Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Transcriptome-wide marker gene expression analysis of stress-responsive Oleidesulfovibrio alaskensis

ABSTRACT: Sulfate-reducing bacteria (SRB) are terminal members of any anaerobic food chain. For example, they critically influence the biogeochemical cycling of carbon, nitrogen, sulfur, and metals (natural environment) as well as the corrosion of civil infrastructure (built environment). The United States alone spends nearly $4 billion to address the biocorrosion challenges of SRB. It is important to analyze the genetic mechanisms of these organisms under environmental stresses. The current study uses transcriptome-wide marker gene panel mapping to decipher the stress mechanisms in SRB. This project contains 3 control samples and 6 test samples of RNA-seq data of Oleidesulfovibrio alaskensis strain G20, exposed to pristine copper and graphene-coated copper.

ORGANISM(S): Oleidesulfovibrio alaskensis

PROVIDER: GSE240798 | GEO | 2023/08/30

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

High-resolution analysis of RNA expression in Desulfovbrio alaskensis G20

Project description:High-resolution tiling analysis of the D. alaskensis G20 transcriptome in lactate/sulfate media, both rich (LS) and defined (LS4D)

2012-07-19 | GSE39471 | GEO

Comparative transcriptional analysis of Desulfovibrio alaskensis G20 and regulator proteins mutants

Project description:Expression data for Desulfovibrio alaskensis strain G20 and mutants in regulator proteins grown on lactate sulfate media. Pellets collected at mid-log growth phase. We aimed to confirm or expand the predicted regulons of each of the transposon interrupted regulator mutants. 12 samples were collected: 10 regulator mutants, 1 mutant in a secretory protein and 1 control sample Desulfovibrio alaskensis G20. 1 replicate for each condition.

2013-08-03 | E-GEOD-49529 | biostudies-arrayexpress

Comparative transcriptional analysis of Desulfovibrio alaskensis G20, a choline utilization regulator and LysX

Project description:Expression data for Desulfovibrio alaskensis strain G20 and mutants in regulator proteins grown on lactate sulfate media and then pelleted and transferred to another media when they reached stationary phase. The Choline mutant was transferred to lacte/sulfate minimal media and choline/sulfate minimal media. The LysX mutant was transferred to minimal media with lysine and rich media. G20 was transferred to minimal media, choline/sulfate minimal media, lactate/choline/sulfate minimal media, minimal media with lysine, and rich media. We aimed to confirm or expand the regulons of each of the transposon interupted regulator mutants and compare gene expression responses of the regulators in different growth conditions. 10 samples were collected: 2 regulator mutants (2 conditions each), Desulfovibrio alaskensis G20 (5 conditions), 2 replicates for G20 minimal media condition. Control sample -G20 rich media.

2013-08-03 | E-GEOD-49528 | biostudies-arrayexpress

Comparative transcriptional analysis of Desulfovibrio alaskensis G20 grown under various syntrophic and fermentative conditions on pyruvate relative to respiratory growth

Project description:Pyruvate fermentation pathway and energetics of Desulfovibrio alaskensis strain G20 under syntrophic coculture and fermentative monoculture conditions Expression data for Desulfovibrio alaskensis strain G20 grown in chemostats on pyruvate under respiratory conditions (sulfate-limited and pyruvate-limited monoculture, dilution rate 0.047 and 0.027 h-1), fermentative conditions (monoculture, dilution rate 0.036 h-1), and syntrophic conditions (coculture with Methanococcus maripaludis or Methanospirillum hungatei, dilution rate of 0.047 and 0.027 h-1)

2013-12-12 | GSE53226 | GEO

Comparative transcriptional analysis of Desulfovibrio alaskensis G20 and mutants in regulator proteins grown in minimal media

Project description:Expression data for Desulfovibrio alaskensis strain G20 and mutants in regulator proteins grown on lactate sulfate media. Pellets collected at mid-log growth phase. We aimed to confirm or expand the predicted regulons of each of the transposon interrupted regulator mutants. 8 samples were collected: 7 regulator mutants and 1 control sample Desulfovibrio alaskensis G20. 1 replicate for each condition.

2013-08-03 | E-GEOD-49527 | biostudies-arrayexpress

Comparative transcriptional analysis of Desulfovibrio alaskensis G20 and regulator proteins mutants

2013-08-03 | GSE49529 | GEO

Oleidesulfovibrio alaskensis G20

Project description:Oleidesulfovibrio alaskensis G20 Raw sequence reads

| PRJNA1138078 | ENA

Oleidesulfovibrio alaskensis G20

Project description:Oleidesulfovibrio alaskensis G20 Raw sequence reads

| PRJNA1135338 | ENA

Transcriptomics and functional analysis of copper stress response in the sulfate-reducing bacteria Desulfovibrio alaskensis G20

Project description:Copper (Cu) is an essential micronutrient required as a co-factor in the catalytic center of many enzymes in bacteria. However, excess Cu is hazardous and can generate pleiotropic effects. Cu has been the metal of choice for piping used in household water distribution systems. Due to its leaching from pipelines, Cu is present at an elevated concentration in groundwater and in soil which is of public health concern. Sulfate-reducing bacteria (SRB) have been demonstrated to remove toxic levels of Cu. However, reports on the toxicity of Cu towards SRB have primarily focused on the degree of toxicity and subsequent elimination. In this study, we show in detail the Cu(II) stress-related effects on a model sulfate reducing bacteria, Desulfovibrio alaskensis G20. Cu(II) stress effects were assessed as alterations in the transcriptome through RNA-Seq at varying Cu(II) concentrations (5µM and 15µM). In the pairwise comparison of control vs 5µM, 61.43% of genes were downregulated and 38.57% genes were upregulated. In 15µM vs control, 49.51% genes were downregulated, and 50.5% genes were upregulated. The results indicated that the expression of inorganic ion transporters and translation machinery was massively modulated. Moreover, changes in important biological processes such as DNA transcription and signal transduction were observed at high Cu(II) concentration. In addition, metabolomics analysis indicated the effect of certain organic acids and amino acids in cellular metal buffering system and reducing oxidative damage to cells. These results will help us better understand the mechanism of Cu(II) stress response and provide avenues for future research.

2022-05-31 | GSE191076 | GEO

Comparative transcriptional analysis of Desulfovibrio alaskensis G20 and mutants in regulator proteins grown in minimal media

2013-08-03 | GSE49527 | GEO