Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Diel cycles of gene expression in oligotrophic, dystrophic, and eutrophic lakes to identify new gene functions and dissect carbon cycling metabolisms

ABSTRACT: Aquatic microbial communities contain a vast amount of genetic diversity and we have much to learn about how this manifests to functional diversity. Existing long-term time series data includes 16S tags, metagenomes, single amplified genomes (SAGs), and genomes from metagenomes (GFMs). Information about functional diversity and metabolic capabilities is often unavailable. The study sites include three lakes that are the subject of intense study through the North Temperate Lakes Long Term Ecological Research site: Sparkling Lake (oligotrophic), Lake Mendota (eutrophic), and Trout Bog Lake (dystrophic). The work (proposal:https://doi.org/10.46936/10.25585/60000947) conducted by the U.S. Department of Energy Joint Genome Institute (https://ror.org/04xm1d337), a DOE Office of Science User Facility, is supported by the Office of Science of the U.S. Department of Energy operated under Contract No. DE-AC02-05CH11231.

INSTRUMENT(S): Q Exactive

ORGANISM(S): Freshwater Lake Microbiome

SUBMITTER: Katherine McMahon

PROVIDER: MSV000093272 | MassIVE | Thu Nov 02 12:44:00 GMT 2023

REPOSITORIES: MassIVE

ACCESS DATA

Json Xml

Similar Datasets

Leveraging pan genomes to investigate diel transcriptomic and metabolomic responses to abiotic stress in Brassica. rapa and B. napus diversity panels.

Project description:Metabolomic analysis of the abiotic stress experiments on tissue from Brassicaceae genotypes. The work (proposal:https://doi.org/10.46936/10.25585/60001202) conducted by the U.S. Department of Energy Joint Genome Institute (https://ror.org/04xm1d337), a DOE Office of Science User Facility, is supported by the Office of Science of the U.S. Department of Energy operated under Contract No. DE-AC02-05CH11231.

2023-11-02 | MSV000093268 | MassIVE

Comparative and Population Genomics of Xylariaceae

Project description:We are examining the metabolites produced during co-culture of Xylariaceae fungi. The work (proposal:https://doi.org/10.46936/10.25585/60001144) conducted by the U.S. Department of Energy Joint Genome Institute (https://ror.org/04xm1d337), a DOE Office of Science User Facility, is supported by the Office of Science of the U.S. Department of Energy operated under Contract No. DE-AC02-05CH11231.

2023-11-02 | MSV000093277 | MassIVE

Global metabolic profile comparison between 2 ecotypes upon inoculation with Azoarcus olearius

Project description:Arabidopsis thaliana associated with Plant Growth Promoting Bacteria (PGPB) Azoarcus olearius (DQS4) innoculated with WS (Wassilewskija) and Col0 (Columbia) ecotypes. The work (proposal:https://doi.org/10.46936/10.25585/60000448) conducted by the U.S. Department of Energy Joint Genome Institute (https://ror.org/04xm1d337), a DOE Office of Science User Facility, is supported by the Office of Science of the U.S. Department of Energy operated under Contract No. DE-AC02-05CH11231.

2023-11-02 | MSV000093274 | MassIVE

Homoserine lactone standards and heterologous expression of LuxI family synthases in E. coli

Project description:This dataset contains spectra of LuxI family synthases heterologously expressed and induced in E. coli as well as commercial homoserine lactones. The work (proposal:https://doi.org/10.46936/10.25585/60001376) conducted by the U.S. Department of Energy Joint Genome Institute (https://ror.org/04xm1d337), a DOE Office of Science User Facility, is supported by the Office of Science of the U.S. Department of Energy operated under Contract No. DE-AC02-05CH11231.

2023-08-04 | MSV000092598 | MassIVE

Exploring the role of drought-induced plant-associated microbes in promoting plant fitness in Sorghum bicolor and Oryza sativa

Project description:We investigate the role of root-associated Actinobacteria in promoting host fitness under drought stress in two plants important to the DOE mission of sustainable biofuels: Sorghum bicolor and Oryza sativa. The work (proposal:https://doi.org/10.46936/10.25585/60001083) conducted by the U.S. Department of Energy Joint Genome Institute (https://ror.org/04xm1d337), a DOE Office of Science User Facility, is supported by the Office of Science of the U.S. Department of Energy operated under Contract No. DE-AC02-05CH11231.

2023-11-02 | MSV000093246 | MassIVE

Genetic, community, and ecosystem consequences of co-introduction of mycorrhizal fungiwith exotic pines

Project description:Suillus luteus mycorrhizae will be experimentally synthesized on the roots of pine seedlings, grown in aseptic conditions from seeds representing either native wild-type European genotypes of Pinus pinaster (a native host of S. luteus) or typical forestry production genotypes of P. radiata. The work (proposal:https://doi.org/10.46936/10.25585/60001406) conducted by the U.S. Department of Energy Joint Genome Institute (https://ror.org/04xm1d337), a DOE Office of Science User Facility, is supported by the Office of Science of the U.S. Department of Energy operated under Contract No. DE-AC02-05CH11231.

2023-11-03 | MSV000093294 | MassIVE

Unearthing the active microbes, viruses, and metabolites in dynamic-redox tropical soils with quantitative SIP and metagenomics

Project description:This research focuses on changes in the microbial communities of tropical soils during aerobic to anaerobic transitions following wetting. Of particular interest is the natural cycling of the soil microbiome through aerobic and anaerobic metabolism over relative short time periods. The work (proposal:https://doi.org/10.46936/10.25585/60000880) conducted by the U.S. Department of Energy Joint Genome Institute (https://ror.org/04xm1d337), a DOE Office of Science User Facility, is supported by the Office of Science of the U.S. Department of Energy operated under Contract No. DE-AC02-05CH11231.

2023-11-02 | MSV000093271 | MassIVE

Botryococcus braunii circadian time course

Project description:Botryococcus braunii is a colony forming green microalga of the order Chlorophyta. During the growth cycle of this organism, the algae synthesizes long chain liquid hydrocarbon isoprenoid compounds and sequesters them in the extracellular matrix of the colony. Metabolomics was done on samples from a circadian time series. The work (proposal:https://doi.org/10.46936/10.25585/60000723) conducted by the U.S. Department of Energy Joint Genome Institute (https://ror.org/04xm1d337), a DOE Office of Science User Facility, is supported by the Office of Science of the U.S. Department of Energy operated under Contract No. DE-AC02-05CH11231.

2023-11-02 | MSV000093267 | MassIVE

Elucidation of the Gene Regulatory Networks Governing Terpenoid-Mediated Plant-Environment Interactions to Enable Advanced Bioenergy Crops

Project description:The proposed project aims to elucidate the gene-regulatory networks (GRNs) underlying terpenoid metabolism in three major bioenergy crops, switchgrass (Panicum virgatum), maize (Zea mays), and sorghum (Sorghum bicolor), to aid crop development for enhanced stress resilience and biofuel production from biomass feedstock. Prior studies identified more than 50 terpene synthases (TPS) and cytochrome P450 monooxygenases (P450), as key enzymes in generating bioactive terpenoids, in several bioenergy plants including switchgrass and maize. This knowledge now enables a precise investigation of the GRNs that govern common and species-specific terpenoid pathways. We will integrate transcription factor (TF) functional studies, TF binding site mapping, transcript and metabolite profiling, and terpenoid pathway engineering to identify the terpenoid-metabolic TF networks mediating stress responses in switchgrass, maize and sorghum. The work (proposal:https://doi.org/10.46936/10.25585/60001378) conducted by the U.S. Department of Energy Joint Genome Institute (https://ror.org/04xm1d337), a DOE Office of Science User Facility, is supported by the Office of Science of the U.S. Department of Energy operated under Contract No. DE-AC02-05CH11231.

2024-02-14 | MSV000094091 | MassIVE

Regional Epigenetic Variation in Asexual Snail Populations among Urban and Rural Lakes

Project description:Epigenetic variation has the potential to control environmentally dependent development and contribute to phenotypic responses to local environments. Environmental epigenetic studies of sexual organisms confirm the responsiveness of epigenetic variation, which should be even more important when genetic variation is lacking. A previous study of an asexual snail, Potamopyrgus antipodarum, demonstrated that different populations derived from a single clonal lineage differed in both shell phenotype and methylation signature when comparing lake versus river populations. Here, we examine methylation variation among lakes that differ in environmental disturbance and pollution histories. The differential DNA methylation regions (DMRs) identified among the different lake comparisons suggested a higher number of DMRs and variation between rural Lake 1 and one urban Lake 2 and between the two urban Lakes 2 and 3, but limited variation between the rural Lake 1 and urban Lake 3. DMR genomic characteristics and gene associations were investigated. Observations suggest there is no effect of geographic distance or any consistent pattern of DMRs between urban and rural lakes. Environmental factors may influence epigenetic response.

2019-09-27 | GSE133502 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data