GEO DataSets

(Submitter supplied) RyhB is a non-coding RNA regulated by the Fur repressor. It has previously been shown to cause the rapid degradation of a number of mRNAs that encode proteins that utilize iron. Here we examine the effect of ectopic RyhB production on global gene expression by microarray analysis. Many of the previously identified targets were found, as well as other mRNAs encoding iron-binding proteins, bringing the total number of regulated operons to at least 18, encoding 56 genes. more...

Organism:

Escherichia coli; Escherichia coli K-12

Type:

Expression profiling by array

Dataset:

GDS1494

Platform:

GPL199

12 Samples

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Analysis of derivatives of strain MG1655: wild-type, fur mutant, and wild-type with added FeSO4, induced to overexpress RyhB. RyhB is a noncoding RNA regulated by the Fur repressor protein. Results suggest that RyhB plays a major role in the regulation of iron metabolism.

Organism:

Escherichia coli; Escherichia coli K-12

Type:

Expression profiling by array, count, 2 agent, 2 genotype/variation, 2 growth protocol sets

Platform:

GPL199

Series:

GSE3105

12 Samples

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(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Escherichia coli str. K-12 substr. MG1655

Type:

Expression profiling by genome tiling array; Genome binding/occupancy profiling by genome tiling array

Platforms:

GPL17024 GPL8708 GPL15010

24 Samples

Download data: PAIR, TXT, WIG

(Submitter supplied) As descirbed in the manuscript "The impact of anaerobiosis on expression of the iron-responsive Fur and RyhB Regulons" we mapped the locations of Fur DNA binding in E. coli K12 under aerobic or anaerobic growth conditions and anerobic iron deficient growth conditions.

Organism:

Escherichia coli str. K-12 substr. MG1655

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL17024 GPL15010

9 Samples

Download data: WIG

(Submitter supplied) As descirbed in the manuscript The impact of anaerobiosis on expression of the iron-responsive Fur and RyhB Regulons we performed a control ChIP-chip experiment in an E. coli strain lacking the transcription factor Fur to identify regions Fur-independent enrichment.

Organism:

Escherichia coli str. K-12 substr. MG1655

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL8708

1 Sample

Download data: PAIR, TXT

(Submitter supplied) As descirbed in the manuscript "The impact of anaerobiosis on expression of the iron-responsive Fur and RyhB Regulons" we profiled the gene expression of E. coli K12 during aerobic or anaerobic growth and in the presence or absence of the transcription factor Fur and/or the small RNA RyhB.

Organism:

Escherichia coli str. K-12 substr. MG1655

Type:

Expression profiling by genome tiling array

Platform:

GPL8708

14 Samples

Download data: PAIR, TXT

(Submitter supplied) Investigation of whole genome gene expression level changes in a Clostridium difficile fur (ferric uptake regulator) mutant, compared to the wild type strain 630 erm. The fur mutant analyzed in this study is further described in Ho and Ellermeier (2015) J. Bacteriology

Organism:

Clostridioides difficile 630

Type:

Expression profiling by array

Platform:

GPL20243

12 Samples

Download data: PAIR

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Cereibacter sphaeroides 2.4.1

Type:

Expression profiling by array; Expression profiling by high throughput sequencing

Platforms:

GPL17213 GPL15457

6 Samples

Download data: TXT, WIG

(Submitter supplied) High intracellular levels of unbound iron can contribute to the production of reactive oxygen species (ROS) in the Fenton reaction, while depletion of iron limits the availability of iron containing proteins, some of which have important functions in the oxidative stress defense. Vice versa increased ROS levels lead to damage of proteins with iron sulfur centers. Thus organisms have to coordinate and balance their responses to oxidative stress and iron availability. more...

Organism:

Cereibacter sphaeroides 2.4.1

Type:

Expression profiling by array

Platform:

GPL15457

2 Samples

Download data: TXT

(Submitter supplied) A total of 4388/4385 genes' transcripts (under aerobic/microaerobic condition, respectively) were identified. Among them, 105 and 71 transcripts were confidently determined to be up- or down-regulated by more than 4 folds with false discovery rate (FDR) p value more than 1, respectively. Additionally, 49 known regulatory non-coding small RNAs (sRNAs) were detected, and 18 sRNAs were differentially abundant (more than 1.5 fold-change). more...

Organism:

Escherichia coli

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL21222 GPL16085

15 Samples

Download data: XLSX

(Submitter supplied) Global tranascriptional profiling of Bacillus subtilis cells comparing fur mutant to mutants of the iron-sparing response: fur fsrA double mutant, fur fbpAB triple mutant, fur fbpC double mutant, and fur fbpABC quadruple mutant Abstract of associated manuscript: The Bacillus subtilis ferric uptake regulator (Fur) protein is the major sensor of cellular iron status. When iron is limiting for growth, derepression of the Fur regulon increases the cellular capacity for iron uptake and mobilizes an iron-sparing response mediated, in large part, by a small non-coding RNA named FsrA. more...

Organism:

Bacillus subtilis

Type:

Expression profiling by array

Platform:

GPL7420

15 Samples

Download data: GPR

(Submitter supplied) Global transcriptome analyses at growth before and after 10 min of photooxidative stress were applied to monitor stress dependent gene expression in the alpha-proteobacterium Rhodobacter capsulatus. Transcriptome profiles of pigmented cultures with high aeration were monitored before and after the onset of singlet oxygen stress.

Organism:

Rhodobacter capsulatus SB 1003

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26909

6 Samples

Download data: XLSX

(Submitter supplied) Global transcriptome analyses at different stages of growth were applied to monitor growth phase-dependent gene expression in the alpha-proteobacterium Rhodobacter sphaeroides. Cultures with low aeration, which underwent strong changes in levels of dissolved oxygen during growth, were compared to aerated cultures, which showed little variation in levels of dissolved oxygen. Cells were in stationary phase for 12 h or for 57 h before dilution into fresh medium. more...

Organism:

Cereibacter sphaeroides 2.4.1

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17213

8 Samples

Download data: WIG

(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