GEO DataSets

(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) 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) 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) 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; Cereibacter sphaeroides 2.4.1

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) 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) 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) 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) We demonstrate here the transcriptional landscape and functional roles of sRNAs specifically in the regulation of the oxidative stress response of the model haloarchaeon Haloferax volcanii. We sequenced 5 biological replicates of H. volcanii strain H53 under no challenge and oxidative stress (H2O2) conditions at mid-exponential phase (OD 0.4). Thousands of sRNAs, both intergenic and antisense, were discovered using strand-specific sRNA-seq, comprising around 30% of the transcriptome during non-challenged and oxidative stress conditions. more...

Organism:

Haloferax volcanii DS2

Type:

Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing

Platform:

GPL21976

16 Samples

Download data: 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) To elucidated the regulatory effect of DsrA on the oxidative resistance in Salmonella enterica serovar Typhimurium. RNA sample of wild-type and DsrA-deletion strain that grown in LB medium or H2O2 stress were extracted. Three biological replicates were carried out per sample. RNA sample was sequenced with Illumina HiSeq 4000 System. DESeq2 method was used to calculate the differentially expressed genes. more...

Organism:

Salmonella enterica subsp. enterica serovar Typhimurium

Type:

Expression profiling by high throughput sequencing

Platform:

GPL27471

12 Samples

Download data: XLS

(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 present the first genome-wide identification and characterizaion of 422 novel sRNAs in R. capsulatus. In addition we report a comparative analysis of conserved sRNAs across 24 bacterial species.

Organism:

Rhodobacter capsulatus

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL20771

2 Samples

Download data: XLS

(Submitter supplied) Bacteria cope with and adapt to stress by modulating gene expression in response to specific environmental cues. In this study the transcriptional response of Pseudomonas putida KT2440 to oxidative, osmotic, and membrane stress conditions at two time points was investigated via identification of differentially expressed mRNAs and sRNAs. A total of 440 small RNA transcripts were detected, where 10% correspond to previously annotated sRNAs, 40% are novel intergenic transcripts and 50% are novel transcripts antisense to annotated genes. more...

Organism:

Pseudomonas putida KT2440

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17091

21 Samples

Download data: TXT, XLSX

(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) Purpose: The goal of this study was the identification of target genes of the Neisseria gonorrhoeae sRNAs NgncR_237, NgncR_162 and NgncR_163. Methods: RNA was isolated from N. gonorrhoeae using the miRNeasy Micro Kit (Qiagen). Enrichment of mRNA was done using the Universal Ribodepletion Kit followed by Next Ultra Directional Library Preparation Kit for Illumina (NEB). The cDNA was sequenced on Illumina HiSeq 3000 platform with 100 bp paired end reads. more...

Organism:

Neisseria gonorrhoeae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL30262

18 Samples

Download data: CSV

(Submitter supplied) The transcription profile of C. acetobutylicum to two major metabolite stress, butanol and butyric acid, was comprehensively investigated at three different concentrations of each metabolite and at four different time points (15, 30, 60 and 75 min post stress). All experiments were performed in 3 parallel biological replicates and the RNA extraction was perfomed in a manner to retain the small RNAs and hence, investigate their role and expression under stress.

Organism:

Clostridium acetobutylicum

Type:

Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing

Platform:

GPL17364

84 Samples

Download data: TXT