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Links from GEO DataSets

Items: 17

1.

Identification of genes regulated by the antitermination factor NasT during denitrification in Bradyrhizobium diazoefficiens.

(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
Series
Accession:
GSE130301
ID:
200130301
2.

The global response regulator RegR controls expression of denitrification genes in Bradyrhizobium japonicum

(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 japonicum; Bradyrhizobium diazoefficiens USDA 110
Type:
Expression profiling by array
Platform:
GPL3401
8 Samples
Download data: CEL, CHP
Series
Accession:
GSE56668
ID:
200056668
3.

Characterization of the Bradyrhizobium japonicum NtrC regulon by DNA Microarray analysis.

(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 diazoefficiens USDA 110; Bradyrhizobium japonicum
Type:
Expression profiling by array
Platform:
GPL5341
24 Samples
Download data: GPR
Series
Accession:
GSE66091
ID:
200066091
4.

Expanding the regulon of the Bradyrhizobium diazoefficiens NnrR transcription factor: New insights into denitrification pathway

(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
Series
Accession:
GSE130684
ID:
200130684
5.

Bj H2O2 shock vs. non-treatment

(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
Series
Accession:
GSE26961
ID:
200026961
6.

Bj H2O2 prolonged exposure vs. non-treatment

(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
Series
Accession:
GSE26960
ID:
200026960
7.

Pleiotropic effects of PhaR regulator in Bradyrhizobium diazoefficiens microaerobic metabolism

(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
Series
Accession:
GSE250298
ID:
200250298
8.

Whole-Genome Transcriptional analysis of Sulfate and Sulfonate assimilation by Bradyrhizobium japonicum USDA 110

(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
Series
Accession:
GSE19039
ID:
200019039
9.

Transcriptional and Physiological Responses of Bradyrhizobium japonicum to Desiccation-Induced Stress

(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
Series
Accession:
GSE9125
ID:
200009125
10.

Metabolomic profiling of Bradyrhizobium diazoefficiens-induced root nodules reveals both host plant-specific and developmental signatures

(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 USDA 110; Bradyrhizobium diazoefficiens
Type:
Expression profiling by array
Platform:
GPL3401
6 Samples
Download data: CEL, CHP, TXT
Series
Accession:
GSE79811
ID:
200079811
11.

Fine-tuning modulation of oxidation-mediated posttranslational control of Bradyrhizobium diazoefficiens FixK2 transcription factor

(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
Series
Accession:
GSE196031
ID:
200196031
12.

Transcriptome response to nitric oxide in Pseudomonas aeruginosa

(Submitter supplied) DNA microarray analysis was employed to investigate the transcriptome response to nitric oxide in Pseudomonas aeruginosa. We focused on the role played by the nitric oxide-response regulators DNR and FhpR and an oxygen-response regulator ANR in the response. The transcriptome profiles of the P. aeruginosa strains before and after exposure to nitric oxide under the microaerobic conditions were analyzed. more...
Organism:
Pseudomonas aeruginosa
Type:
Expression profiling by array
Platform:
GPL84
20 Samples
Download data: CEL
Series
Accession:
GSE58862
ID:
200058862
13.

Iron- and Irr-regulated genes in Bradyrhizobium japonicum

(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
9 Samples
Download data
Series
Accession:
GSE4156
ID:
200004156
14.

Comparison of Bradyrhizobium japonicum parent strain LO with irr mutant strain LODTM5

(Submitter supplied) The purpose of the study is to identify Irr-responsive genes in the bacterium Bradyrhizobium japonicum. Parent strain LO was compared to irr mutant strain LODTM5 by whole genome microarray analysis. Both cell types were grown in iron-limited media. Keywords: Comparison of B. japonicum wild type and mutant cells
Organism:
Bradyrhizobium diazoefficiens USDA 110; Bradyrhizobium japonicum
Type:
Expression profiling by array
Dataset:
GDS2389
Platform:
GPL3401
6 Samples
Download data
Series
Accession:
GSE4155
ID:
200004155
15.

Comparison of Bradyrhizobium japonicum parent strain LO grown under low or high iron conditions

(Submitter supplied) The purpose of the study is to identify iron-responsive genes in the bacterium Bradyrhizobium japonicum. Parent strain LO was grown under iron limitation or under iron sufficiency and compared to each other by whole genome microarray analysis. Keywords: Comparison of cells grown under low or high iron conditons
Organism:
Bradyrhizobium japonicum; Bradyrhizobium diazoefficiens USDA 110
Type:
Expression profiling by array
Dataset:
GDS2388
Platform:
GPL3401
6 Samples
Download data
Series
Accession:
GSE4143
ID:
200004143
16.
Full record GDS2389

Iron limitation effect on iron response regulator mutant

Analysis of parent strain LO and the iron response regulator (Irr) mutant strain LODMT5 grown in iron-limited or iron-replete medium. Results provide insight into the scope of Irr's role in iron metabolism.
Organism:
Bradyrhizobium japonicum; Bradyrhizobium diazoefficiens USDA 110
Type:
Expression profiling by array, count, 2 strain sets
Platform:
GPL3401
Series:
GSE4155
6 Samples
Download data
17.
Full record GDS2388

Iron limitation effect

Analysis of parent strain LO cells grown in iron-limited or iron-replete media. Results provide insight into the structure of the iron regulon.
Organism:
Bradyrhizobium japonicum; Bradyrhizobium diazoefficiens USDA 110
Type:
Expression profiling by array, count, 2 growth protocol sets
Platform:
GPL3401
Series:
GSE4143
6 Samples
Download data
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