GEO DataSets

(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) Hfq is a ubiquitous Sm-like RNA-binding protein in bacteria involved in physiological fitness and pathogenesis, while its in vivo binding nature remains elusive. Here we reported genome-wide Hfq-bound RNAs in Yersinia pestis, a causative agent of plague, by using cross-linking immunoprecipitation coupled with deep sequencing (CLIP-seq) approach. We show that the Hfq binding density is enriched in more than 80% mRNAs of Y. more...

Organism:

Yersinia pestis

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL21403

8 Samples

Download data: TXT

(Submitter supplied) Grad-seq of Pseudomonas aerugionosa PAO1 at OD 0.3 with and without infection with ΦKZ bacteriophage

Organism:

Phikzvirus phiKZ; Pseudomonas aeruginosa PAO1

Type:

Expression profiling by high throughput sequencing; Other

Platforms:

GPL23999 GPL28760

44 Samples

Download data: TDF

(Submitter supplied) The molecular roles of many RNA‐binding proteins in bacterial post‐transcriptional gene regulation are not well understood. Approaches combining in vivo UV crosslinking with RNA deep sequencing (CLIP‐seq) have begun to revolutionize the transcriptome‐wide mapping of eukaryotic RNA‐binding protein target sites. We have applied CLIP‐seq to chart the target landscape of two major bacterial post‐transcriptional regulators, Hfq and CsrA, in the model pathogen Salmonella Typhimurium. more...

Organism:

Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20056

12 Samples

Download data: WIG

(Submitter supplied) We report the identification of new noncoding RNAs in Brucella suis 1330 and that are associated to the chaperone protein Hfq

Organism:

Brucella suis 1330

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20974

2 Samples

Download data: GR

(Submitter supplied) A key challenge for understanding the role(s) played by short, non-coding RNAs (sRNAs) in bacteria is identifying the mRNA targets regulated by the sRNAs. Because the Hfq protein mediates the interactions between many sRNAs and the corresponding target mRNAs, one apporach to identify the mRNA targets of sRNAs is to capture sRNA:mRNA interactions occuring on Hfq by exposing cells to UV-irradiation, which forms cross-links between nucleic acids and proteins. more...

Organism:

Pseudomonas aeruginosa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL33271

9 Samples

Download data: BW

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

Organism:

Pseudomonas aeruginosa PAO1; Pseudomonas aeruginosa

Type:

Expression profiling by high throughput sequencing; Other

Platforms:

GPL33271 GPL23999

33 Samples

Download data: BW

(Submitter supplied) A key challenge for understanding the role(s) played by short, non-coding RNAs (sRNAs) in bacteria is identifying the mRNA targets regulated by the sRNAs. Because the Hfq protein mediates the interactions between many sRNAs and the corresponding target mRNAs, one apporach to identify the mRNA targets of sRNAs is to capture sRNA:mRNA interactions occuring on Hfq by exposing cells to UV-irradiation, which forms cross-links between nucleic acids and proteins. more...

Organism:

Pseudomonas aeruginosa PAO1

Type:

Expression profiling by high throughput sequencing

Platform:

GPL23999

12 Samples

Download data: BW

(Submitter supplied) A key challenge for understanding the role(s) played by short, non-coding RNAs (sRNAs) in bacteria is identifying the mRNA targets regulated by the sRNAs. Because the Hfq protein mediates the interactions between many sRNAs and the corresponding target mRNAs, one apporach to identify the mRNA targets of sRNAs is to capture sRNA:mRNA interactions occuring on Hfq by exposing cells to UV-irradiation, which forms cross-links between nucleic acids and proteins. more...

Organism:

Pseudomonas aeruginosa PAO1

Type:

Other; Expression profiling by high throughput sequencing

Platform:

GPL23999

12 Samples

Download data: BED, BW

(Submitter supplied) The Gram-positive bacterium Clostridium difficile, a leading cause of antibiotic-associated pseudomembranous colitis, has received increasing attention due to a rising incidence of clinical C. difficile infections (CDI). Despite progress understanding bacterial factors that promote CDI-associated morbidity and mortality, many fundamental aspects of C. difficile biology remain to be explored. Compared to other Gram-positive pathogens, little is known about the bacterium’s transcriptome architecture and in particular mechanisms of post-transcriptional control. more...

Organism:

Clostridioides difficile 630

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL28932

39 Samples

Download data: WIG

(Submitter supplied) Determination of the RNA interacting with vfr mRNA at two different time-points during growth on the three strains PAO1, PA14 and IHMA87, representing the three major P. aeruginosa phylogenetic lineages, using rGRIL-seq.

Organism:

Pseudomonas aeruginosa

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL21297

12 Samples

Download data: XLSX

(Submitter supplied) Determination of the RNA interactome of the RNA-binding protein Hfq at three different time-point during growth on the three strains PAO1, PA14 and IHMA87, representing the three major P. aeruginosa phylogenetic lineages, using RIP-seq.

Organism:

Pseudomonas aeruginosa

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL21297

36 Samples

Download data: XLSX

(Submitter supplied) Purpose: Pseudomonas aeruginosa is a motile species that initiates swarming motility in response to specific environmental cues, i.e., a semisolid surface with amino acids as a nitrogen source (relevant to the human lung). Swarming is an intricately regulated process, but to date post-transcriptional regulation has not been extensively investigated. Small non-coding RNAs (sRNA) are hypothesized to play post-transcriptional regulatory roles, largely through suppression of translation, and we previously demonstrated 20 sRNA species that were dysregulated under swarming conditions. more...

Organism:

Pseudomonas aeruginosa PAO1

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18782

10 Samples

Download data: TXT

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

Organism:

Vibrio cholerae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25180

14 Samples

Download data

(Submitter supplied) In this study we determined the target spectrum of Vibrio cholerae FarS sRNA via pulse-expression followed by RNA-sequencing.

Organism:

Vibrio cholerae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25180

6 Samples

Download data: XLSX

(Submitter supplied) In this study we used RNA co-immunoprecipitation followed by RNA-sequencing (RIP-seq) to identify Hfq-binding RNAs in Vibrio cholerae.

Organism:

Vibrio cholerae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25180

8 Samples

Download data: XLSX

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

Organism:

Staphylococcus aureus

Type:

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

Platforms:

GPL25144 GPL19531

14 Samples

Download data: TXT