GEO DataSets

(Submitter supplied) Shewanella oneidensis MR-1 exhibits diverse metal ion-reducing capabilities and thus is of potential utility as a bioremediation agent. Knowledge of the molecular components and regulatory mechanisms dictating cellular responses to heavy metal stress, however, remains incomplete. In a previous work, the S. oneidensis so2426 gene, annotated as a DNA-binding response regulator, was demonstrated to be specifically responsive at both the transcript and protein levels to acute chromate [Cr(VI)] challenge. more...

Organism:

Shewanella oneidensis MR-1

Type:

Expression profiling by array

Platform:

GPL7055

6 Samples

Download data: TXT

(Submitter supplied) Time-series transcriptional profiles of Shewanella oneidensis type strain MR-1 under iron depletion and repletion conditions. Iron homeostasis of Shewanella oneidensis, a gamma-proteobacterium possessing high iron content, is regulated by a global transcription factor Fur. However, knowledge is incomplete about other biological pathways that respond to changes in iron concentration, as well as details of the responses. more...

Organism:

Shewanella oneidensis MR-1

Type:

Expression profiling by array

Platform:

GPL3253

52 Samples

Download data: TXT

(Submitter supplied) In limiting oxygen as an electron acceptor, the dissimilatory metal-reducing bacterium Shewanella oneidensis MR-1 rapidly forms nanowires, extensions of its outer membrane containing the cytochromes MtrC and OmcA needed for extracellular electron transfer. RNA-Seq analysis was employed to determine differential gene expression over time from cultures maintained in a chemostat and limited for oxygen. more...

Organism:

Shewanella oneidensis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21696

16 Samples

Download data: TXT

(Submitter supplied) The ArrayIt® brand SuperAmine 2 Microarray Substrates line represents the highest quality amine-containing substrate in the microarray industry. All of our substrates are polished to atomic flatness and manufactured in a state-of-the-art class 100 cleanrooms, with strict controls on particulate, biological and static contaminants, as well as temperature and humidity control.  These pristine glass substrates with reactive amine groups offer quality and performance that cannot be obtained from any other vendor. more...

Organism:

Shewanella oneidensis MR-1

9 Series

166 Samples

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(Submitter supplied) Comparisson of expression profiling of a etrA deletion mutant strain (experimental sample) with that of the wild type Shewanella oneidensis MR-1 strain to assess global direct/indirect genetic regulation EtrA in Shewanella oneidensis MR-1 shares 73.6% and 50.8% amino acid sequence identity with the oxygen-sensing regulator Fnr in E. coli and Anr in Pseudomonas aeruginosa, respectively; however, its regulatory role of anaerobic metabolism in Shewanella spp. more...

Organism:

Shewanella oneidensis MR-1

Type:

Expression profiling by array

Platform:

GPL3253

6 Samples

Download data: TXT

(Submitter supplied) Using gene expression changes at mid-log phase data from microarray experiments, we investigated the roles of global transcription regulators in D. vulgaris.

Organism:

Nitratidesulfovibrio vulgaris str. Hildenborough

Type:

Expression profiling by array

Platform:

GPL5214

5 Samples

Download data: TXT

(Submitter supplied) In the alpha subclass of proteobacteria iron homeostasis is controlled by diverse iron responsive regulators. Caulobacter crescentus, an important freshwater α-proteobacterium, uses the ferric uptake repressor (Fur) for such purpose. However, the impact of the iron availability on the C. crescentus transcriptome and an overall perspective of the regulatory networks involved remain unknown. In this work we report the identification of iron-responsive and Fur-regulated genes in C. more...

Organism:

Caulobacter vibrioides NA1000; Caulobacter vibrioides CB15

Type:

Expression profiling by array

Platform:

GPL10469

4 Samples

Download data: TXT

(Submitter supplied) This study presents a global transcriptional analysis of the cold shock response of Shewanella oneidensis MR-1 after a temperature downshift from 30 to 8 or 15oC based on time-series microarray experiments. More than 700 genes were found to be significantly affected (p < 0.05) upon cold shock challenge, especially at 8oC. The temporal gene expression patterns of the classical cold-shock genes varied and only some of them, most notably so1648 and so2787, were differentially regulated in response to temperature downshift. more...

Organism:

Shewanella oneidensis MR-1

Type:

Expression profiling by array

Platform:

GPL3253

60 Samples

Download data

(Submitter supplied) We undertook a transcriptional profiling to identify genes coping with H2O2-induced oxidative stress in S. oneidensis. The data revealed that the well conserved scavenging genes such as as ahpCF, katB, and katG formed the first line of defense while iron-sulfur protecting proteins may not play a significant role.

Organism:

Shewanella oneidensis MR-1; Shewanella oneidensis

Type:

Expression profiling by array

Platform:

GPL3253

8 Samples

Download data: TXT

(Submitter supplied) Shewanella oneidensis MR-1 exhibits extracellular electron transfer (EET) activity that is influenced by various cellular components, including outer-membrane cytochromes, cell-surface polysaccharides (CPS), and regulatory proteins. Here, a random transposon-insertion mutant library of S. oneidensis MR-1 was screened after extended cultivation in electrochemical cells (ECs) with a working electrode poised at +0.2 V (vs. more...

Organism:

Shewanella oneidensis; Shewanella oneidensis MR-1

Type:

Expression profiling by array

Platform:

GPL17650

6 Samples

Download data: TXT

(Submitter supplied) 5' RNA-Seq of mRNA from S. oneidensis MR-1 grown aerobically in defined lactate medium

Organism:

Shewanella oneidensis MR-1

Type:

Expression profiling by high throughput sequencing

Platform:

GPL15825

1 Sample

Download data: WIG

(Submitter supplied) High-resolution tiling analysis of the MR-1 transcriptome in defined lactate minimal medium

Organism:

Shewanella oneidensis MR-1

Type:

Expression profiling by genome tiling array

Platform:

GPL15823

2 Samples

Download data: FTR, TXT

(Submitter supplied) Comparison of gene expression and mutant fitness in Shewanella oneidensis MR-1

Organism:

Shewanella oneidensis MR-1

Type:

Expression profiling by array

Platform:

GPL15821

36 Samples

Download data: FTR

(Submitter supplied) Anaerobic respiration in the metal reducer Shewanella oneidensis MR-1, unlike other bacteria, is regulated by the cAMP receptor protein, CRP. Three putative genes, cyaA, cyaB, and cyaC, predicted to encode class I, class IV, and class III adenylate cyclases respectively, have been identified in the genome sequence of this bacterium. Functional validation through complementation of an E. coli cya mutant confirmed that these genes encode proteins with adenylate cyclase activities. more...

Organism:

Shewanella oneidensis MR-1

Type:

Expression profiling by genome tiling array

Platform:

GPL8434

6 Samples

Download data: CEL

(Submitter supplied) Initial attachment to a surface marks the onset of a bacterial life style switch from planktonic to biofilm mode of growth. Among dissimilatory iron reducing bacteria, S. oneidensis MR-1 is notable due to its extensive respiratory versatility. It has been hypothesized that direct interaction of Shewanella cells with, or close proximity to, an appropriate surface facilitates the deposition of electrons. more...

Organism:

Shewanella oneidensis MR-1

Type:

Expression profiling by array

Platform:

GPL10101

8 Samples

Download data: TXT

(Submitter supplied) The purpose of this study was to determine what S. agalactiae genes are under the control of the MtaR regulatory protein. Inactivation of the Streptococcus agalactiae mtaR gene resulted in the downregulation of 11 genes and the upregulation of 1 gene in the mtaR mutant. Genes involved in the uptake of methionine and a gene involved in the degradation of peptides were downregulated. Also, genes involved in the transport and biosynthesis of arginine were downregulated. more...

Organism:

Streptococcus agalactiae

Type:

Expression profiling by array

Platform:

GPL7515

6 Samples

Download data: CEL, CHP

(Submitter supplied) The sumitted data compares gene expression profile of Shewnaella oneidensis MR-1 on two different sets of media conditions (nutritionally rich LB medium and Lactate minimal medium)

Organism:

Shewanella oneidensis MR-1

Type:

Expression profiling by array

Platform:

GPL8434

84 Samples

Download data: CEL

(Submitter supplied) To identify the transcriptional targets of the DNA-binding response regulator HnoC (SO_2540), mRNA transcript levels in Shewanella oneidensis were measured using whole genome microarray analysis. Transcript levels were compared between WT Shewanella oneidensis and a hnoC deletion strain.

Organism:

Shewanella oneidensis MR-1

Type:

Expression profiling by array

Platform:

GPL16721

8 Samples

Download data: TXT

(Submitter supplied) The TyrR transcription factor controls the expression of genes for the uptake and biosynthesis of aromatic amino acids in Escherichia coli. In the plant-associated and clinically significant proteobacterium Enterobacter ludwigii UW5, the TyrR orthologue was previously shown to regulate genes that encode enzymes for synthesis of the plant hormone indole-3-acetic acid and gluconeogenesis, indicating a broader function for the transcription factor. more...

Organism:

Enterobacter ludwigii

Type:

Expression profiling by high throughput sequencing

Platform:

GPL29272

8 Samples

Download data: TXT, XLSX

(Submitter supplied) The availability of oxygen is a major environmental factor for many microbes, in particular for bacteria, such as Shewanella species, which thrive in redox-stratified environments. One of the best studied systems involved in mediating the response to changes in environmental oxygen levels is the Arc two-component system of Escherichia coli, consisting of the sensor kinase ArcB and the cognate response regulator ArcA. more...

Organism:

Shewanella oneidensis MR-1

Type:

Expression profiling by array

Platform:

GPL10101

6 Samples

Download data: TXT