GEO DataSets

(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) Oxidative stress responsive small non-coding RNAs (sRNAs) have been reported in the model archaeon, Haloferax volcanii, but targets and mechanisms of actions have not been elucidated. While haloarchaea are highly resistant to oxidative stress, a comprehensive understanding of the mechanisms regulating this remarkable response is lacking. Here, using a combination of high throughput and reverse molecular genetic approaches we elucidated the functional role of the most up-regulated intergenic sRNA during oxidative stress in H. more...

Organism:

Haloferax volcanii DS2

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21976

16 Samples

Download data: TXT, XLSX

(Submitter supplied) Three biological replicates of H. volcanii grown under optimal conditions to mid-exponential growth phase were used to determine the primary transcriptome and map 5’-ends of transcripts. In total, 4,749 potential transcriptional start sites (TSS) were detected. A position weight matrix was derived for promoter prediction, showing that 64% of the TSS were preceded by stringent or relaxed basal promoters. more...

Organism:

Haloferax volcanii

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25010

6 Samples

Download data: WIG

(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) We report the transcriptomic profile of Escherichia coli when the small RNA RydC is overexpressedand how this can be used to identify putative mRNA targets. This technique allowed us to identify potential mRNA targets to further validate in vivo.

Organism:

Escherichia coli str. K-12 substr. MG1655

Type:

Expression profiling by high throughput sequencing

Platform:

GPL15010

6 Samples

Download data: TXT, WIG

(Submitter supplied) Small RNAs have been studied in detail in Bacteria and Eukarya domain, but in the case of Archaea domain the knowledge is scarce and the physiological function of the majority is still uncertain. To extend the knowledge of sRNAs in Archaea domain and its possible role in the regulation of the nitrogen assimilation metabolism in haloarchaea, Haloferax mediterranei has been used as a model microorganism. more...

Organism:

Haloferax mediterranei

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL20667

15 Samples

Download data: GFF3, 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) Small RNAs (sRNAs) have emerged as important regulatory molecules and have been studied in several bacteria. However, to date, there have been no whole-transcriptome studies on sRNAs in any of the Soft Rot Enterobacteriaceae (SRE) group of pathogens. Although the main ecological niches for these pathogens are plants, a significant part of their life cycle is undertaken outside their host within the adverse soil environment. more...

Organism:

Pectobacterium atrosepticum SCRI1043

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL20147

2 Samples

Download data: TAB, XLSX

(Submitter supplied) Investigation of gene expression in ∆glpR mutant strains vs wild type in response to glycerol and glucose.

Organism:

Haloferax volcanii

Type:

Expression profiling by array

Platform:

GPL21414

12 Samples

Download data: PAIR

(Submitter supplied) The oral commensal Fusobacterium nucleatum can spread to extra-oral sites where it is associated with pathologies as diverse as pre-term birth or cancer. Due to the evolutionary distance of F. nucleatum to other model bacteria, we lack a deeper understanding of RNA regulatory networks that allow this bacterium to adapt to different environmental niches. As a first step in that direction, we recently showed that F. more...

Organism:

Fusobacterium nucleatum subsp. nucleatum ATCC 23726

Type:

Expression profiling by high throughput sequencing

Platform:

GPL33873

15 Samples

Download data: WIG

(Submitter supplied) Small RNAs are the non-coding RNAs known to regulate various biological functions such as stress adaptation, metabolism, virulence as well as pathogenicity across wide range of bacteria, mainly by controlling mRNA stabilization or regulating translation. Identification and functional characterization of sRNAs that has been carried out in various plant growth promoting bacteria have shown to help the bacterial cell cope up with environmental stress. more...

Organism:

Azospirillum baldaniorum

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL25390

2 Samples

Download data: TXT

(Submitter supplied) Small RNAs and L7Ae co-immunoprecipitated RNA were isolated from the thermophilic archaeon Sulfolobus acidocaldarius and subjected to Illumina sequencing. The sRNome revealed a high abundance of C/D box sRNAs and CRISPR RNAs. The L7Ae-RNA interactome showed enrichment of all known interactors of the L7Ae protein, i.e. C/D box sRNAs, H/ACA box sRNAs, RNaseP, rRNA. A high abundance of reads for the SRP RNA was found, suggesting L7Ae´s interaction with this universal RNA. more...

Organism:

Sulfolobus acidocaldarius

Type:

Other; Non-coding RNA profiling by high throughput sequencing

Platforms:

GPL23051 GPL23429

5 Samples

Download data: WIG

(Submitter supplied) These data were obtained using a recently-developed high throughput method to probe regional RNA accessibility by mimicking in vivo antisense hybridization. The method (INTERFACE) is an engineered RNA system (for use in E. coli) that exploits conserved bacterial mechanisms of translational stalling and Rho-dependent transcription termination mechanisms to quantify RNA hybridization (via an asRNA targeting an RNA region of interest) via a transcriptional elongation response. more...

Organism:

Escherichia coli

Type:

Other

Platform:

GPL21222

12 Samples

Download data: BED, FA

(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) Regulatory small RNAs (sRNAs) represent a major class of regulatory molecules that play large-scale and essential roles in many cellular processes across all domains of life. Microbial sRNAs have been primarily investigated in a few model organisms and little is known about the dynamics of sRNA synthesis in natural environments, and the roles of these short transcripts at the community level. Analyzing the metatranscriptome of a model extremophilic community inhabiting halite nodules (salt rocks) from the Atacama Desert, sampled over two years with different weather conditions, with SnapT – a new sRNA annotation pipeline – we discovered hundreds of intergenic (itsRNAs) and antisense (asRNAs) sRNAs expressed.

Organism:

halite metagenome

Type:

Expression profiling by high throughput sequencing

Platform:

GPL27449

45 Samples

Download data: GFF, TXT

(Submitter supplied) Identification of global gene expression profiling when Haloferax volcanii H26 strain is grown in minimal medium supplemented with two nitrogen sources, 10 mM L-alanine and 10 mM ammonium chloride.

Organism:

Haloferax volcanii

Type:

Expression profiling by array

Platform:

GPL21414

6 Samples

Download data: CALLS, PAIR

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

Organism:

Pseudomonas aeruginosa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21297

18 Samples

Download data: WIG

(Submitter supplied) Bacterial small non-coding RNAs (sRNAs) play post-transcriptional regulatory roles in cellular responses to changing environmental cues and in adaptation to harsh conditions. Generally, the RNA-binding protein Hfq helps sRNAs associate with target mRNAs to modulate their translation and to modify global RNA pools depending on physiological state. Here, a combination of in vivo UV crosslinking immunoprecipitation followed by high-throughput sequencing (CLIP-seq) and total RNA-seq showed that Hfq interacts with different regions of the P. more...

Organism:

Pseudomonas aeruginosa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21297

6 Samples

Download data: XLSX

(Submitter supplied) Bacterial small non-coding RNAs (sRNAs) play post-transcriptional regulatory roles in cellular responses to changing environmental cues and in adaptation to harsh conditions. Generally, the RNA-binding protein Hfq helps sRNAs associate with target mRNAs to modulate their translation and to modify global RNA pools depending on physiological state. Here, a combination of in vivo UV crosslinking immunoprecipitation followed by high-throughput sequencing (CLIP-seq) and total RNA-seq showed that Hfq interacts with different regions of the P. more...

Organism:

Pseudomonas aeruginosa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21297

12 Samples

Download data: WIG

(Submitter supplied) We report the use of Next Generation RNA Sequencing to identifiy novel sRNAs in the human pathogen Staphylococcus aureus

Organism:

Staphylococcus aureus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL18481 GPL19531

10 Samples

Download data: TXT