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ABSTRACT:
PROVIDER: PRJEB88482 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:SpaceX Inspiration4 Oral, Nasal, and Skin Metagenomic and Metatranscriptomic Microbial Swabs
| PRJNA1134112 | ENA
Project description:For analyzing the exploratory nasal commensal viruses, we performed the metatranscriptomic analysis of the nose swabs from the enrolled AR patients both before and after treatments, as well as sequenced the nose swabs from a set of healthy volunteers without AR history.Simultaneously, to assess the expression of interferon-stimulated genes in patients with allergic rhinitis, we analyzed the gene expression of host reads.
2024-08-21 | GSE275114 | GEO
Project description:To understand the ecophysiology of Sulfurihydrogenibium spp. in situ, integrated metagenomic, metatranscriptomic and metaproteomic analyses were conducted on a microbial community from Narrow Gauge at Mammoth Hot Springs, Yellowstone National Park.
2020-05-26 | PXD004323 | Pride
Project description:Sequencing the metatranscriptome can provide information about the response of organisms to varying environmental conditions. We present a methodology for obtaining random whole-community mRNA from a complex microbial assemblage using Pyrosequencing. The metatranscriptome had, with minimum contamination by ribosomal RNA, significant coverage of abundant transcripts, and included significantly more potentially novel proteins than in the metagenome. Keywords: metatranscriptome, mesocosm, ocean acidification This experiment is part of a much larger experiment. We have produced 4 454 metatranscriptomic datasets and 6 454 metagenomic datasets. These were derived from 4 samples. The experiment is an ocean acidification mesocosm set up in a Norwegian Fjord in 2006. We suspended 6 bags containing 11,000 L of sea water in a Coastal Fjord and then we bubbled CO2 through three of these bags to simulate ocean acidification conditions in the year 2100. The other three bags were bubbled with air. We then induced a phytoplankton bloom in all six bags and took measurements and performed analyses of phytoplankton, bacterioplankton and physiochemical characteristics over a 22 day period. We took water samples from the peak of the phytoplankton bloom and following the decline of the phytoplankton bloom to analyses using 454 metagenomics and 454 metatranscriptomics. Day 1, High CO2 Bag and Day 1, Present Day Bag, refer to the metatranscriptomes from the peak of the bloom. Day 2, High CO2 Bag and Day 2, Present Day Bag, refer to the metatranscriptomes following the decline of the bloom. Obviously High CO2 refers to the ocean acidification mesocosm and Present Day refers to the control mesocosm. Raw data for both the metagenomic and metatranscriptomic components are available at NCBI's Short Read Archive at ftp://ftp.ncbi.nlm.nih.gov/sra/Studies/SRP000/SRP000101
2008-02-08 | E-GEOD-10119 | biostudies-arrayexpress
Project description:Febrile patients PCR positive for H1N1 swine flu, seasonal H1N1 and seasonal H3N2 in nasal swabs and controls consisting of febrile patients with rhinovirus infection or febrile patients of non-viral etiology (nasal swabs PCR negative for common respiratory viruses and blood PCR negative for dengue and parvovirus B19) were assessed consecutively for global transcriptional changes in whole blood
2014-04-01 | GSE29385 | GEO
Project description:Evaluation of short-read-only, long-read-only, and hybrid assembly approaches on metagenomic samples demonstrating how they affect gene and protein prediction which is relevant for downstream functional analyses. For a human gut microbiome sample, we use complementary metatranscriptomic, and metaproteomic data to evaluate the metagenomic-based protein predictions.
2022-02-17 | PXD025505 | Pride
Project description:Asymptomatic colonization of the upper respiratory tract is a common trait of the two exclusive human pathogens, Neisseria gonorrhoeae and Neisseria meningitidis. In vivo models of pathogenic neisserial infections are heterologous systems that permit short-term persistence but do not fully recapitulate infections in humans. Studying Neisseria musculi (Nmus), an oral commensal, in laboratory mice allows investigation of Neisseria-host interactions that avoids host restriction barriers. Nmus produces smooth and rough morphotypes on solid media. We compared the in vitro phenotypes, biofilm transcriptomes, and in vivo colonization patterns and burdens of the Nmus morphotypes. We observed that the two morphotypes differ in biofilm formation, aggregation, pilin production, and transformation frequency in vitro. These phenotypes strongly correlated with differential expression of a set of genes in the Nmus biofilms including those that encoded factors for bacterial attachment. In vivo, the smooth morphotype stably colonized the oral cavities of all inoculated A/J and C57BL/6J mice at higher burdens compared to the rough. Following nasal inoculations, we detected transient Nmus nasal colonization. The smooth morphotype was able to reach higher burdens more quickly in the nasal cavity and on oral swabs following dissemination to the oral cavity. Gut colonization burdens fluctuated over time. Interestingly, both morphotypes colonized the oral cavities of A/Js at higher magnitudes than in C57BL/6Js. Collectively, our results demonstrate that colonization by Nmus can be affected by various factors including Nmus morphotypes, inoculation routes, anatomical niches, and host backgrounds. The Nmus-mouse model can use variable morphotype-host combinations to study the dynamics of neisserial asymptomatic colonization and persistence in multiple extragenital niches.
2024-09-15 | GSE184230 | GEO
Project description:Febrile patients PCR positive for H1N1 swine flu, seasonal H1N1 and seasonal H3N2 in nasal swabs and controls consisting of febrile patients with rhinovirus infection or febrile patients of non-viral etiology (nasal swabs PCR negative for common respiratory viruses and blood PCR negative for dengue and parvovirus B19) were assessed consecutively for global transcriptional changes in whole blood Peripheral whole blood collected in PAX-gene tubes and extracted for total RNA
2014-04-01 | E-GEOD-29385 | biostudies-arrayexpress
Project description:The thermophilic Aquificales inhabit and play important biogeochemical roles in the geothermal environments globally. Although intensive studies on physiology, microbial ecology, biochemistry, metagenomics and metatranscriptomics of the Aquificales¬ species and Aquificales-containing environmental samples have been conducted, comprehensive understandings about their ecophysiology, especially in the natural niches have been limited. In the present study, an integrated suite of metagenomic, metatranscriptomic and metaproteomic analyses, for the first time, were conducted on a filamentous microbial community from the Apron and Channel Facies (ACF) of CaCO3 (travertine) deposition at Narrow Gauge, Mammoth Hot Springs, Yellowstone National Park.
2020-05-26 | PXD006506 | Pride