GEO DataSets

(Submitter supplied) The Bradyrhizobium japonicum NtrC regulatory protein influences gene expression in response to changes in intracellular nitrogen status. Under conditions of low nitrogen, phosphorylation of NtrC results in up-regulation of a number of genes involved in nitrogen metabolism and nitrogen acquisition. To better define the exact nature of NtrC’s influence on gene expression, a ntrC mutation was created in B. more...

Organism:

Bradyrhizobium japonicum; Bradyrhizobium diazoefficiens USDA 110

Type:

Expression profiling by array

Platform:

GPL5341

24 Samples

Download data: GPR

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

Organism:

Caulobacter vibrioides NA1000

Type:

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

Platform:

GPL33463

16 Samples

Download data

(Submitter supplied) Caulobacter species are dimorphic Gram-negative bacteria that inhabit diverse terrestrial and aquatic ecosystems. A suite of molecular sensory systems enables these microbes to control growth, development, and reproduction in response to levels of essential elements, including carbon, nitrogen, and phosphorus. Although the enhancer binding protein NtrC and its cognate sensor histidine kinase NtrB are well-established regulators of bacterial nitrogen assimilation, their precise functions in Caulobacter metabolism and cell development remained largely undefined. more...

Organism:

Caulobacter vibrioides NA1000

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL33463

2 Samples

Download data: BIGWIG

(Submitter supplied) Caulobacter species are dimorphic Gram-negative bacteria that inhabit diverse terrestrial and aquatic ecosystems. A suite of molecular sensory systems enables these microbes to control growth, development, and reproduction in response to levels of essential elements, including carbon, nitrogen, and phosphorus. Although the enhancer binding protein NtrC and its cognate sensor histidine kinase NtrB are well-established regulators of bacterial nitrogen assimilation, their precise functions in Caulobacter metabolism and cell development remained largely undefined. more...

Organism:

Caulobacter vibrioides NA1000

Type:

Expression profiling by high throughput sequencing

Platform:

GPL33463

14 Samples

Download data: TXT

(Submitter supplied) The ability of Bradyrhizobium japonicum and B. elkanii strains to utilize alkane and aromatic sulfonates as sole sources of sulfur for growth was investigated. All of the strains tested were able to utilize alkane sulfonates, but not aromatic sulfonates for growth. Whole-genome transcriptional profiling was used to assess B. japonicum USDA 110 genes involved in growth on alkane sulfonates, as compared to growth on sulfate and cysteine. more...

Organism:

Bradyrhizobium japonicum

Type:

Expression profiling by array

Platform:

GPL5341

12 Samples

Download data: GPR

(Submitter supplied) Purpose: Identification of genes regulated by NasT during denitrifying growth in B. diazoefficiens.  Methods: Two biological replications were processed for each strain (wild-type USDA 110 and ΔnasT mutant). Sequencing was performed in an Illumina HiSeq 2000 Sequencing System in paired-end mode running 100x2 cycles (performed by Hokkaido System Science Co., Ltd.). Mapping of reads to the reference genome, read counting, normalization to RPKM (reads per kilobase per million mapped reads), and calculations of expression values were performed with default values with the CLC Genomic Workbench software 9.5.3. more...

Organism:

Bradyrhizobium diazoefficiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26569

4 Samples

Download data: TXT, XLS

(Submitter supplied) The growth and persistence of rhizobia and bradyrhizobia in soils are negatively impacted by drought conditions. In this study, we used genome-wide transcriptional analyses to obtain a comprehensive understanding of the response of Bradyrhizobium japonicum to drought. Desiccation of cells resulted in the differential expression of 15 to 20% of the 8,480 B. japonicum open reading frames, with considerable differentiation between early (after 4 h) and late (after 24 and 72 h) expressed genes. more...

Organism:

Bradyrhizobium japonicum; Bradyrhizobium diazoefficiens USDA 110

Type:

Expression profiling by array

Platform:

GPL5341

18 Samples

Download data: GPR

(Submitter supplied) Members of the genus Burkholderia are versatile bacteria capable of colonizing highly diverse environmental niches. In this study, we investigated the global response of the opportunistic pathogen Burkholderia cenocepacia H111 to nitrogen limitation at the transcript and protein expression level. In addition to a classical response to nitrogen starvation, including the activation of glutamine synthetase, PII proteins and the two component regulatory system ntrBC, B. more...

Organism:

Burkholderia cenocepacia H111

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16128

5 Samples

Download data: TXT

(Submitter supplied) Corynebacterium glutamicum, a gram-positive soil bacterium used for the industrial production of amino acids such as L-glutamate and L-lysine, is able to use a number of different nitrogen sources, such as ammonium, urea, or creatinine. In this communication, we show that L-glutamine serves as an excellent nitrogen source for C. glutamicum and allows similar growth rates in glucose minimal medium as ammonium. more...

Organism:

Corynebacterium glutamicum ATCC 13032

Type:

Expression profiling by array

Platform:

GPL9860

3 Samples

Download data: GPR

(Submitter supplied) part of GSE8478: Genome-wide transcript analysis of Bradyrhizobium japonicum bacteroids in soybean root nodules This SuperSeries is composed of the SubSeries listed below.

Organism:

Bradyrhizobium japonicum; Bradyrhizobium diazoefficiens USDA 110; Glycine max

Type:

Expression profiling by array

Platform:

GPL3401

72 Samples

Download data: CEL, CHP

(Submitter supplied) Analysis of a mutant in the Bradyrhizobium japonicum response regulator RegR. RegR is known to control expression of the gene encoding the key regulator of nitrogen fixation NifA. This study provides insights into the RegR regulon under free-living conditions and during symbiosis. Cells of the regR mutant and the wild type were grown to mid-exponential phase in full medium (PSY) under different oxygen conditions (aerobic and microaerobic) in culture. more...

Organism:

Bradyrhizobium japonicum; Bradyrhizobium diazoefficiens USDA 110

Type:

Expression profiling by array

Platform:

GPL3401

23 Samples

Download data: CEL, CHP

(Submitter supplied) Expression data from B. japonicum soybean root nodules including a nodulation time-course experiment with soybean nodules harvested at 10, 13, 21 and 31 dpi and transcriptome of bacteroids formed by a mutant defective in the RNA polymerase transcription factor sigma 54. Two reference data sets were established using B. japonicum cells grown in PSY medium under either aerobic or micro-aerobic conditions. more...

Organism:

Glycine max; Bradyrhizobium diazoefficiens USDA 110; Bradyrhizobium japonicum

Type:

Expression profiling by array

Datasets:

GDS3120 GDS3121 GDS3122

Platform:

GPL3401

71 Samples

Download data: CEL, CHP

Comparison of sigma54-deficient mutant strain N50-97 bacteroids with wild type bacteroids, both at 21 days postinoculation. The mutants are able to elicit soybean nodules but unable to carry out symbiotic nitrogen fixation. Results provide insight into the sigma 54 regulon in symbiosis.

Organism:

Bradyrhizobium japonicum; Bradyrhizobium diazoefficiens USDA 110

Type:

Expression profiling by array, count, 2 genotype/variation, 3 growth protocol sets

Platform:

GPL3401

Series:

GSE8478

59 Samples

Download data: CEL, CHP

Analysis of soybean nodules at 10, 13, 21, and 31 days postinoculation, having relative symbiotic nitrogen-fixation activities of 9, 95, 100, and 61%, respectively. Results provide insight into genes expressed early and late in bacteroid development.

Organism:

Bradyrhizobium japonicum; Bradyrhizobium diazoefficiens USDA 110

Type:

Expression profiling by array, count, 4 time sets

Platform:

GPL3401

Series:

GSE8478

13 Samples

Download data: CEL, CHP

Analysis of bacteroids harvested from soybean nodules at 21 days postinoculation (dpi), a timepoint of maximal nitrogen-fixation activity. Free-living cells grown in aerobic or microaerobic culture also examined. Results provide insight into the genetic basis underlying the conversion to symbiosis.

Organism:

Bradyrhizobium japonicum; Bradyrhizobium diazoefficiens USDA 110

Type:

Expression profiling by array, count, 3 growth protocol sets

Platform:

GPL3401

Series:

GSE8478

42 Samples

Download data: CEL, CHP

(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:

Glycine max; Bradyrhizobium diazoefficiens USDA 110; Bradyrhizobium japonicum

Type:

Expression profiling by array

Platform:

GPL3401

97 Samples

Download data: CEL, CHP

(Submitter supplied) Analysis of a Bradyrhizobium japonicum pmtA mutant. PmtA catalyzes the first of three consecutive methylation reactions leading to phosphatidylcholine (PC) formation in B. japonicum. Disruption of the pmtA gene results in a significantly reduced PC content causing a defect in symbiosis with the soybean host. This study provides the first insight into global transcriptomic changes of a bacterial phosphatidylcholine biosynthesis mutant. more...

Organism:

Bradyrhizobium diazoefficiens USDA 110; Bradyrhizobium japonicum

Type:

Expression profiling by array

Platform:

GPL3401

10 Samples

Download data: CEL, CHP

(Submitter supplied) PhyR is an unusual type of response regulator consisting of a receiver domain and an extracytoplasmic function (ECF) sigma factor-like domain. It was recently described as a master regulator of general stress response in Methylobacterium extorquens. Orthologues of this regulator are present in essentially all free-living Alphaproteobacteria. In most of them, phyR is genetically closely linked to a gene encoding an ECF sigma factor. more...

Organism:

Bradyrhizobium japonicum; Bradyrhizobium diazoefficiens USDA 110

Type:

Expression profiling by array

Platform:

GPL3401

18 Samples

Download data: CEL, CHP

(Submitter supplied) Genome-wide transcriptional profiling of cells subjected to a H2O2 shock treatment (10 mM for 10 minutes).

Organism:

Bradyrhizobium japonicum; Bradyrhizobium diazoefficiens USDA 110

Type:

Expression profiling by array

Platform:

GPL5341

6 Samples

Download data: GPR

(Submitter supplied) Genome-wide transcriptional profiling of cells exposed to 0.3 mM H2O2 from time of inoculation.

Organism:

Bradyrhizobium japonicum; Bradyrhizobium diazoefficiens USDA 110

Type:

Expression profiling by array

Platform:

GPL5341

6 Samples

Download data: GPR