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GEO DataSets

Functional Genomics Studies

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Items: 1 to 20 of 2593

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Select item 2002332921.

Soil bacterial diversity around a hospital and university precinct in South India over a 12-month period.

(Submitter supplied) This study identified and compared the bacterial diversity and clinically relavent bacterial strains around a newly developed hospital and university precinct in southern India for a period of twelve months.

Organism:: Bacteria

Type:: Other

Platform:: GPL24661
120 Samples

Download data: CSV

Series

Accession:: GSE233292

ID:: 200233292

Select item 2001829282.

Functional responses of coral microbial communities to ocean acidification

(Submitter supplied) DNA samples of G. fascicularis were used to investigate the GeoChip 5.0 based functional gene arrays, which contains 57,000 probes and covered over 144,000 gene sequences from 393 functional gene families associated with a variety of microbial functional traits, such as carbon, nitrogen, phosphorus, sulfur cycling, pathogenicity and secondary metabolism.

Organism:: Archaea; Eukaryota; Viruses; Bacteria; Galaxea fascicularis

Type:: Other

Platform:: GPL30559
9 Samples

Download data: TXT

Series

Accession:: GSE182928

ID:: 200182928

Analyze with GEO2R

Select item 2002688693.

Intestinal Microbiota Composition is Predictive of Radiotherapy-induced Acute Gastrointestinal Toxicity in Prostate Cancer Patients

(Submitter supplied) The search for factors beyond the radiotherapy dose that could identify patients more at risk of developing radio-induced toxicity is essential to establish personalised treatment protocols for improving the quality-of-life of survivors. To investigate the role of the intestinal microbiota in the development of radiotherapy-induced gastrointestinal toxicity, the MicroLearner observational cohort study characterised the intestinal microbiota of 136 (discovery) and 79 (validation) consecutive prostate cancer patients at baseline radiotherapy. more...

Organism:: Bacteria

Type:: Other

Platform:: GPL34542
215 Samples

Download data: TXT

Series

Accession:: GSE268869

ID:: 200268869

PubMed Full text in PMC Similar studies

Select item 2002662634.

Designing Molecular RNA Switches with Restricted Boltzmann Machines

(Submitter supplied) Riboswitches are structured allosteric RNA molecules that change conformation in response to a metabolite binding event, eventually triggering a regulatory response. Computational modelling of the structure of these molecules is complicated by a complex network of tertiary contacts, stabilized by the presence of their cognate metabolite. In this work, we focus on the aptamer domain of SAM-I riboswitches and show that Restricted Boltzmann machines (RBM), an unsupervised machine learning architecture, can capture intricate sequence dependencies induced by secondary and tertiary structure, as well as a switching mechanism between open and closed conformations. more...

Organism:: Bacteria; synthetic construct

Type:: Other; Expression profiling by high throughput sequencing

Platforms:: GPL19424 GPL34432
22 Samples

Download data: TAR

Series

Accession:: GSE266263

ID:: 200266263

Select item 2002254195.

Exploring the diversity and antibiogram of the soil around a tertiary care hospital and a university precinct in southern In-dia: A pilot study

(Submitter supplied) This study identified and compared the bacterial diversity and the antimicrobial resistance profile of clinically relevant isolates around a newly developed hospital and university precinct

Organism:: Bacteria

Type:: Other

Platform:: GPL24661
8 Samples

Download data: CSV, TXT

Series

Accession:: GSE225419

ID:: 200225419

Select item 2002520716.

Salmonella manipulates the host to drive pathogenicity via induction of interleukin 1β

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:: Bacteria; Mus musculus

Type:: Expression profiling by high throughput sequencing; Other

Platforms:: GPL24661 GPL21626
18 Samples

Download data

Series

Accession:: GSE252071

ID:: 200252071

PubMed Full text in PMC Similar studies

Select item 2002520707.

Salmonella manipulates the host to drive pathogenicity via induction of interleukin 1β [16S]

(Submitter supplied) Acute gastrointestinal infection with intracellular pathogens like Salmonella Typhimurium triggers the release of the proinflammatory cytokine interleukin 1β (IL-1β). However, the role of IL-1β in intestinal defense against Salmonella remains unclear. Here, we show that IL-1b production is detrimental during Salmonella infection. Mice lacking IL-1b (IL-1b -/-) failed to recruit neutrophils to the gut during infection, which reduced tissue damage and prevented depletion of short-chain fatty acid-producing commensals. more...

Organism:: Bacteria

Type:: Other

Platform:: GPL24661
1 Sample

Download data: TSV

Series

Accession:: GSE252070

ID:: 200252070

PubMed Full text in PMC Similar studies

Select item 2002469658.

Biofilm Heterogeneity-Adaptive Photoredox Catalysis Enables Red Light-Triggered Nitric Oxide Release for Combating Drug-Resistant Infections

(Submitter supplied) The formation of biofilms is closely associated with persistent and chronic infections, and physiological heterogeneity such as pH and oxygen gradients renders biofilms highly resistant to conventional antibiotics. To date, effectively treating biofilm infections remains a significant challenge. Herein, we report the fabrication of micellar nanoparticles adapted to heterogeneous biofilm microenvironments, enabling nitric oxide (NO) release through two distinct photoredox catalysis mechanisms. more...

Organism:: Bacteria

Type:: Expression profiling by high throughput sequencing

Platform:: GPL32770
6 Samples

Download data: TXT

Series

Accession:: GSE246965

ID:: 200246965

PubMed Full text in PMC Similar studies

Select item 2002163869.

Osteopontin Exacerbates High-Fat Diet-induced Metabolic Disorders in a microbiome-dependent Manner

(Submitter supplied) Gut microbiota is involved in metabolic disorders. However, microbiome-based therapeutic interventions are not always effective, which might be due to interference of the host factors. Here, we first identified a strong positive correlation between OPN levels and BMI in humans. Next, we confirmed that OPN could aggravate high-fat diet induced metabolic disorders in mice. Importantly, we found that fecal microbiota transplantation from OPN-deficient mice significantly alleviated metabolic disorders in WT mice. more...

Organism:: Mus musculus; Bacteria; feces metagenome

Type:: Other; Expression profiling by high throughput sequencing

4 related Platforms
126 Samples

Download data: TXT, XLS, XLSX

Series

Accession:: GSE216386

ID:: 200216386

PubMed Full text in PMC Similar studies

Select item 20020325410.

The Effects of Bacillus licheniformis-fermented Products on Chronic Feline Diarrhea and Intestinal Microbiota

(Submitter supplied) Bacillus licheniformis-fermented products (BLFP) are probiotics with antibacterial, antiviral, and anti-inflammatory properties that can improve growth performance. This study aimed to, firstly, compare the fecal microbiota of cats with chronic diarrhea (n = 8) with that of healthy cats (n = 4) from the same household using next-generation sequencing and, secondly, evaluate the effectiveness of oral administration of BLFP in relieving clinical signs and altering the intestinal microbiota in diarrheal cats. more...

Organism:: Bacteria

Type:: Other

Platform:: GPL24661
24 Samples

Download data: FASTA, TXT

Series

Accession:: GSE203254

ID:: 200203254

PubMed Full text in PMC Similar studies

Select item 20014704111.

Differential effects of nitrogen addition on soil organic carbon decomposition correlate with changes in microbial C-degradation functional potentials in a Pinus tabulaeformis forest

(Submitter supplied) Anthropogenic nitrogen (N) deposition may affect soil organic carbon (SOC) decomposition, thus affecting the global terrestrial carbon (C) cycle. However, it remains unclear how the level of N deposition affects SOC decomposition by regulating microbial community composition and function, especially C-cycling functional genes structure. We investigated the effects of short-term N addition on soil microbial C-cycling functional gene composition, SOC-degrading enzyme activities, and CO2 emission in a 5-year field experiment established in an artificial Pinus tabulaeformis forest on the Loess Plateau, China.

Organism:: Archaea; Bacteria; Eukaryota; Viruses; uncultured soil microorganism

Type:: Other

Platform:: GPL28276
16 Samples

Download data: XLS

Series

Accession:: GSE147041

ID:: 200147041

Analyze with GEO2R

Select item 20019549012.

Monthly dynamics of microbial functional diversity and composition in a tall-grass prairie, 2012

(Submitter supplied) We carried out an in-depth analysis of the monthly variations of a temperate grassland ecosystem to examine a range of biotic and abiotic factors that underpin soil respiration changes in response to warming.

Organism:: Bacteria; Eukaryota; Viruses; uncultured soil bacterium; Archaea

Type:: Other

Platform:: GPL22866
96 Samples

Download data: TXT, XLSX

Series

Accession:: GSE195490

ID:: 200195490

PubMed Full text in PMC Similar studies

Select item 20018688013.

Reuterin in the healthy gut microbiome suppresses colorectal cancer growth through altering redox balance

(Submitter supplied) Microbial dysbiosis is a colorectal cancer (CRC) hallmark and contributes to inflammation, tumor growth, and therapy response. Gut microbes signal via metabolites, but how the metabolites impact CRC is largely unknown. We interrogated fecal metabolites associated with mouse models of colon tumorigenesis with varying mutational load. We found that microbial metabolites from healthy mice or humans were growth-repressive, and this response was attenuated in mice and patients with CRC. more...

Organism:: Bacteria; feces metagenome; synthetic construct; mouse gut metagenome

Type:: Other

4 related Platforms
71 Samples

Download data: TXT

Series

Accession:: GSE186880

ID:: 200186880

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 20015678414.

Enhanced metabolic potentials and functional gene interactions of microbial stress response towards high elevation in freshwater lakes

(Submitter supplied) Here, we applied a microarray-based metagenomics technology termed GeoChip 5.0 to examined functional gene structure of microbes in four lakes at low and high elevations of approximately 530 and 4,600 m a.s.l., respectively.

Organism:: Bacteria; Eukaryota; Viruses; Archaea; uncultured microorganism

Type:: Other

Platform:: GPL29063
24 Samples

Download data: TXT

Series

Accession:: GSE156784

ID:: 200156784

PubMed Full text in PMC Similar studies Analyze with GEO2R

Select item 20013515315.

soil mcirobial functional communities

(Submitter supplied) To study the soil mcirobial functional communities and the nutrient cycles couplings changes after exposure to different contaminant

Organism:: Bacteria; Eukaryota; Viruses; uncultured soil microorganism; Archaea

Type:: Genome variation profiling by array

Platform:: GPL22263
15 Samples

Download data: TXT

Series

Accession:: GSE135153

ID:: 200135153

Select item 20015558216.

Climate warming and nutrient enrichment jointly affect microbial functional potentials important to nutrient cycling in shallow-lake mesocosms

(Submitter supplied) Here, we applied a microarray-based metagenomics technology termed GeoChip 5.0 to investigate spring microbial functional genes in mesocosm-simulated shallow lake ecosystems having been undergoing nutrient enrichment and warming for nine years.

Organism:: Bacteria; Archaea; Eukaryota; Viruses; uncultured soil microorganism

Type:: Other

Platform:: GPL28957
16 Samples

Download data: TXT

Series

Accession:: GSE155582

ID:: 200155582

Analyze with GEO2R

Select item 20011783117.

Survey functional genes in Arctic marine sediment communities

(Submitter supplied) The objective was to identify functional genes encoded by Fungi and fungal-like organisms to assess putative ecological roles Using the GeoChip microarray, we detected fungal genes involved in the complete assimilation of nitrate and the degradation of lignin, as well as evidence for Partitiviridae (a mycovirus) that likely regulates fungal populations in the marine environment. These results demonstrate the potential for fungi to degrade terrigenously-sourced molecules, such as permafrost and compete with algae for nitrate during blooms. more...

Organism:: Archaea; Bacteria; Eukaryota; Viruses; synthetic construct; marine sediment metagenome

Type:: Other

Platform:: GPL25397
2 Samples

Download data: TXT

Series

Accession:: GSE117831

ID:: 200117831

PubMed Full text in PMC Similar studies Analyze with GEO2R

Select item 20012882618.

The functional diversity of stream microbes on mountainsides across Eurasia based on Geochip 4.0

(Submitter supplied) Understanding the biogeographical patterns and underlying drivers of microbial functional diversity is essential for anticipating climate change impacts on ecosystem functioning worldwide. However, this matter remains scarcely addressed in freshwater ecosystems. Using the high-throughput gene array GeoChip 4.0, we show that functional gene alpha diversity and compositon differ across mountains, alpha diversity declines towards high elevations and compositional turnover increases with larger elevational distances. more...

Organism:: Bacteria; Archaea; biofilm metagenome; Fungi

Type:: Other

Platform:: GPL26346
52 Samples

Download data: TXT

Series

Accession:: GSE128826

ID:: 200128826

PubMed Full text in PMC Similar studies Analyze with GEO2R

Select item 20014843119.

Endophytic and rhizophytic prokaryotic communities in S. alterniflora and petroleum degradation

(Submitter supplied) The experiment was designed to test the interactions of Spartina alterniflora, its microbiome, and the interaction of the plant-microbe relationship with oil from the Deepwater Horizon oil spill (DWH). Total RNA was extracted from leaf and root microbiome of S. alterniflora in soils that were oiled in DWH oil spill with or without added oil, as well as those grown in unoiled soil with or without added oil. more...

Organism:: uncultured bacterium; Archaea; Bacteria; Eukaryota; Viruses; synthetic construct

Type:: Expression profiling by array

Platform:: GPL28373
24 Samples

Download data: TXT

Series

Accession:: GSE148431

ID:: 200148431

Analyze with GEO2R

Select item 20013380020.

Effect of biogas slurry combined with biochar on soil microbial function gene

(Submitter supplied) The functional diversity of soil microbial communities was explored for a poplar plantation, which was treated solely with biogas slurry, or combined with biochar at different fertilization intensities over several years.