GEO DataSets

(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) In this study we analyzed the effects of reduced RNase E activity, lacking RNase III activity or chromosomal deletion of the sRNA StsR on the transcriptome of Cereibacter sphaeroides. Samples for total RNA sequencing were collected during exponential and late stationary growth phase (72 hours) under microaerobic or phototrophic condtions. Transcriptome profiles were compared to corresponding wild type controls.

Organism:

Cereibacter sphaeroides 2.4.1

Type:

Expression profiling by high throughput sequencing

Platform:

GPL34692

30 Samples

Download data: TSV

(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) 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 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

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(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) In previous studies we identified the small RNA-binding protein CcaF1 that is involved in sRNA maturation and RNA turnover in Rhodobacter sphaeroides under microaerobic growth conditions (Grützner et al., 2021, Nucleic Acids Res. 49(6), doi: 10.1093/nar/gkab146). In this study we analysed the the small RNA-binding protein CcaF1 under phototrophic growth condtions to identify new RNA binding partners.

Organism:

Cereibacter sphaeroides

Type:

Other

Platform:

GPL33350

4 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) 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) 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) Comparison of wild type and mutant strain with temperature-sensitive RNase E. Goal: to study the effect of RNase E on the transcriptome

Organism:

Cereibacter sphaeroides

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24048

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) 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) Bordetella pertussis has been shown to encode regulatory RNAs, yet the post-transcriptional regulatory circuits on which they act remain to be fully elucidated. We generated mutants lacking the endonucleases RNase III and RNase E and assessed their individual impact on the B. pertussis transcriptome. RNA-Seq analysis showed differential expression of ~25% of the B. pertussis transcriptome in each mutant with only 28% overlap between data sets. more...

Organism:

Bordetella pertussis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL29570

15 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

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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

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(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