Warning: The NCBI web site requires JavaScript to function. more...

U.S. flag

An official website of the United States government

Dot gov

The .gov means it's official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you're on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

GEO DataSets

Functional Genomics Studies

Search database

Search term

Format

Summary
Summary (text)
Unique Identifier List

Sort by

Default order
Number of Samples (High to Low)
Number of Samples (Low to High)

Send to:

Choose Destination

File
Clipboard
Collections

Format
Sort by

Search results

Items: 1 to 20 of 365

<< First< Prev

Page of 19

Next > Last >>

Select item 2001829281.

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 2001470412.

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 2001954903.

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 2001567844.

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 2001351535.

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 2001555826.

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 2001178317.

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 2001288268.

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 2001484319.

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 20013380010.

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.

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

Type:: Other

Platform:: GPL19950
15 Samples

Download data: TXT

Series

Accession:: GSE133800

ID:: 200133800

Select item 20014628911.

Microbial communities of vineyard BRO11-BRO12 soils (GeoChip)

(Submitter supplied) In this work, we used a functional gene microarray approach (GeoChip) to assess the soil microbial community functional potential related to the different wine quality. In order to minimize the soil variability, this work was conducted at a "within-vineyard" scale, comparing two similar soils (BRO11 and BRO12) previously identified with respect to pedological and hydrological properties within a single vineyard in Central Tuscany and that yielded highly contrasting wine quality upon cultivation of the same Sangiovese cultivar

Organism:: Archaea; Bacteria; Viruses; soil metagenome; Fungi

Type:: Genome variation profiling by array

Platform:: GPL28213
6 Samples

Download data: TXT

Series

Accession:: GSE146289

ID:: 200146289

Analyze with GEO2R

Select item 20014280612.

Regulation of nitrous oxide production in low oxygen waters off the coast of Peru

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below. [SUBMITTER_CITATION]: Frey, C., Bange, H. W., Achterberg, E. P., Jayakumar, A., Löscher, C. R., Arévalo-Martínez, D. L., León-Palmero, E., Sun, M., Sun, X., Xie, R. C., Oleynik, S., and Ward, B. B.: Regulation of nitrous oxide production in low-oxygen waters off the coast of Peru, Biogeosciences, 17, 2263-2287

Organism:: synthetic construct; seawater metagenome; Archaea

Type:: Other

Platforms:: GPL20807 GPL27963
74 Samples

Download data: TXT

Series

Accession:: GSE142806

ID:: 200142806

Analyze with GEO2R

Select item 20014280513.

Regulation of nitrous oxide production in low oxygen waters off the coast of Peru [BC016]

(Submitter supplied) Oxygen deficient zones (ODZs) are major sites of net natural oceanic nitrous oxide (N2O) production and emissions. In order to understand changes in the magnitude of N2O production in response to global change, knowledge on the individual contributions of the major microbial pathways (nitrification and denitrification) to N2O production and their regulation is needed. In the ODZ of the coastal area off Peru, the sensitivity of N2O production to oxygen and organic matter was investigated using 15N-tracer experiments in combination with qPCR and microarray analysis of total and active functional genes targeting archaeal amoA and nirS as marker genes for nitrification and denitrification, respectively. more...

Organism:: synthetic construct; seawater metagenome; Archaea

Type:: Other

Platform:: GPL20807
32 Samples

Download data: TXT

Series

Accession:: GSE142805

ID:: 200142805

Analyze with GEO2R

Select item 20014280414.

Regulation of nitrous oxide production in low oxygen waters off the coast of Peru [BC015]

Organism:: Archaea; synthetic construct; seawater metagenome

Type:: Other

Platform:: GPL27963
42 Samples

Download data: TXT

Series

Accession:: GSE142804

ID:: 200142804

Analyze with GEO2R

Select item 20010037915.

Artificial reforestation has less diverse soil nitrogen-cycling genes than natural restoration

(Submitter supplied) Reforestation is effective in restoring ecosystem functions and enhancing ecosystem services of degraded land. The three most commonly employed reforestation methods of natural reforestation, artificial reforestation with native Masson pine (Pinus massoniana Lamb.), and introduced slash pine (Pinus elliottii Engelm.) plantations were equally successful in biomass yield in southern China. However, it is not known if soil ecosystem functions, such as nitrogen (N) cycling, are also successfully restored. more...

Organism:: Archaea; Fungi; Bacteria; Viruses

Type:: Genome variation profiling by array

Platform:: GPL23836
42 Samples

Download data: XLSX

Series

Accession:: GSE100379

ID:: 200100379

Analyze with GEO2R

Select item 20013283916.

Gene expression-based, through the hybridization of microbial DNA onto the designed probes on microarrys, i.e., GeoChip

(Submitter supplied) A total of 81515 genes belonging to 31 gene categories were detected in a total of 80 samples

Organism:: manure metagenome; Archaea; compost metagenome; Bacteria; Eukaryota; soil metagenome

Type:: Other

Platform:: GPL26791
79 Samples

Download data: TXT

Series

Accession:: GSE132839

ID:: 200132839

Analyze with GEO2R

Select item 20009710717.

Functional gene abundance of tundra soil microbial communities sampled at the EML Thaw Gradient site, AK in May 2004

(Submitter supplied) Permafrost soil in high latitude tundra is one of the largest terrestrial carbon (C) stocks and is highly sensitive to climate warming. Understanding microbial responses to warming induced environmental changes is critical to evaluating their influence on soil biogeochemical cycles. In this study, a functional gene array (i.e. GeoChip 4.2) was used to analyze the functional capacities of soil microbial communities collected from a naturally degrading permafrost region in Central Alaska. more...

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

Type:: Genome variation profiling by array

Platform:: GPL23230
107 Samples

Download data: FTR

Series

Accession:: GSE97107

ID:: 200097107

Select item 20012999018.

Advanced biofilm analysis in streams receiving organic deicer runoff

(Submitter supplied) Prolific heterotrophic biofilm growth is a common occurrence in airport receiving streams containing deicer and anti-icer runoff. This study investigated relations of heterotrophic biofilm prevalence and community composition to environmental conditions at stream sites upstream and downstream of Milwaukee Mitchell International Airport in Milwaukee, WI, during two deicing seasons (2009–2010 and 2010–2011). more...

Organism:: Bacteria; Archaea; biofilm metagenome

Type:: Other

Platform:: GPL26517
11 Samples

Download data: CEL

Series

Accession:: GSE129990

ID:: 200129990

PubMed Full text in PMC Similar studies Analyze with GEO2R

Select item 20012401819.

Profiles of antibiotic resistance genes (ARGs) and virulence genes (VGs) and their temporal interactions in OD and MBR

(Submitter supplied) Antibiotic resistance genes (ARGs) and virulence genes (VGs) associated with bacterial pathogens are of great concern in WWTPs, while current knowledge of their profiles and co-occurrence patterns in different time intervals is barely sufficient. Moreover, the impacts of treatment process on ARG/VGs diversity also remain clear. To this end, this study was launched to address the differences of the ARG/VGs diversity between an oxidation ditch (OD) and an membrane bioreactor (MBR) and the co-occurrence patterns in different time intervals using a functional gene array-GeoChip.

Organism:: Archaea; Eukaryota; Viruses; Bacteria; activated sludge metagenome

Type:: Other

Platform:: GPL25953
48 Samples

Download data: TXT

Series

Accession:: GSE124018

ID:: 200124018

Select item 20009851220.

Antagonistic interactive effects of CO2 and nitrogen on microbial community enhance the persistence of soil C storage

(Submitter supplied) To study long-term elevated CO2 and enriched N deposition interactive effects on microbial community and soil ecoprocess, here we investigated soil microbial community in a grassland ecosystem subjected to ambient CO2 (aCO2, 368 ppm), elevated CO2 (eCO2, 560 ppm), ambient nitrogen deposition (aN) or elevated nitrogen deposition (eN) treatments for a decade. There exist antagonistic ×ばつN interactions on microbial functional genes associated with C, N, P S cycling processes. more...