1.0.2, and any bin with a contamination above 10% were excluded. The final MAGs were classified as Low-quality (<50% completeness, <10% contamination), medium-quality (>50% completeness, <10% contamination) and high-quality (>90% completeness, <5% contamination), as recommended by the MIMAG specification . Finally, the MAGs were dereplicated using an dRep v 3.4.3 with an ANI of 95% and classified using gtdb-tk v2.4.0 using the gtdb database release220.<br></span></span></p> <p><span><span>Files:</span></span></p> <ul> <li><span><span>The <strong>MAGs_sequences_v1.0.0 </strong>contains the fasta sequence for the individual MAGs assembled in this project</span></span></li> <li><span><span>The <strong>MAGs_catalogue_v1.0.0.xlsx</strong> contains a description of the quality, taxonomic annotation and characteristics of each MAGs in the dataset</span></span></li> </ul>
Metagenome assembled genome (MAG) annotations for Columbia River sediment bacteria and archaea
<p>Excel spreadsheet containing all annotations for metagenome assembled genomes (MAGs) that form part of a publication to be submitted titled: "<strong>Microbial genome-resolved metaproteomic analyses frame intertwined carbon and nitrogen cycles in river hyporheic sediments". </strong></p>
Metagenome-assembled genomes(MAGs) generated from CRC human gut (PRJEB27928).
<p>MAGs generated from CRC human gut (PRJEB27928) with Maxbin2, VAMB, Metabat2, SemiBin(single-sample binning) and VAMB, SemiBin(multi-sample binning).</p> <p>Single-sample binning: Maxbin2.tar.gz, Metabat2.tar.gz, VAMB.tar.gz and SemiBin(_pretrain).tar.gz. </p> <p>Multi-sample binning: VAMB_multi.tar.gz and SemiBin_multi.tar.gz.</p>
Metagenome-assembled genomes(MAGs) generated from dog gut (PRJEB20308).
<p>MAGs generated from dog gut (PRJEB20308) with Maxbin2, VAMB, Metabat2, SemiBin(single-sample binning) and VAMB, SemiBin(multi-sample binning).</p> <p>Single-sample binning: Maxbin2.tar.gz, Metabat2.tar.gz, VAMB.tar.gz and SemiBin(_pretrain).tar.gz. </p> <p>Multi-sample binning: VAMB_multi.tar.gz and SemiBin_multi.tar.gz.</p>
Metagenome-assembled genomes(MAGs) generated from ocean (PRJEB1787).
<p>MAGs generated from ocean (PRJEB1787) with Maxbin2, VAMB, Metabat2, SemiBin(single-sample binning) and VAMB, SemiBin(multi-sample binning).</p> <p>Single-sample binning: Maxbin2.tar.gz, Metabat2.tar.gz, VAMB.tar.gz and SemiBin(_pretrain).tar.gz. </p> <p>Multi-sample binning: VAMB_multi.tar.gz and SemiBin_multi.tar.gz.</p>
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International Brain Laboratory public data
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OpenNeuro
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