GEO DataSets

(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) 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 GPL15010 GPL8708

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) Pathogenicity islands and plasmids encode genes for pathogenesis of various Escherichia coli pathotypes.Although there is a basic understanding of the contribution of these virulence factors to disease, less is known about variation in regulatory networks in determining disease phenotypes. Here we dissected aregulatory network directed by the conserved iron homeostasis regulator, Ferric Uptake Regulator (Fur), inuropathogenic E. more...

Organism:

Escherichia coli CFT073

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL18955

19 Samples

Download data: TXT, WIG

(Submitter supplied) Ferric uptake regulator (Fur) is the major regulator of iron acquisition in Escherichia coli and other bacteria. In the present study, the role of Fur in anaerobic S. enterica serovar Typhimurium was determined by transcriptome analysis, reporter assays, and enzymatic assays. In anaerobic Δfur, 298 genes were differentially expressed. In general, Fur repressed genes required for iron acquisition/storage, metabolism, electron transport, oxidative/nitrosative stress, and modulators of virulence. more...

Organism:

Salmonella enterica subsp. enterica serovar Typhimurium; Salmonella

Type:

Expression profiling by array

Platform:

GPL1835

6 Samples

Download data: CSV

(Submitter supplied) In this study wild-type, fur mutant, and complemented fur mutant strains of the human pathogen Neisseria gonorrhoeae F62 were grown under high (100 uM iron) or low (100 uM desferal) iron conditions to identify genes whose expression was regulated by iron and/or Fur

Organism:

Neisseria gonorrhoeae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20721

10 Samples

Download data: TXT

(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 K-12; Escherichia coli

Type:

Expression profiling by array

Dataset:

GDS1494

Platform:

GPL199

12 Samples

Download data

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

Download data

(Submitter supplied) The goal of this study is to obtain a genomic view of the Fur regulatory network under both iron replete and iron deficient conditions in Bacillus subtilis using ChIP-seq. Besides the known Fur target sites, 70 putative DNA binding sites were identified, and the vast majority had higher occupancy under iron sufficient conditions. In addition,we discovered a role for catechol degradation in bacillibactin metabolism, and provided evidence that catechol 2,3-dioxygenase can detoxify endogenously produced catechol substrates in addition to its more widely studied role in biodegradation of environmental aromatic compounds and pollutants.

Organism:

Bacillus subtilis

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL24109

5 Samples

Download data: WIG

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

Organism:

Escherichia coli str. K-12 substr. MG1655

Type:

Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing

Platform:

GPL17439

20 Samples

Download data: GFF

(Submitter supplied) The ferric uptake regulator (Fur) plays a critical role in the transcriptional regulation of iron metabolism in many bacteria. However, the full regulatory potential of Fur beyond iron metabolism remains undefined. Here, we comprehensively reconstructed the Fur transcriptional regulatory network in Escherichia coli K-12 MG1655 in response to iron availability using genome-wide measurements (ChIP-exo and RNA-seq). more...

Organism:

Escherichia coli str. K-12 substr. MG1655

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17439

8 Samples

Download data: CSV

(Submitter supplied) The ferric uptake regulator (Fur) plays a critical role in the transcriptional regulation of iron metabolism in many bacteria. However, the full regulatory potential of Fur beyond iron metabolism remains undefined. Here, we comprehensively reconstructed the Fur transcriptional regulatory network in Escherichia coli K-12 MG1655 in response to iron availability using genome-wide measurements (ChIP-exo and RNA-seq). more...

Organism:

Escherichia coli str. K-12 substr. MG1655

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL17439

12 Samples

Download data: GFF

(Submitter supplied) To get a high resolution understanding of the effect of Fur on global gene expression, we compared by high-resolution RNAseq the transcriptomes of a wild-type E. coli K-12 strain and its Fur deletion derivative grown in minimal medium with or without supplementation of iron. Three independent total RNA extraction and RNAseq assays were performed for each strain in each condition.

Organism:

Escherichia coli

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25368

12 Samples

Download data: 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) The study aimed to identify role of OxyR during growth on different electron acceptors when E. coli are growing anaerobically.

Organism:

Escherichia coli str. K-12 substr. MG1655; Escherichia coli

Type:

Expression profiling by array

Platform:

GPL3154

8 Samples

Download data: CEL, CHP

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

Organism:

Escherichia coli; Escherichia coli str. K-12 substr. MG1655

Type:

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

Platforms:

GPL3154 GPL8387

12 Samples

Download data: CEL, PAIR

(Submitter supplied) We integrated transcription factor binding regions and mRNA transcript abundance to elucidate the PurR regulon experimentally. To measure transcription factor binding at a genome scale, we employed a ChIP-chip method to derivative strains of E. coli K-12 MG1655 harboring PurR-8myc under various conditions.

Organism:

Escherichia coli str. K-12 substr. MG1655

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL8387

4 Samples

Download data: PAIR

(Submitter supplied) Expression profiling of wild type and purR deletion strains of E. coli K-12 MG1655 under both M9 minimal media and addition of adenine.

Organism:

Escherichia coli str. K-12 substr. MG1655; Escherichia coli

Type:

Expression profiling by array

Platform:

GPL3154

8 Samples

Download data: CEL