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50 results for “Metatranscriptomics”
Data from: A metatranscriptomic analysis of diseased social wasps (Vespula vulgaris) for pathogens, with an experimental infection of larvae and nests
Social wasps are a major pest in many countries around the world. Pathogens may influence wasp populations and could provide an option for population management via biological control. We investigated the pathology of nests of apparently healthy common wasps, Vespula vulgaris, with nests apparently suffering disease. First, next-generation sequencing and metatranscriptomic analysis were used to examine pathogen presence. The transcriptome of healthy and diseased V. vulgaris showed 27 known microbial phylotypes. Four of these were observed in diseased larvae alone (Aspergillus fumigatus, Moellerella wisconsensis, Moku virus, and the microsporidian Vavraia culicis). Kashmir Bee Virus (KBV) was found to be present in both healthy and diseased larvae. Moellerella wisconsensis is a human pathogen that was potentially misidentified in our wasps by the MEGAN analysis: it is more likely to be the related bacteria Hafnia alvei that is known to infect social insects. The closest identification to the putative pathogen identified as Vavraia culicis was likely to be another microsporidian Nosema vulgaris. PCR and subsequent Sanger sequencing using published or our own designed primers, confirmed the identity of Moellerella sp. (which may be Hafnia alvei), Aspergillus sp., KBV, Moku virus and Nosema. Secondly, we used an infection study by homogenising diseased wasp larvae and feeding them to entire nests of larvae in the laboratory. Three nests transinfected with diseased larvae all died within 19 days. No pathogen that we monitored, however, had a significantly higher prevalence in diseased than in healthy larvae. RT-qPCR analysis indicated that pathogen infections were significantly correlated, such as between KBV and Aspergillus sp. Social wasps clearly suffer from an array of pathogens, which may lead to the collapse of nests and larval death.
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>
Metatranscriptomic Next Generation Sequencing in First Trimester Trophoblast With Increased Fetal Nuchal Translucency (METAHCN)
ClinicalTrials.gov study NCT05388968. IPD Sharing: NO. Countries: 1. Publications: 4.
Data from: Metatranscriptomics yields new genomic resources and sensitive detection of infections for diverse blood parasites
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Data from: A metatranscriptomic analysis of diseased social wasps (Vespula vulgaris) for pathogens, with an experimental infection of larvae and nests
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Data for: Longitudinal metatranscriptomic sequencing of Southern California wastewater representing 16 million people from August 2020-21 reveals widespread transcription of antibiotic resistance genes
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Data from: Metatranscriptomics of the human oral microbiome during health and disease
The human microbiome plays important roles in health, but when disrupted these same indigenous microbes can cause disease. The composition of the microbiome changes during the transition from health to disease; however, these changes are often not conserved among patients. Since microbiome-associated diseases like periodontitis cause similar patient symptoms despite inter-patient variability in microbial community composition, we hypothesized that human-associated microbial communities undergo conserved changes in metabolism during disease. Here we used patient-matched healthy and diseased samples to compare gene expression of 160,000 genes in healthy and diseased periodontal communities. We show that healthy and diseased communities exhibit defined differences in metabolism that are conserved between patients. In contrast, individual species metabolic gene expression was highly variable between patients. These results demonstrate that despite high inter-patient variability in microbial composition, diseased communities display conserved metabolic profiles that are generally accomplished by a patient-specific cohort of microbes.
Data from: Metatranscriptomics of the human oral microbiome during health and disease
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Data from: Eukaryotic metatranscriptomes of alpine soils and their links to the functioning of ecosystems
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Next Generation Metatranscriptome Sequencing of an Anaerobic Hexadecane-Degrading Microbial Consortia
GEO Series GSE49830. mixed culture KAZ_0815. 3 samples. Type: Expression profiling by high throughput sequencing.
Fecal metatranscriptomics from healthy adults before and after supplementation with bovine milk oligosaccharides
GEO Series GSE108809. feces metagenome. 24 samples. Type: Other.
Evaluating the Lettuce Metatranscriptome with MinION Sequencing for Future Spaceflight Food Production Application.
GEO Series GSE152914. Lactuca sativa. 3 samples. Type: Expression profiling by high throughput sequencing.
Metagenomic, metatranscriptomic and metaproteomic study of enrichment culture of M. oxyfera (denitrifying methanotroph)
GEO Series GSE18535. Candidatus Methylomirabilis oxygeniifera. 1 samples. Type: Expression profiling by high throughput sequencing.
Abundant and diverse non-coding small RNAs identified in an extremophilic microbial community using metatranscriptomics
GEO Series GSE137164. halite metagenome. 45 samples. Type: Expression profiling by high throughput sequencing.
De novo metatranscriptome assembly and coral gene expression profile of Montipora capitata with growth anomaly
GEO Series GSE97888. coral metagenome. 27 samples. Type: Expression profiling by high throughput sequencing.
Metatranscriptomic analysis of an anaerobic ammonium oxidizing community dominated by Kuenenia stuttgartiensis
GEO Series GSE15408. Candidatus Kuenenia stuttgartensis. 1 samples. Type: Expression profiling by high throughput sequencing.
Metatranscriptomics of the macaque juvenile gut microbiome in health and chronic diarrhea
GEO Series GSE108572. Macaca mulatta. 24 samples. Type: Expression profiling by high throughput sequencing.
Metatranscriptomics provides insight into the physiologies of the digestive tract symbionts within the medicinal leech, Hirudo verbana
GEO Series GSE23786. Hirudo verbana; gut metagenome. 2 samples. Type: Expression profiling by high throughput sequencing.
Simultaneous acclimation to nitrogen and iron scarcity in open ocean cyanobacteria revealed by sparse tensor decomposition of metatranscriptomes
<h2>Description</h2> <p>This dataset contains all of the supplementary files necessary to reproduce the findings published in the research article entitled <em>Simultaneous acclimation to nitrogen and iron scarcity in open ocean cyanobacteria revealed by sparse tensor decomposition of metatranscriptomes. </em>The scripts necessary for reproducing the published analyses can be found in the <a href="https://github.com/blasks/barnacle-manuscript">GitHub repository associated with the article</a>. Below is the article abstract and a description of the files included in this dataset.</p> <h2>Abstract</h2> <p>Microbes respond to changes in their environment by adapting their physiology through coordinated adjustments to the expression levels of functionally related genes. To detect these shifts in situ, we developed a sparse tensor decomposition method that derives gene co-expression patterns from inherently complex whole community RNA-sequencing data. Application of the method to metatranscriptomes of the abundant marine cyanobacteria <em>Prochlorococcus</em> and <em>Synechococcus</em> identified responses to scarcity of two essential nutrients, nitrogen and iron, including increased transporter expression, restructured photosynthesis and carbon metabolism, and mitigation of oxidative stress. Further, expression profiles of the identified gene clusters suggest that both cyanobacteria populations experience simultaneous nitrogen and iron stresses in a transition zone between North Pacific oceanic gyres. The results demonstrate the power of our approach to infer organism responses to environmental pressures, hypothesize functions of uncharacterized genes, and extrapolate ramifications for biogeochemical cycles in a changing ecosystem.</p> <h2>Legends for data S1 to S11</h2> <h3>Data S1. <em>Prochlorococcus</em> component profiles.</h3> <p>Median weight profiles for each <em>Prochlorococcus</em> component, including list of associated CyCOGs with corresponding gene weight, bootstrap support, and consensus annotation.</p> <h3>Data S2. <em>Synechococcus</em> component profiles.</h3> <p>Median weight profiles for each <em>Synechococcus</em> component, including list of associated CyCOGs with corresponding gene weight, bootstrap support, and consensus annotation.</p> <h3>Data S3. Enrichment analysis.</h3> <p>Significantly enriched KEGG pathways associated with each component, and compiled consensus annotations for each CyCOG.</p> <h3>Data S4. MED4 CyCOGs.</h3> <p>Mapping of <em>Prochlorococcus</em> MED4 genes to associated CyCOGs.</p> <h3>Data S5. Nitrogen and iron acclimation clusters.</h3> <p>CyCOGs, genes, and annotations for clusters associated with acclimation to nitrogen and iron scarcity.</p> <h3>Data S6. Sample metadata.</h3> <p>Metadata file detailing sampling conditions for all metatranscriptomes used in this study.</p> <h3>Data S7. Genome metadata.</h3> <p>Metadata file for CyCOG v6 reference genomes, including updated clade assignments.</p> <h3>Data S8. CyCOG v6 database.</h3> <p>Tarball of CyCOG v6 database, including reference genomes and annotation data.</p> <h3>Data S9. Reference sequence phylogenies.</h3> <p>Tarball of <em>Prochlorococcus</em> and <em>Synechococcus</em> reference genome phylogenies, used to update clade assignments.</p> <h3>Data S10. <em>Prochlorococcus</em> transcript abundance data.</h3> <p>A netCDF file of raw and normalized <em>Prochlorococcus</em> transcript abundance data, aggregated by CyCOG and organized into an `xarray.Dataset' tensor data structure.</p> <h3>Data S11. <em>Synechococcus</em> transcript abundance data.</h3> <p>A netCDF file of raw and normalized <em>Synechococcus</em> transcript abundance data, aggregated by CyCOG and organized into an `xarray.Dataset' tensor data structure.</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>
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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.