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915 results for “metagenomics”
Metagenomic analysis of Mesolithic chewed pitch reveals poor oral health among stone age individuals
<p>Prehistoric chewed pitch has proven to be a useful source of ancient DNA, both from humans and their microbiomes. Here we present the metagenomic analysis of three pieces of chewed pitch from Huseby Klev, Sweden, that were dated to 9,890–9,540 before present. The metagenomic profle exposes a Mesolithic oral microbiome that includes opportunistic oral pathogens. We compared the data with healthy and dysbiotic microbiome datasets and we identifed increased abundance of periodontitisassociated microbes. In addition, trained machine learning models predicted dysbiosis with 70–80% probability. Moreover, we identifed DNA sequences from eukaryotic species such as red fox, hazelnut, red deer and apple. Our results indicate a case of poor oral health during the Scandinavian Mesolithic, and show that pitch pieces have the potential to provide information on material use, diet and oral health.</p>
Metagenome-assembled genomes from two genera of pitcher plants and three freshwater lakes
<p>Illumina shotgun metagenome sequences from <em>Sarracenia </em>and <em>Nepenthes </em>pitcher plants (originally published in Bittleston et al. 2018, MG-RAST RRID: SCR_004814; mgp15454) and three freshwater lakes (Consensus Lake, New York, USA (SRR15064816), Lake Mendota, Wisconsin, USA (SRR11647637), and Lake Samiti, Sikkim, India (SRR10757258)) were binned using CONCOCT v1.1.0 (Alneberg et al. 2014). Bins were further refined using anvi’o’s interactive interface v7.1 (Eren et al. 2015).</p>
Exploring the Atmospheric Microbiome in the Eastern Mediterranean through Metagenomic Analysis
<p><span>Dataset</span><span> S5 (separate file)</span><span>. </span><span>Genome coverage depth information for each specific position across the entire genome of potential pathogens.</span></p>
Rapid Inference of Antibiotic Susceptibility Phenotype of Uropathogens using Metagenomic Sequencing with Neighbour Typing - RASE Databases for E. coli and Klebsiella spp
<p>RASE databases used for the prediction of antibiotic phenotype in the paper titled "Rapid Inference of Antibiotic Susceptibility Phenotype of Uropathogens using Metagenomic Sequencing with Neighbour Typing". A database for each of <em>Escherichia coli </em>and <em>Klebsiella spp.</em> are available, including the original metadata and genetic trees used to create the databases.</p>
Correlation figure of metagenomics and metatranscriptomics sample
<p>Visualization codes from the 2nd "speeding up science workshop". This repository contains codes to plot and calculate correlation (linear regression) between metagenomic and metatranscriptomic sequencing results acquired from the same sample.</p> <p>There is an example of visualizing gene abundances (DNA) compared to their expression levels (RNA) included in the binder. The data are from one Mediterranean site from the TARA Oceans project (https://science.sciencemag.org/content/348/6237/1261359.long). The metagenomics come from sample accession SAMEA2619782, and the metatransciptomics come from SAMEA2619784.</p>
Simulated metagenomes used in "CRISPR spacers indicate preferential matching of specific virioplankton genes"
<p>A simulated 454 and simulated Illumina sequencing run for 10 known microbial genomes that were used to test the accuracy of different CRISPR spacer prediction programs.</p>
Metagenomic assembly (Galaxy Training Material)
<p>The tutorial aims to train how to perform assembly of metagenomic samples. (https://training.galaxyproject.org/training-material/)</p>
Validation of StrainIQ software performance using metagenomic data from ATCC staggered mix genomes
<p>StrainIQ (Strain Identification and Quantification) is a novel tool that implements a new <em>n</em>-gram based algorithm for predicting and quantifying strain-level taxa from whole genome metagenomic sequencing data. We tested our method using simulated (GI tract reference genomes) and mock metagenomic datasets (from ATCC microbial genomic mix) and compared its performance with existing methods. Here, the gut_mix.zip file contains the metagenomic sequence data from the ATCC 20 strain staggered genomic mix (MSA-1003). From this original sequencing sequence (nearly 120X), we created additional datasets with 90X, 60X, 30X, 5X, 3X, and 1X coverage and tested StrainIQ performance on those varying sequencing datasets.</p> <p>Please find the new link for this data at https://zenodo.org/record/8132164</p>
Metagenome-assembled genomes (MAGs) from Acropora pharaonis holobiont
<p>These metagenome-assembled genomes were assembled from the Acropora pharonis metagenomes. Reads were simultaneously mapped to <em>Acropora</em>, <em>Cladocopium</em> genomes before the reads were individually assembled and binned. The resulting genomes were dereplicated and filtered for contamination and completeness. A high-quality MAG for Endozoicomonas was obtained and used along with paired metabolomic data to investigate the roles Endozoicomonas play in the coral holobiont during thermal stress. </p>
Genomics and Metagenomics of Asthma Severity
ClinicalTrials.gov study NCT04501926. IPD Sharing: NO. Countries: 1. Publications: 0.
Study of the Composition and Bacterial Diversity of the Vaginal Microbiota in Healthy Versus Pathological Conditions (Bacterial Vaginosis) Using a Targeted Metagenomic Approach (RNA 16s)
ClinicalTrials.gov study NCT04989543. IPD Sharing: NO. Countries: 1. Publications: 0.
Respiratory Virus Metagenomics After COVID-19
ClinicalTrials.gov study NCT05126589. IPD Sharing: Not stated. Countries: 1. Publications: 0.
Metagenomic Next-Generation Sequencing for Diagnosis of Ascites Infection in End-stage Liver Diseases
ClinicalTrials.gov study NCT04125654. IPD Sharing: Not stated. Countries: 1. Publications: 0.
A Metagenome-wide Association Study of Gut Microbiota in Gastrointestinal Non-Hodgkin's Lymphoma Patients
ClinicalTrials.gov study NCT03930043. IPD Sharing: Not stated. Countries: 1. Publications: 0.
Metagenomic Study in Parapneumonic Effusion
ClinicalTrials.gov study NCT05394220. IPD Sharing: NO. Countries: 1. Publications: 0.
The Gut Metagenome Research of Schizophrenia
ClinicalTrials.gov study NCT02708316. IPD Sharing: Not stated. Countries: 1. Publications: 0.
AlloSure Lung Assessment and Metagenomics Outcomes Study
ClinicalTrials.gov study NCT05050955. IPD Sharing: Not stated. Countries: 2. Publications: 0.
Metagenomic Analysis of the Link Between Periodontitis and Smoking: Case-control Study
ClinicalTrials.gov study NCT05995158. IPD Sharing: NO. Countries: 1. Publications: 0.
Metagenomic Sequencing in Clinical Infectious Diseases
ClinicalTrials.gov study NCT05353634. IPD Sharing: NO. Countries: 1. Publications: 0.
Metagenomic Evaluation of the Gut Microbiome in Patients With Lynch Syndrome and Other Hereditary Colonic Polyposis Syndromes
ClinicalTrials.gov study NCT02371135. IPD Sharing: Not stated. Countries: 1. Publications: 0.
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.