GEO DataSets

(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) 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 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) To determine the regulon of RSP1056-RSP0847 TCS (response regulator with DNA-binding domains) we used ChIP-seq to determine the genomic occupancy of RSP0847 in strains with a hyperactive (RSP0847(D56E)), WT, and low activity (ΔRSP1056, RSP0847(D56A)) TCS. We then correlated cenR binding sites with changes in global gene expression between WT and strains with a hyperactive (RSP1056(D56E)) or low activity (ΔRSP1056, RSP0847(D56A)) TCS in RNA-seq experiments.

Organism:

Cereibacter sphaeroides 2.4.1

Type:

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

Platforms:

GPL30898 GPL30899

53 Samples

Download data: TXT, 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) 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) 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 alphaproteobacteria have metabolic activities and lifestyles of societal and industrial importance that differ from those in many other bacteria. Here we report the genome-wide identification of transcription start sites (TSSs) from two alphaproteobacteria grown under conditions that result in significant changes in gene expression. TSSs that were identified as present in one condition or both will be an important resource for future studies of these, and possibly other, alphaproetobacteria.

Organism:

Novosphingobium aromaticivorans; Cereibacter sphaeroides 2.4.1

Type:

Other

Platforms:

GPL28624 GPL18842

24 Samples

Download data: TXT

(Submitter supplied) To investigate the R. sphaeroides NtrYX two component system on RNA transcript levels, we used global RNA sequencing (RNA-seq) to compare transcript abundance in parent and DntrYX strains grown under aerobic conditions. Our previous studies were performed in strains deficient at synthesizing the polyhydroxybutyrate, so we used strains D0382 and DNtrYXD0382, herein referred to as parent and DntrYX, respectively. more...

Organism:

Cereibacter sphaeroides 2.4.1

Type:

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

Platforms:

GPL18842 GPL28141

11 Samples

Download data: WIG, XLSX

(Submitter supplied) We investigated an improved method that combines competitive PCR and microarray techniques. This approach allowed us to quantify specific bacterial groups mounted on DNA chips with accuracy close to that of real-time PCR, despite a measurement at the end point of PCR, and also to estimate the bacterial DNA content in sample DNA.

Organism:

Neisseria meningitidis; Porphyromonas gingivalis; Fusobacterium nucleatum; Clostridium beijerinckii; Lactobacillus gasseri; Tannerella forsythia; Treponema denticola; Cereibacter sphaeroides; Streptococcus gordonii; Streptococcus agalactiae; Enterococcus faecalis; Bifidobacterium adolescentis; Homo sapiens; Prevotella intermedia; Prevotella nigrescens; Campylobacter rectus; Helicobacter pylori; Pseudomonas aeruginosa; Aggregatibacter actinomycetemcomitans; Phocaeicola vulgatus; Capnocytophaga gingivalis; Deinococcus radiodurans; Streptococcus mutans; Streptococcus intermedius; Cutibacterium acnes; Bacteria; Acinetobacter baumannii; Escherichia coli; Staphylococcus aureus; Staphylococcus epidermidis; Bacillus cereus; Schaalia odontolytica; Fusobacterium nucleatum subsp. nucleatum

Type:

Other

Platform:

GPL25612

178 Samples

Download data: CSV

(Submitter supplied) The identification of DNA G-quadruplexes (G4s) in the genome is important to study different biological processes in which these structures play a role, such as genome rearrangement, transcriptional regulation and DNA replication. G4-seq allowed the high-throughput experimental mapping of G-quadruplexes in the human genome. We developed here an improved version of this method, named G4-seq2, which we applied to generate G-quadruplexes genomic maps for 12 species, selected as important models organism to study development or as pathogens of clinical relevance. more...

Organism:

Escherichia coli; Cereibacter sphaeroides; Arabidopsis thaliana; Caenorhabditis elegans; Drosophila melanogaster; Leishmania major; Plasmodium falciparum; Mus musculus; Saccharomyces cerevisiae; Trypanosoma brucei; Danio rerio; Homo sapiens

Type:

Other

12 related Platforms

24 Samples

Download data: BED, BEDGRAPH

(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) 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) To learn more about the function of Pos19, we constructed an over-expression strain. For this purpose, the Pos19 gene together with its native RpoE promoter was cloned into the middle-copy plasmid pBBR1 and expressed in the R. sphaeroides wild-type 2.4.1 background. The corresponding strain consequently exhibits a singlet oxygen-induced Pos19 over-expression compared to an empty vector control. Total RNA from the over-expression (pPos19) and from the empty vector control (pBBR) strain was extracted after 7 min of singlet oxygen stress and used for microarray analysis to investigate Pos19-induced changes on transcriptome level.

Organism:

Cereibacter sphaeroides 2.4.1

Type:

Expression profiling by array

Platform:

GPL21931

2 Samples

Download data: TXT

(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) 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) 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