GEO DataSets

(Submitter supplied) We performed microarray analyses to investigate the extent of genes regulated by the Prr system. We compared the transcriptome and proteome profiles of the wild type (WT) and mutant PrrA2 cells grown anaerobically, in the dark, with DMSO as electron acceptor. Approximately 25% of the genes present in the genome are PrrA-regulated, at the transcriptional level, either directly or indirectly, by ≥ 2-fold relative to wild type. more...

Organism:

Cereibacter sphaeroides 2.4.1

Type:

Expression profiling by array

Platform:

GPL162

6 Samples

Download data: CEL

(Submitter supplied) mRNA levels were measured in Rhodobacter sphaeroides 2.4.1 at 20% O2 and 0.5% O2, Rhodobacter sphaeroides 2.4.1 App11 (AppA-null), Rhodobacter sphaeroides 2.4.1 (pPNs) and PpsR mutant PPS2-4. The mRNA samples were prepared from cultures supplied with 20% O2, 1% CO2, and 79% N2, and grown in the dark to an OD of 0.18. The mRNA levels for each strain was measured three times. Keywords: repeat sample

Organism:

Cereibacter sphaeroides; Cereibacter sphaeroides 2.4.1

Type:

Expression profiling by array

Dataset:

GDS1709

Platform:

GPL162

15 Samples

Download data: CEL

Analysis of PpsR overexpressing and mutant strains grown at normal 20% oxygen. Expression examined in wild type cells at 0.5% oxygen. PpsR represses the transcription of a subset of biosynthetic genes in photosystem (PS) formation. Results suggest that PpsR is a master regulator of PS development.

Organism:

Rhodobacter sphaeroides; Rhodobacter sphaeroides 2.4.1

Type:

Expression profiling by array, count, 4 genotype/variation, 2 growth protocol, 3 other sets

Platform:

GPL162

Series:

GSE1515

15 Samples

Download data: CEL

(Submitter supplied) The expression of genes involved in photosystem development in Rhodobacter sphaeroides is dependent upon three major regulatory networks: FnrL, the PrrBA two-component system and the AppA-PpsR pathway. A PrrA- mutant strain of R. sphaeroides is unable to develop under photosynthetic conditions, but when combined with a ppsR mutation, is able to resume growth. In an effort to better characterize the ppsR regulon and to unravel the relationship between the PrrBA and the AppA-PpsR networks, we compared transcriptome profiles from the wild type, PrrA- and PrrA-PpsR- strains under a permissive, common, growth condition: anaerobic-dark-DMSO. more...

Organism:

Cereibacter sphaeroides 2.4.1

Type:

Expression profiling by array

Platform:

GPL162

3 Samples

Download data: CEL

(Submitter supplied) Transcriptional profiling of R. sphaeroides pRKPcrZ compared to control R. sphaeroides pRK4352 under low oxygen conditions. In this study we compared the transcriptome of a PcrZ over-expression strain to a control strain. PcrZ is the first small non-coding RNA, which is involved in the complex regulatory network of photosynthesis gene regulation in Rhodobacter sphaeroides. It counteracts the formation of photosynthetic complexes in a redox dependent manner.

Organism:

Cereibacter sphaeroides; Cereibacter sphaeroides 2.4.1

Type:

Expression profiling by array

Platform:

GPL15457

2 Samples

Download data: TXT

(Submitter supplied) Transcriptome profiling of Rhodobacter sphaeroides cells (WT and delta-oxyR mutant) grown in semiaerobic conditions, 7 and 30 min after addition of H2O2 up to 1 mM Keywords: time series

Organism:

Cereibacter sphaeroides 2.4.1; Cereibacter sphaeroides

Type:

Expression profiling by array

Dataset:

GDS1908

Platform:

GPL162

15 Samples

Download data

Expression profiling of oxyR deletion mutant and wild type cells following treatment with 1 mM hydrogen peroxide. OxyR is a transcription factor that senses oxidative stress. Results provide insight into the mechanisms involved in oxidative stress tolerance.

Organism:

Rhodobacter sphaeroides; Rhodobacter sphaeroides 2.4.1

Type:

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

Platform:

GPL162

Series:

GSE2829

15 Samples

Download data

(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) Data used in "Responses of the Rhodobacter sphaeroides Transcriptome to Blue Light Under Semiaerobic Conditions" paper. Cells are grown at 10% O2 (see detailed description in the paper and in the sample info). Keywords: time-course

Organism:

Cereibacter sphaeroides; Cereibacter sphaeroides 2.4.1

Type:

Expression profiling by array

Dataset:

GDS718

Platform:

GPL162

9 Samples

Download data: CEL

The phototrophic anoxygenic proteobacterium Rhodobacter sphaeroides 2.4.1 grown under 10% O2 semi-aerobic conditions in the dark, then illuminated with blue light for 5, 45 or 135 minutes before harvesting.

Organism:

Rhodobacter sphaeroides; Rhodobacter sphaeroides 2.4.1

Type:

Expression profiling by array, count, 4 time sets

Platform:

GPL162

Series:

GSE1480

9 Samples

Download data: CEL

(Submitter supplied) Iron-sulphur (Fe-S) clusters are ensembles of iron and sulphide centres. They are found in all life forms and are important components of many enzymes involved in diverse cellular processes, including respiration, DNA synthesis or gene regulation. However, the increase in oxygen after the emergence of oxygenic photosynthesis created a threat to Fe–S proteins and, consequently, to the organisms relying on them. more...

Organism:

Cereibacter sphaeroides 2.4.1

Type:

Expression profiling by array

Platform:

GPL15457

2 Samples

Download data: TXT

(Submitter supplied) Global transcriptome analyses at different stages of growth were applied to monitor growth phase-dependent gene expression in the alpha-proteobacterium Rhodobacter sphaeroides. Low aerated cultures with strong changes in levels of dissolved oxygen during growth, were compared to aerated cultures showing little variation in oxygen levels. Cells were in stationary phase for 12 h or for 57 h before dilution into fresh medium. more...

Organism:

Cereibacter sphaeroides 2.4.1

Type:

Expression profiling by array

Platform:

GPL15457

19 Samples

Download data: TXT

(Submitter supplied) we performed time series microarray analyses to investigate transcriptome dynamics during the transition from anaerobic photosynthesis to aerobic respiration. Published on J. Bacteriol., 190 (1), 286-299, 2008. Major changes in gene expression profiles occurred in the initial 15 min after the shift from anaerobic-light to aerobic-dark conditions, with changes continuing to occur up to 4 hours postshift. more...

Organism:

Cereibacter sphaeroides 2.4.1

Type:

Expression profiling by array

Dataset:

GDS3296

Platform:

GPL162

24 Samples

Download data: CEL

Analysis of the facultative photosynthetic anaerobe Rhodobacter sphaeroides at various time points during the transition from anaerobic-light to aerobic-dark growth conditions. Results provide insight into molecular mechanisms underlying the transition from one homeostatic state to another.

Organism:

Rhodobacter sphaeroides 2.4.1

Type:

Expression profiling by array, count, 2 growth protocol, 6 time sets

Platform:

GPL162

Series:

GSE12269

24 Samples

Download data: CEL

(Submitter supplied) Investigation of whole genome gene expression level changes in Thermoplasma acidophilum cultured under aerobic and anaerobic conditions. The analysis are further described in Na Sun, Cuiping Pan, Stephan Nickell, Matthias Mann, Wolfgang Baumeister, and István Nagy, Quantitative proteome and transcriptome analysis of the archaeon Thermoplasma acidophilum cultured under aerobic and anaerobic conditions (submitted).

Organism:

Thermoplasma acidophilum DSM 1728

Type:

Expression profiling by array

Platform:

GPL10453

6 Samples

Download data: TXT

(Submitter supplied) Global transcriptome analyses at different stages of growth were applied to monitor growth phase-dependent gene expression in the alpha-proteobacterium Rhodobacter sphaeroides. Cultures with low aeration, which underwent strong changes in levels of dissolved oxygen during growth, were compared to aerated cultures, which showed little variation in levels of dissolved oxygen. Cells were in stationary phase for 12 h or for 57 h before dilution into fresh medium. more...

Organism:

Cereibacter sphaeroides 2.4.1

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17213

8 Samples

Download data: WIG

(Submitter supplied) DNA microarray analysis was employed to investigate the transcriptome response to nitrosative stress in a non-denitrifying facultative photosynthetic bacterium Rhodobacter sphaeroides 2.4.1. We focused on the role played by a nitric oxide-response transcriptional regulator NnrR in the response. The transcriptome profiles of R. sphaeroides 2.4.1 and its nnrR mutant before and after exposure to nitrosating agents S-nitrosoglutathione (GSNO) or sodium nitroprusside (SNP) under semiaerobic conditions were analyzed.

Organism:

Cereibacter sphaeroides 2.4.1

Type:

Expression profiling by array

Platform:

GPL162

12 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