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; Bradyrhizobium diazoefficiens USDA 110

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) 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) 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) 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) 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 diazoefficiens USDA 110; Bradyrhizobium japonicum

Type:

Expression profiling by array

Platform:

GPL3401

21 Samples

Download data: CEL, CHP

(Submitter supplied) Expression data from B. japonicum bll2758::aphII strain (7414) grown micro-oxically. This study includes also the expression data of a fixK2 and a fixJ mutant grown in free-living micro-oxic condition (samples GSM313721 to GSM313734 in GEO record number GSE12491) and the wild type strain grown micro-oxically (samples GSM210246 to GSM210268 in GEO record number GSE8478).

Organism:

Bradyrhizobium japonicum; Bradyrhizobium diazoefficiens USDA 110

Type:

Expression profiling by array

Platform:

GPL3401

40 Samples

Download data: CEL, CHP

(Submitter supplied) Certain alpha- and beta-proteobacteria, the rhizobia, are able to infect legume roots, elicit root nodules, and live therein as endosymbiotic, nitrogen-fixing bacteroids. Host recognition and specificity are the results of consecutive programming events in bacteria and host plants in which important signaling molecules, e.g. plant flavonoids and rhizobial lipooligosaccharides, play key roles. Here, we introduce a new aspect of this symbiosis: the adaptive response to hosts. more...

Organism:

Glycine max; Bradyrhizobium diazoefficiens USDA 110; Vigna unguiculata subsp. unguiculata; Bradyrhizobium japonicum; Macroptilium atropurpureum

Type:

Expression profiling by array

Platform:

GPL3401

15 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 diazoefficiens USDA 110; Bradyrhizobium japonicum

Type:

Expression profiling by array

Platform:

GPL3401

18 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) 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; Glycine max; Bradyrhizobium diazoefficiens USDA 110

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 diazoefficiens USDA 110; Bradyrhizobium japonicum

Type:

Expression profiling by array

Platform:

GPL3401

23 Samples

Download data: CEL, CHP

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

Organism:

Bradyrhizobium japonicum; Bradyrhizobium diazoefficiens USDA 110

Type:

Expression profiling by array

Platform:

GPL3401

12 Samples

Download data: CEL

(Submitter supplied) An initializing step in the rhizobia-legume symbiosis is the secretion of flavonoids by plants that leads to the expression of nodulation genes in rhizobia. Here we report the genome-wide transcriptional response of Bradyrhizobium japonicum to genistein, an isoflavone secreted by soybean. About 100 genes were induced in the wild type. This included all nod box-associated genes, the flagellar cluster and several genes that are likely to be involved in transport processes. more...

Organism:

Bradyrhizobium diazoefficiens USDA 110; Bradyrhizobium japonicum

Type:

Expression profiling by array

Platform:

GPL3401

6 Samples

Download data: CEL

(Submitter supplied) An initializing step in the rhizobia-legume symbiosis is the secretion of flavonoids by plants that leads to the expression of nodulation genes in rhizobia. Here we report the genome-wide transcriptional response of Bradyrhizobium japonicum to genistein, an isoflavone secreted by soybean. About 100 genes were induced in the wild type. This included all nod box-associated genes, the flagellar cluster and several genes that are likely to be involved in transport processes. more...

Organism:

Bradyrhizobium diazoefficiens USDA 110; Bradyrhizobium japonicum

Type:

Expression profiling by array

Platform:

GPL3401

6 Samples

Download data: CEL

(Submitter supplied) An initializing step in the rhizobia-legume symbiosis is the secretion of flavonoids by plants that leads to the expression of nodulation genes in rhizobia. Here we report the genome-wide transcriptional response of Bradyrhizobium japonicum to genistein, an isoflavone secreted by soybean. About 100 genes were induced in the wild type. This included all nod box-associated genes, the flagellar cluster and several genes that are likely to be involved in transport processes. more...

Organism:

Bradyrhizobium diazoefficiens USDA 110; Bradyrhizobium japonicum

Type:

Expression profiling by array

Platform:

GPL3401

6 Samples

Download data: CEL