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Items: 1 to 20 of 576

1.

Engineered cell elongation promotes extracellular electron transfer of Shewanella oneidensis

(Submitter supplied) To investigate how cell elongation impacts extracellular electron transfer (EET) of electroactive microorganisms (EAMs), the division of model EAM Shewanella oneidensis MR-1 was engineered by reducing the formation of cell divisome. Specially, by blocking the translation of division proteins via anti-sense RNAs or expressing division inhibitors, the cellular length and output power density were all increased. more...
Organism:
Shewanella oneidensis MR-1
Type:
Expression profiling by high throughput sequencing
Platform:
GPL33796
12 Samples
Download data: XLSX
Series
Accession:
GSE244261
ID:
200244261
2.

Supplementation with amino acid sources facilitates fermentative growth of Shewanella oneidensis MR-1 in defined media

(Submitter supplied) Shewanella oneidensis MR-1 is a facultative anaerobe that grows by respiration using a variety of electron acceptors. This organism serves as a model to study how bacteria thrive in redox-stratified environments. A glucose-utilizing engineered derivative of MR-1 has been reported to be unable to grow in glucose minimal medium (GMM) in the absence of electron acceptors, despite this strain having a complete set of genes for reconstructing glucose to lactate fermentative pathways. more...
Organism:
Shewanella oneidensis; Shewanella oneidensis MR-1
Type:
Expression profiling by array
Platform:
GPL27952
8 Samples
Download data: TXT
Series
Accession:
GSE220284
ID:
200220284
3.

Elevated intracellular cyclic-di-GMP level in Shewanella oneidensis increases expression of c-type cytochromes

(Submitter supplied) Transcriptomic analysis used to understand the influence of elevated intracellular cyclic-di-GMP in Shewanella oneidensis on expression of c-type cytochrome at transcript level.
Organism:
Shewanella oneidensis
Type:
Expression profiling by high throughput sequencing
Platform:
GPL24121
12 Samples
Download data: XLSX
Series
Accession:
GSE138586
ID:
200138586
4.

Identification of an ECF sigma factor that facilitates electroactive biofilm formation by Shewanella oneidensis MR-1

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Shewanella oneidensis; Shewanella oneidensis MR-1
Type:
Expression profiling by array
Platform:
GPL27952
16 Samples
Download data: TXT
Series
Accession:
GSE142643
ID:
200142643
5.

Identification of an ECF sigma factor that facilitates electroactive biofilm formation by Shewanella oneidensis MR-1: Experiment 2

(Submitter supplied) Shewanella oneidensis MR-1 was grown on electrodes in electrochemical flow cells (EFC), and the transcriptome profiles of electrode-attached MR-1 cells were compared under electrolyte-flow and static (non-flow) conditions. The results revealed that the SO_3096 gene encoding a putative extracytoplasmic function (ECF) sigma factor, as well as genes related to cyclic-di-guanosine monophosphate and flagella synthesis (e.g., SO_3556 and flrC) and c-type cytochrome maturation (dsbD), was significantly up-regulated under the electrolyte-flow condition. more...
Organism:
Shewanella oneidensis; Shewanella oneidensis MR-1
Type:
Expression profiling by array
Platform:
GPL27952
8 Samples
Download data: TXT
Series
Accession:
GSE142642
ID:
200142642
6.

Identification of an ECF sigma factor that facilitates electroactive biofilm formation by Shewanella oneidensis MR-1: Experiment 1

(Submitter supplied) Shewanella oneidensis MR-1 was grown on electrodes in electrochemical flow cells (EFC), and the transcriptome profiles of electrode-attached MR-1 cells were compared under electrolyte-flow and static (non-flow) conditions. The results revealed that the SO_3096 gene encoding a putative extracytoplasmic function (ECF) sigma factor, as well as genes related to cyclic-di-guanosine monophosphate and flagella synthesis (e.g., SO_3556 and flrC) and c-type cytochrome maturation (dsbD), was significantly up-regulated under the electrolyte-flow condition. more...
Organism:
Shewanella oneidensis MR-1; Shewanella oneidensis
Type:
Expression profiling by array
Platform:
GPL27952
8 Samples
Download data: TXT
Series
Accession:
GSE142641
ID:
200142641
7.

Transcriptome analysis of Wild Type and ΔfadR in Shewanella oneidensis MR-1

(Submitter supplied) Purpose: The goals of this study are to find out the differential expression genes in the fadR mutant strain(ΔfadR) compared with wild-type (WT) and to further explore the regulation mechanisms of fadR. Methods: Shewanella oneidensis MR-1 WT and ΔfadR were collected in log phage(OD~0.6). RNA extraction was performed using the RNeasy minikit (Qiagen) and the RNA was quantified by using a NanoVue spectrophotometer (GE Healthcare). more...
Organism:
Shewanella oneidensis
Type:
Expression profiling by high throughput sequencing
Platform:
GPL26851
2 Samples
Download data: XLS
Series
Accession:
GSE133375
ID:
200133375
8.

Overexpression of the adenylate cyclase gene cyaC facilitates current generation by Shewanella oneidensis in bioelectrochemical systems

(Submitter supplied) Electrochemically active bacteria (EAB) are capable of electrochemical interactions with electrodes via extracellular electron transfer (EET) pathways and serve as essential components in bioelectrochemical systems. Previous studies have suggested that EAB, such as Shewanella oneidensis MR-1, use cyclic AMP (cAMP) receptor proteins for coordinately regulating the expression of catabolic and EET-related genes, allowing us to hypothesize that the intracellular cAMP concentration is an important factor determining electrochemical activities of EAB. more...
Organism:
Shewanella oneidensis; Shewanella oneidensis MR-1
Type:
Expression profiling by array
Platform:
GPL17650
8 Samples
Download data: TXT
Series
Accession:
GSE129679
ID:
200129679
9.

Electrochemically active bacteria sense electrode potentials for regulating catabolic pathways

(Submitter supplied) Electrochemically active bacteria (EAB) receive considerable attention for their utility in bioelectrochemical processes. Although electrode potentials are known to affect the metabolic activity of EAB, it is unclear whether EAB are able to sense and respond to electrode potentials. Here, we show that, in the presence of a high-potential electrode, a model EAB Shewanella oneidensis MR-1 can utilize NADH-dependent catabolic pathways and a background formate-dependent pathway to achieve high growth yield. more...
Organism:
Shewanella oneidensis; Shewanella oneidensis MR-1
Type:
Expression profiling by array
Platform:
GPL17650
22 Samples
Download data: TXT
Series
Accession:
GSE102264
ID:
200102264
10.

CpdA is involved in amino acid metabolism in Shewanella oneidensis MR-1

(Submitter supplied) Cyclic 3',5'-adenosine monophosphate (cAMP) phosphodiesterase (CPD) is an enzyme that catalyzes the hydrolysis of cAMP, a signaling molecule affecting diverse cellular and metabolic processes in bacteria. Some CPDs are also known to function in cAMP-independent manners, while their physiological roles remain largely unknown. Here, we investigated physiological roles of CPD in Shewanella oneidensis MR-1, a model environmental bacterium, and report that CPD is involved in amino-acid metabolism. more...
Organism:
Shewanella oneidensis MR-1; Shewanella oneidensis
Type:
Expression profiling by array
Platform:
GPL17650
8 Samples
Download data: TXT
Series
Accession:
GSE97220
ID:
200097220
11.

The small RNA RyhB is a regulator of cytochrome expression in Shewanella oneidensis

(Submitter supplied) Study of the roles played by Fur and RyhB in Shewanella oneidensis
Organism:
Shewanella oneidensis
Type:
Expression profiling by high throughput sequencing
Platform:
GPL24121
15 Samples
Download data: TXT
Series
Accession:
GSE104952
ID:
200104952
12.

Syntrophic interactions within the multi-species exoelectrogenic biofilm community in bio-electrochemical systems

(Submitter supplied) Anode-associated multi-species exoelectrogenic biofilms are essential to the function of bioelectrochemical systems (BESs). The investigation of electrode-associated biofilms is critical to advance understanding of the function of individual members within communities that thrive using an electrode as the terminal electron acceptor. This study focusses on the analysis of a model biofilm community consisting of Shewanella oneidensis, Geobacter sulfurreducens and Geobacter metallireducens. more...
Organism:
Shewanella oneidensis; Geobacter metallireducens; Geobacter sulfurreducens
Type:
Expression profiling by high throughput sequencing
4 related Platforms
18 Samples
Download data: TXT
Series
Accession:
GSE79750
ID:
200079750
13.

Regulation of Gene Expression During Electron Acceptor Limitation and Bacterial Nanowire Formation in Shewanella oneidensis MR-1

(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
Series
Accession:
GSE79964
ID:
200079964
14.

Comparative transcriptome analysis of Shewanella MR-1 under oxic vs. suboxic conditions

(Submitter supplied) To understand how cell physiological state affects mRNA translation, we used the bacterium Shewanella oneidensis MR-1 grown under steady state conditions at either 20% or 8.5% O2. Using a combination of quantitative proteomics and RNA-Seq, we generated high-confidence data on >1000 mRNA and protein pairs. By using a steady state model, we found that differences in protein–mRNA ratios were primarily due to differences in the translational efficiency of specific genes. more...
Organism:
Shewanella oneidensis MR-1
Type:
Expression profiling by high throughput sequencing
Platforms:
GPL19663 GPL19662
18 Samples
Download data: TXT
Series
Accession:
GSE65062
ID:
200065062
15.

Electrochemical selection and characterization of a high current-generating Shewanella oneidensis mutant with altered cell-surface morphology and biofilm-related gene expression

(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
Series
Accession:
GSE50443
ID:
200050443
16.

dRNA-seq of Shewanella oneidensis MR-1

(Submitter supplied) We combined high-resolution tiling microarrays and 5'-end RNA sequencing to obtain a genome-wide map of transcription start sites (TSSs) for Shewanella oneidensis MR-1. To test the reliability of these TSSs, we compared our result to those from differential RNA sequencing (dRNA-seq), which discriminates primary and processed ends of transcripts. We found that our identified TSSs tend to have significantly more mapped reads in the TEX(+) sample than the TEX(-) sample. more...
Organism:
Shewanella oneidensis MR-1
Type:
Expression profiling by high throughput sequencing
Platform:
GPL18765
4 Samples
Download data: WIG
Series
Accession:
GSE58292
ID:
200058292
17.

Conservation of transcription start sites within genes across a bacterial genus

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Shewanella sp. W3-18-1; Shewanella sp. MR-4; Shewanella sp. MR-7; Shewanella sp. ANA-3; Shewanella oneidensis MR-1; Shewanella putrefaciens CN-32; Shewanella loihica PV-4; Shewanella amazonensis SB2B
Type:
Expression profiling by genome tiling array; Expression profiling by high throughput sequencing
10 related Platforms
26 Samples
Download data: FTR, WIG
Series
Accession:
GSE58337
ID:
200058337
18.

Genomic Array Footprinting of Shewanella oneidensis grown under aerobic conditions

(Submitter supplied) We undertook a genomic array footprinting to identify genes important for aerobic growth of S. oneidensis. The data revealed that removal of 96 genes resulted in significant impacts on aerobic growth.
Organism:
Shewanella oneidensis MR-1; Shewanella oneidensis
Type:
Expression profiling by array
Platform:
GPL3253
6 Samples
Download data: TXT
Series
Accession:
GSE42479
ID:
200042479
19.

Transcriptional targets of Shewanella oneidensis HnoC (SO_2540)

(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
Series
Accession:
GSE44689
ID:
200044689
20.

Transcript structures in Shewanella oneidensis MR-1

(Submitter supplied) 5' RNASeq of mRNA from S. oneidensis MR-1 grown aerobically in Luria-Bertani broth (LB) and defined lactate minimal medium
Organism:
Shewanella oneidensis MR-1
Type:
Expression profiling by high throughput sequencing
Platform:
GPL16837
3 Samples
Download data: WIG
Series
Accession:
GSE45313
ID:
200045313
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