GEO DataSets

(Submitter supplied) In this study, we performed a ChIP-chip experiment to determine the regulon of FnrL in Rhodobacter sphaeroides. We grew R. sphaeroides under anaerobic photosnthetic conditions, in which FnrL is expected to bind DNA and contol gene expression, and immuno-precipitated FnrL, but also sigma70 and the Beta' subunits of RNA polymerase to determine transcription activity.

Organism:

Cereibacter sphaeroides 2.4.1

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL10463

9 Samples

Download data: GFF, PAIR

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

Organism:

Cereibacter sphaeroides; Cereibacter sphaeroides 2.4.1

Type:

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

Platforms:

GPL18840 GPL162 GPL18841

32 Samples

Download data: CEL, WIG

(Submitter supplied) To gain a deeper understanding of the transcription factors that regulate photosynthesis in Rhodobacter sphaeroides ChIP-seq was used to determine the genome-wide binding locations of 4 transcription factors (FnrL, PrrA, CrpK and RSP_2888) known or predicted to be involved in the regulation of photosynthesis.

Organism:

Cereibacter sphaeroides

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL18841 GPL18840

12 Samples

Download data: WIG

(Submitter supplied) To gain a deeper understanding of the transcription factors that regulate photosynthesis in Rhodobacter sphaeroides global gene expression analysis was used to determine the expression profiles of the deletion mutants of 4 transcription factors (FnrL, PrrA, CrpK and RSP_2888) known or predicted to be involved in the regulation of photosynthesis.

Organism:

Cereibacter sphaeroides; Cereibacter sphaeroides 2.4.1

Type:

Expression profiling by array

Platform:

GPL162

20 Samples

Download data: CEL, TXT

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

Organism:

Cereibacter sphaeroides 2.4.1; Cereibacter sphaeroides

Type:

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

Platforms:

GPL162 GPL18842 GPL17213

15 Samples

Download data: CEL, WIG

(Submitter supplied) By integrating sequence information from closely related bacteria with a compendium of high-throughput gene expression datasets, a large-scale transcriptional regulatory networks was constructed for Rhodobacter sphaeroides. Predictions from this network were validated in part using genome-wide analysis for 3 transcription factors (PpsR, RSP_0489 and RSP_3341).

Organism:

Cereibacter sphaeroides 2.4.1

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL17213 GPL18842

4 Samples

Download data: WIG

(Submitter supplied) Rhodobacter sphaeroides is the best studied photosynthetic bacterium, yet much remains unknown about its transcriptional regulatory processes on a genome-scale. We developed a work-flow for genome-scale reconstruction of transcriptional regulatory networks and applied it to sequence and gene expression data sets available for R. sphaeroides. To assess the predictive performance of our reconstructed model, we generated global transcript level and/or protein-DNA interaction data for 3 transcription factors (PpsR, RSP_0489 and RSP_3341). more...

Organism:

Cereibacter sphaeroides 2.4.1; Cereibacter sphaeroides

Type:

Expression profiling by array

Platform:

GPL162

11 Samples

Download data: CEL, TXT

(Submitter supplied) The anaerobic metabolism of the opportunistic pathogen Pseudomonas aeruginosa is important for growth and survival during persistent infections. The two Fnr-type transcription factors Anr and Dnr regulate different parts of the underlying network. Both are proposed to bind to a non-distinguishable DNA sequence named Anr box. The aim of this study was the identification of genes induced under anaerobic conditions in the P. more...

Organism:

Pseudomonas aeruginosa

Type:

Expression profiling by array

Platform:

GPL84

8 Samples

Download data: CEL

(Submitter supplied) In Rhodobacter sphaeroides a transcriptional response to the reactive oxygen species singlet oxygen is controlled by the group IV sigma factor RpoE and the anti-sigma factor ChrR. In this study, we integrated various large datasets to identify genes within the singlet oxygen stress response that contain RpoE-dependent promoters within R. sphaeroides. Transcript pattern clustering and a RpoE-binding sequence model were used to predict candidate promoters that respond to singlet oxygen stress in R. more...

Organism:

Cereibacter sphaeroides 2.4.1

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL10463

6 Samples

Download data: GFF, TXT

(Submitter supplied) Oligo probes are 45bp in average, tiling the genome sequences with about 35-bp overlap between consecutive probes. Every other probe hybridizes to the reverse strand. Native array description file: 2007-06-20_R_sphaeroides_long85_v2.ndf Native array description file: 2007-06-20_R_sphaeroides_long85_v2.pos Protocol: See manufacturer's web site (www.nimblegen.com)

Organism:

Cereibacter sphaeroides 2.4.1

4 Series

21 Samples

Download data: NDF, POS

(Submitter supplied) Transcriptional response of the QS-negative D. shibae strain ∆luxI1 towards externally added 500nM autoinducer (AI) 3-oxo-C14-HSL over a time period of 3 hours.

Organism:

Dinoroseobacter shibae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25762

27 Samples

Download data: TXT

(Submitter supplied) The adaptation strategies and regulatory networks behind the adaptation of D. shibae DFL12T to changing oxygen regimes was investigated. Moreover, the essential role of 4 Crp/ Fnr like regulators within this adaptation process was revealed using transcriptional analysis of regulator knock out strains.

Organism:

Dinoroseobacter shibae DFL 12 = DSM 16493

Type:

Expression profiling by array

Platform:

GPL11243

30 Samples

Download data: TXT

(Submitter supplied) Wild-type E. coli are prototrophic for all amino acid and nucleotides. These are synthesized by a network of interconnected metabolic pathways from a handful precursors molecules, which are regulated at the level of gene expression. It was hypothesized in this study, that since metabolic pathways are interconnected, transcriptional regulation should be shared across multiple pathways. To uncover these regulatory interactions, cells growing at steady state were perturbed by the addition of an end-metabolite (aa or nt), and were allowed to recover. more...

Organism:

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

Type:

Expression profiling by array

Platform:

GPL3503

22 Samples

Download data: GPR

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

Organism:

Cereibacter sphaeroides 2.4.1; Cereibacter sphaeroides

Type:

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

Platforms:

GPL18841 GPL162 GPL18840

13 Samples

Download data: CEL, WIG

(Submitter supplied) To gain a better understanding of the transcription factors that regulate central carbon metabolism in Rhodobacter sphaeroides ChIP-seq was used to determine the genome-wide binding locations of 2 transcription factors: CceR (RSP_1663) and AkgR (RSP_0981) both predicted to be involved in the regulation of of central carbon and energy metabolism.

Organism:

Cereibacter sphaeroides

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL18841 GPL18840

4 Samples

Download data: WIG

(Submitter supplied) To gain a better understanding of the transcription factors that regulate central carbon metabolism in Rhodobacter sphaeroides global gene expression analysis was used to determine genes under the regulatory influence of 2 transcription factors: CcmR (RSP_1663) and AkgR (RSP_0981) both predicted to be involved in the regulation of central carbon and energy metabolism.

Organism:

Cereibacter sphaeroides 2.4.1; Cereibacter sphaeroides

Type:

Expression profiling by array

Platform:

GPL162

12 Samples

Download data: CEL

(Submitter supplied) Genome-wide transcription profiling of B. japonicum fixJ, fixK2, and fixK1 mutant strains which were grown in free-living microoxic condition, and in the case of the fixK1 mutant also in anoxic condition. Transcriptomes of nodules from soybean plants infected with the fixJ or fixK2 mutant strains were investigated, too. This study includes also the expression data of a nifA mutant grown in free-living anoxic condition. more...

Organism:

Bradyrhizobium japonicum; Glycine max; Bradyrhizobium diazoefficiens USDA 110

Type:

Expression profiling by array

Platform:

GPL3401

97 Samples

Download data: CEL, CHP

(Submitter supplied) The level of the Central glycolytic gene regulator (CggR) was engineered in Lactobacillus plantarum NC8 and WCFS1 by over-expression and in-frame mutation of the cggR gene in order to evaluate its regulatory role on the glycolytic gap operon and the glyco

Organism:

Lactiplantibacillus plantarum; Lactiplantibacillus plantarum WCFS1

Type:

Expression profiling by array

Platform:

GPL4318

28 Samples

Download data: TXT

(Submitter supplied) Transcriptional regulation is a critical process to ensure expression of genes necessary for growth and survival in diverse environments. Transcription is mediated by multiple transcriptional factors including activators, repressors and sigma factors. Accurate computational prediction of the regulon of target genes for transcription factors is difficult and experimental identification is a laborious process and not scalable. more...

Organism:

Streptomyces coelicolor A3(2)

Type:

Expression profiling by high throughput sequencing

Platform:

GPL30648

68 Samples

Download data: CSV

(Submitter supplied) Transcriptional regulation is a critical process to ensure expression of genes necessary for growth and survival in diverse environments. Transcription is mediated by multiple transcriptional factors including activators, repressors and sigma factors. Accurate computational prediction of the regulon of target genes for transcription factors is difficult and experimental identification is a laborious process and not scalable. more...

Organism:

Streptomyces coelicolor A3(2)

Type:

Other

Platform:

GPL30647

51 Samples

Download data: CSV