GEO DataSets

(Submitter supplied) To learn more about the function of SorX, we constructed an over-expression strain. For this purpose, the sorX gene together with its 28-bp upstream region was cloned into the over-expression vector pRK4352 and expressed in the R. sphaeroides wild-type 2.4.1 background. The corresponding strain consequently exhibits a SorX over-expression that is driven by the constitutive 16S rRNA (RSP_4352) promoter. more...

Organism:

Cereibacter sphaeroides 2.4.1

Type:

Expression profiling by array

Platform:

GPL15457

3 Samples

Download data: TXT

(Submitter supplied) Exposure to oxygen and light generates photooxidative stress by the bacteriochlorophyll a mediated formation of singlet oxygen (1O2) in the facultative photosynthetic bacterium Rhodobacter sphaeroides. We have identified SorY as an sRNA, which is induced under several stress conditions and confers increased resistance against 1O2. SorY by direct interaction decreases the levels of takP mRNA, encoding a TRAP-T transporter. more...

Organism:

Cereibacter sphaeroides 2.4.1

Type:

Expression profiling by array

Platform:

GPL15457

2 Samples

Download data: TXT

(Submitter supplied) Transcriptional profiling of R. sphaeroides pRCcsR1-4 comparing to control R. sphaeroides 2.4.1 pRK415 under aerobic conditions

Organism:

Cereibacter sphaeroides; 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. 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) The polynucleotide phosphorylase (PNPase) is conserved among both Gram-positive and Gram-negative bacteria. As a core part of the degradosome, the PNPase is involved in maintaining proper RNA levels within the bacterial cell. It plays a major role in RNA homeostasis and decay since it acts as a 3’- to 5’-exoribonuclease. Furthermore PNPase can catalyze the reverse reaction by elongating RNA molecules in 5’- to 3’-end direction which finally has a destabilizing effect on the prolonged RNA molecule. more...

Organism:

Cereibacter sphaeroides

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24048

9 Samples

Download data: BED, CSV, WIG

(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) The sRNA UdsC ist derived from the 3´ UTR of RSP_7527. To analyse the effect of the sRNA on the transcriptome of R. sphaeroides we performed the RNAseq analysis with a chromosomal knockout and an inducible overexpression of this sRNA.

Organism:

Cereibacter sphaeroides

Type:

Expression profiling by high throughput sequencing

Platform:

GPL32157

9 Samples

Download data: WIG

(Submitter supplied) The conserved endoribonuclease RNase E is essential in Rhodobacter sphaeroides and acts as global regulator of the transcriptome. By comparison of an RNase E mutant (showing reduced enzyme activity) with the Rhodobacter sphaeroides wild type, both grown under three different growth conditions, we analysed the impact of RNase E on the adaption of Rhodobacter sphaeroides to different growth conditions.

Organism:

Cereibacter sphaeroides

Type:

Expression profiling by high throughput sequencing

Platform:

GPL32157

18 Samples

Download data: CSV

(Submitter supplied) Transcriptional profiling of R. sphaeroides pBBRUpsMx2 compared to control R. sphaeroides pBBR under high oxygen and singlet oxygen conditions.

Organism:

Cereibacter sphaeroides 2.4.1

Type:

Expression profiling by array

Platform:

GPL22542

4 Samples

Download data: TXT

(Submitter supplied) The facultatively photosynthetic bacterium Rhodobacter sphaeroides harbors an unusual LOV (light, oxygen, voltage) domain protein, RsLOV. While showing a characteristic photocycle, the protein misses a C - terminal output domain, similar to PpSB2 in Pseudomonas putida. Oxygen tension and light quantity are the two main responsible factors controlling the expression of photosynthesis genes in Rhodobacter sphaeroides. more...

Organism:

Cereibacter sphaeroides 2.4.1

Type:

Expression profiling by array

Platforms:

GPL14782 GPL14796

6 Samples

Download data: GPR, TXT

(Submitter supplied) Transcriptional profiling of R. sphaeroides Δlov compared to control R. sphaeroides 2.4.1 under singlet oxygen stress, aerobic conditions

Organism:

Cereibacter sphaeroides 2.4.1

Type:

Expression profiling by array

Platform:

GPL14796

2 Samples

Download data: TXT

(Submitter supplied) Transcriptional profiling of R. sphaeroides Δlov compared to control R. sphaeroides 2.4.1 under blue light, semiaerobic conditions.

Organism:

Cereibacter sphaeroides 2.4.1

Type:

Expression profiling by array

Platform:

GPL14796

2 Samples

Download data: TXT

(Submitter supplied) Transcriptional profiling of R. sphaeroides Δlov comparing to control R. sphaeroides 2.4.1 under microarobic conditions

Organism:

Cereibacter sphaeroides 2.4.1

Type:

Expression profiling by array

Platform:

GPL14782

2 Samples

Download data: GPR

(Submitter supplied) Many protein domains are conserved among different classes and are found in numerous species, but their function remains obscure. Data bases list more than 17,000 DUF1127 proteins but to date no biological function could be assigned to any of these proteins. This study demonstrates that the 71 amino acid DUF1127 protein CcaF1 from the alphaproteobacterium Rhodobacter sphaeroides participates in the maturation of the CcsR sRNAs that are processed from the 3´ UTR of the ccaF mRNA and have a role in the oxidative stress defense. more...

Organism:

Cereibacter sphaeroides 2.4.1

Type:

Other

Platform:

GPL28141

4 Samples

Download data: CSV, WIG

(Submitter supplied) Many protein domains are conserved among different classes and are found in numerous species, but their function remains obscure. Data bases list more than 17,000 DUF1127 proteins but to date no biological function could be assigned to any of these proteins. This study demonstrates that the 71 amino acid DUF1127 protein CcaF1 from the alphaproteobacterium Rhodobacter sphaeroides participates in the maturation of the CcsR sRNAs that are processed from the 3´ UTR of the ccaF mRNA and have a role in the oxidative stress defense. more...

Organism:

Cereibacter sphaeroides

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24048

9 Samples

Download data: CSV

(Submitter supplied) RNase III is an important and highly conserved endoribonuclease known to impact rRNA, mRNA and ncRNA abundances by RNA processing. In this study we analyzed the effects of an inactivation of RNase III (inactivated through substitution of two strictly conserved amino acids within the active enzyme center) on the transcriptome of the facultative phototrophic model organism Rhodobacter sphaeroides.

Organism:

Cereibacter sphaeroides

Type:

Expression profiling by high throughput sequencing

Platform:

GPL33350

9 Samples

Download data: WIG

(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

(Submitter supplied) Oligo probes are 45bp in average, tiling the genome sequences with about 35-bp overlap between consecutive probes. Every other probe hybridizes to the reverse strand. Native array description file: 2007-06-20_R_sphaeroides_long85_v2.ndf Native array description file: 2007-06-20_R_sphaeroides_long85_v2.pos Protocol: See manufacturer's web site (www.nimblegen.com)

Organism:

Cereibacter sphaeroides 2.4.1

4 Series

21 Samples

Download data: NDF, POS

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

Organism:

Cereibacter sphaeroides 2.4.1

Type:

Expression profiling by array

Platforms:

GPL14782 GPL14796

7 Samples

Download data: GPR, TXT

(Submitter supplied) Transcriptional profiling of R. sphaeroides delta-cryB compared to control R. sphaeroides 2.4.1 under blue light, semiaerobic conditions.

Organism:

Cereibacter sphaeroides 2.4.1

Type:

Expression profiling by array

Platform:

GPL14796

2 Samples

Download data: TXT