GEO DataSets

(Submitter supplied) Genome-wide transcription profiling of B. diazoefficiens (formerly B. japonicum) and a phaR mutant, both cultured under microoxic conditions (0.5% O2) in Götz minimal medium supplemented with mannitol. Keywords: microoxia, polyhydroxybutyrate, protein-DNA interaction, proteomics, Rhizobia, transcriptomics

Organism:

Bradyrhizobium diazoefficiens USDA 110; Bradyrhizobium diazoefficiens

Type:

Expression profiling by array

Platform:

GPL3401

6 Samples

Download data: CEL, CHP

(Submitter supplied) Genome-wide transcription profiling of B. diazoefficiens (formerly B. japonicum) wild type and a C183D FixK2 encoding strain which were cultured under microoxic conditions (0.5% O2). For comparison, this work also includes the expression data samples GSM210246 to GSM210268, and samples GSM313727 to GSM313734 in GEO record number GSE12491. Keywords: CRP/FNR proteins, in vitro transcription, microoxia, posttranslational control, protein-DNA interaction, Rhizobia, transcriptomics

Organism:

Bradyrhizobium diazoefficiens; Bradyrhizobium diazoefficiens USDA 110

Type:

Expression profiling by array

Platform:

GPL3401

6 Samples

Download data: CEL, CHP

(Submitter supplied) Expression data from B. japonicum wild-type and Dblr1880 (6498) strains under free-living and symbiotic conditions

Organism:

Bradyrhizobium japonicum; Bradyrhizobium diazoefficiens USDA 110

Type:

Expression profiling by array

Platform:

GPL3401

20 Samples

Download data: CEL, CHP

(Submitter supplied) Legume plants can form root organs called nodules where they house intracellular symbiotic rhizobium bacteria. Within nodule cells, rhizobia differentiate into bacteroids, which fix nitrogen for the benefit of the plant. Depending on the combination of host plants and rhizobial strains, the output of rhizobium-legume interactions is varying from non-fixing associations to symbioses that are highly beneficial for the plant. more...

Organism:

Bradyrhizobium diazoefficiens USDA 110

Type:

Expression profiling by high throughput sequencing

Platform:

GPL29495

9 Samples

Download data: TXT

(Submitter supplied) Expression data from B. japonicum stress response; aerobic treatment of B. japoncium culture under different stress conditons; pH stress (8 and 4; 4 h); salt stress (80 mM NaCl; 4 h); heat shock (43 °C; 15 min) and temperature stress (35.2 °C; 48 h); as reference wildtype without treatment (AG media; pH 6.9; without NaCl; 28 °C) was used heat shock data were verified by using rpoH-mutant strains B. japonicum 5009; B. japonicum 5032 and B. japonicum 09-32 as described in Narberhaus et al. 1997

Organism:

Bradyrhizobium japonicum; Bradyrhizobium diazoefficiens USDA 110

Type:

Expression profiling by array

Platform:

GPL3401

34 Samples

Download data: CEL, CHP

(Submitter supplied) Genome-wide transcription profiling of B. diazoefficiens (formerly B. japonicum) wild type and nnrR mutant strain which were grown in free-living anoxic denitrifying conditions (using nitrate as final electron aceptor). This study includes also the expression data of the wild type strain grown oxically (samples GSM210269 to GSM210283 in GEO record number GSE8478). Keywords: CRP/FNR proteins, in vitro transcription, microoxia, nitrogen oxides, Rhizobia, transcriptomics

Organism:

Bradyrhizobium diazoefficiens; Bradyrhizobium diazoefficiens USDA 110

Type:

Expression profiling by array

Platform:

GPL3401

6 Samples

Download data: CEL, CHP

(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) Metabolomics and transcriptomics of Bradyrhizobium diazoefficiens-induced root nodules Bradyrhizobium diazoefficiens is a nitrogen-fixing endosymbiont, which can grow inside root-nodule cells of the agriculturally important soybean and other host plants. Our previous studies described B. diazoefficiens host-specific global expression changes occurring during legume infection at the transcript and protein level. more...

Organism:

Bradyrhizobium diazoefficiens; Bradyrhizobium diazoefficiens USDA 110

Type:

Expression profiling by array

Platform:

GPL3401

6 Samples

Download data: CEL, CHP, TXT

(Submitter supplied) Background: During the symbiosis with legumes, Bradyrhizobium japonicum cells infect roots where they induce the formation of root nodules and differentiate into intracellular nitrogen-fixing bacteroids. We used differential RNA-seq (dRNA-seq) for the genome-wide detection of transcriptional start sites (TSSs) in B. japonicum USDA 110 cells grown free-living or as bacteroids in soybean root nodules. more...

Organism:

Bradyrhizobium diazoefficiens USDA 110

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20219

4 Samples

Download data: WIG

(Submitter supplied) Differential gene expression was analyzed between B. japonicum wild type (Bj110) and aceA mutant (BjΔaceA) exposed to desiccation stress to find AceA regulons under the culture condition.

Organism:

Bradyrhizobium japonicum; Bradyrhizobium diazoefficiens USDA 110

Type:

Expression profiling by array

Platform:

GPL5341

6 Samples

Download data: GPR

(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) A time-course transcriptomic analysis of bacteroids isolated from soybean plants inoculated with B. japonicum USDA 110, relative to cells cultured in HM-arabinose medium was performed to characterize senescence genes.

Organism:

Bradyrhizobium diazoefficiens USDA 110; Bradyrhizobium japonicum

Type:

Expression profiling by array

Platform:

GPL5341

46 Samples

Download data: GPR

(Submitter supplied) A transcriptomic analysis of bacteroids isolated from soybean plants inoculated with B. japonicum USDA 110, relative to cells cultured in HM-arabinose medium was performed and the results combined with two other transcriptomic analyses to form a reiterated pool of transcripts that define genes essential for symbiotic nitrogen fixation.

Organism:

Bradyrhizobium diazoefficiens USDA 110; Bradyrhizobium japonicum

Type:

Expression profiling by array

Platform:

GPL5341

8 Samples

Download data: GPR

(Submitter supplied) Bradyrhizobium japonicum RegSR regulatory proteins belong to the family of two-component regulatory systems, and orthologs are present in many Proteobacteria where they globally control gene expression mostly in a redox-responsive manner. In this work, we have performed a transcriptional profiling of wild-type and regR mutant cells grown under anoxic denitrifying conditions. The comparative analyses of wild-type and regR strains revealed that almost 620 genes induced in the wild type under denitrifying conditions were regulated (directly or indirectly) by RegR, pointing out the important role of this protein as a global regulator of denitrification. more...

Organism:

Bradyrhizobium diazoefficiens USDA 110; Bradyrhizobium japonicum

Type:

Expression profiling by array

Platform:

GPL3401

8 Samples

Download data: CEL, CHP

(Submitter supplied) Transcriptional profiling of mid-logarithmic phase cultures exposed to a 1 mM shock treatment of indole-3-acetic acid for 3 hours.

Organism:

Bradyrhizobium japonicum; Bradyrhizobium diazoefficiens USDA 110

Type:

Expression profiling by array

Platform:

GPL5341

6 Samples

Download data: GPR

(Submitter supplied) Copper-limiting growth conditions were thought to cause an induction of genes possibly involved in copper uptake and sorting. This rationale in mind, we performed microarray analyses on B. japonicum cells grown in three variations of the BVM minimal medium. Variant 1 contained 2 μM CuSO4 (copper excess). Variant 2 was prepared in HCl-treated glassware without any copper added (copper starvation). The residual copper concentration in this copper-starvation medium was analyzed by GF-AAS and determined to be 5 nM. more...

Organism:

Bradyrhizobium japonicum; Bradyrhizobium diazoefficiens USDA 110

Type:

Expression profiling by array

Platform:

GPL3401

9 Samples

Download data: CEL, CHP

(Submitter supplied) Expression data from B. japonicum strains 110spc4 (wild type), 0202 (Dbll1028), 9688 (Dblr3038-39) grown micro-oxically unstressed or stressed with 2 mM H2O2 for 10 min and strain 9692 (Dblr3039) grown micro-oxically

Organism:

Bradyrhizobium japonicum; Bradyrhizobium diazoefficiens USDA 110

Type:

Expression profiling by array

Platform:

GPL3401

21 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

(Submitter supplied) Genome-wide transcriptional profiling of Bj110 cells treated with P6 (20 uM for 24 h).

Organism:

Bradyrhizobium diazoefficiens USDA 110; Bradyrhizobium japonicum

Type:

Expression profiling by array

Platform:

GPL5341

6 Samples

Download data: GPR