GEO DataSets

(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) 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) 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) 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) 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) In this study, we performed a ChIP-chip experiment to determine the regulon of FnrL in Rhodobacter sphaeroides. We grew R. sphaeroides under anaerobic photosnthetic conditions, in which FnrL is expected to bind DNA and contol gene expression, and immuno-precipitated FnrL, but also sigma70 and the Beta' subunits of RNA polymerase to determine transcription activity.

Organism:

Cereibacter sphaeroides 2.4.1

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL10463

9 Samples

Download data: GFF, PAIR

(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) 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) 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) We identified genome-wide binding regions of NdgR in Streptomyces coelicolor using chromatin immunoprecipitation sequencing (ChIP-seq). We constructed 6×myc-tagged NdgR strain using homologous recombination with myc-tagging vector. Analysis of the sequencing data aligned to Streptomyces coelicolor genome database (NC_003888).

Organism:

Streptomyces coelicolor

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL18886

1 Sample

Download data: GFF

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

Organism:

Cereibacter sphaeroides 2.4.1; Cereibacter sphaeroides

Type:

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

Platforms:

GPL162 GPL18842 GPL17213

15 Samples

Download data: CEL, WIG

(Submitter supplied) By integrating sequence information from closely related bacteria with a compendium of high-throughput gene expression datasets, a large-scale transcriptional regulatory networks was constructed for Rhodobacter sphaeroides. Predictions from this network were validated in part using genome-wide analysis for 3 transcription factors (PpsR, RSP_0489 and RSP_3341).

Organism:

Cereibacter sphaeroides 2.4.1

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL17213 GPL18842

4 Samples

Download data: WIG

(Submitter supplied) Rhodobacter sphaeroides is the best studied photosynthetic bacterium, yet much remains unknown about its transcriptional regulatory processes on a genome-scale. We developed a work-flow for genome-scale reconstruction of transcriptional regulatory networks and applied it to sequence and gene expression data sets available for R. sphaeroides. To assess the predictive performance of our reconstructed model, we generated global transcript level and/or protein-DNA interaction data for 3 transcription factors (PpsR, RSP_0489 and RSP_3341). more...

Organism:

Cereibacter sphaeroides 2.4.1; Cereibacter sphaeroides

Type:

Expression profiling by array

Platform:

GPL162

11 Samples

Download data: CEL, TXT

(Submitter supplied) The sRNA StsR (formerly RSs0827) was first described as an sRNA induced upon iron starvation and was later demonstrated to be the most highly induced RNA in late stationary phase in the phototrophic Alphaproteobacterium R. sphaeroides. StsR is under control of RpoHI/RpoHII and therefore induced by multiple stress factors. To investigate the function of this sRNA on the hole transcriptome of R. sphaeroides we performed RNAseq with cultures of the exponential growth (6 h) phase, stationary growth phase (72 h / 144 h) and outgrowth phase. more...

Organism:

Cereibacter sphaeroides 2.4.1

Type:

Expression profiling by high throughput sequencing

Platform:

GPL28141

24 Samples

Download data

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

Organism:

Cereibacter sphaeroides 2.4.1; Cereibacter sphaeroides

Type:

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

Platforms:

GPL18841 GPL162 GPL18840

13 Samples

Download data: CEL, WIG

(Submitter supplied) To gain a better understanding of the transcription factors that regulate central carbon metabolism in Rhodobacter sphaeroides ChIP-seq was used to determine the genome-wide binding locations of 2 transcription factors: CceR (RSP_1663) and AkgR (RSP_0981) both predicted to be involved in the regulation of of central carbon and energy metabolism.

Organism:

Cereibacter sphaeroides

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL18841 GPL18840

4 Samples

Download data: WIG