GEO DataSets

(Submitter supplied) Hfq is an RNA chaperone and an important post-transcriptional regulator in bacteria. Using chromatin immunoprecipitation together with DNA sequencing (ChIP-Seq), we show that Hfq associates with hundreds of different regions of the Pseudomonas aeruginosa chromosome. These associations are abolished when transcription is inhibited, indicating they reflect Hfq binding to transcripts during their synthesis. more...

Organism:

Pseudomonas aeruginosa PAO1

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL18782

20 Samples

Download data: BED, WIG

(Submitter supplied) In the opportunistic pathogen Pseudomonas aeruginosa RsmA is an RNA-binding protein that plays critical roles in the control of virulence, interbacterial interactions and biofilm formation. Although RsmA is thought to exert its regulatory effects by binding full-length transcripts, the extent to which RsmA binds nascent transcripts has not been addressed. Moreover, which transcripts are direct targets of this key post-transcriptional regulator is largely unknown. more...

Organism:

Pseudomonas aeruginosa PAO1

Type:

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

Platforms:

GPL23999 GPL18782

30 Samples

Download data: BED, BW, TXT, WIG

(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) 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) S. typhimurium 14028 wt, hfq and smpB were harvested from log phase LB (LBlog); (2), stationary phase LB (LBstat); (3) 4h MgM medium pH 5.0 after resuspension of LB stat culture (MgMshock); and (4) log phase MgM medium pH5.0 after 100fold dilution of an LB stat culture (MgMDil). Total RNA was extracted, cDNA labeled and hybridized to a non-redundant Salmonella whole genome PCR product ORF array.

Organism:

Salmonella enterica subsp. enterica serovar Typhimurium; Salmonella enterica

Type:

Expression profiling by array

Platform:

GPL6868

36 Samples

Download data

(Submitter supplied) The small RNAs associated with protein Hfq constitute one of the largest classes of post-transcriptional regulators known to date. Most previously investigated members of this class are encoded by conserved free-standing genes. Here, deep sequencing of Hfq-bound transcripts from multiple stages of growth of Salmonella Typhimurium revealed a plethora of new small RNA species from within mRNA loci, including DapZ which overlaps with the 3’ region of the biosynthetic gene, dapB. more...

Organism:

Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344

Type:

Other

Platform:

GPL15732

14 Samples

Download data: WIG

(Submitter supplied) To determine the targets of the small regulatory RNA DapZ in S. Typhimurium, we looked at the effect of a short pulse of DapZ over-expression on the Salmonella transcriptome, as well as a DapZ variant that lacks the GcvB-like R1 region. To achieve over-expression, the wild-type DapZ and its variant were cloned in the pBAD plasmid and induced with 0.2% L-arabinose for 10 min. We then extracted the total RNA for transcriptional profiling. more...

Organism:

Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344

Type:

Expression profiling by array

Platform:

GPL11416

6 Samples

Download data: TXT

(Submitter supplied) The alpha-proteobacterium Caulobacter crescentus thrives in oligotrophic environments and is able to optimally exploit minimal resources by entertaining an intricate network of gene expression control mechanisms. Numerous transcriptional activators and repressors have been reported to contribute to these processes, but only few studies have focused on regulation at the post-transcriptional level in C. more...

Organism:

Caulobacter vibrioides

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL24555

2 Samples

Download data: XLSX

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

Organism:

Caulobacter vibrioides

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL21016 GPL28356

10 Samples

Download data

(Submitter supplied) In this study we determined the target spectrum of C. crescentus sRNA R0199 via pulse-expression followed by RNA-sequencing.

Organism:

Caulobacter vibrioides

Type:

Expression profiling by high throughput sequencing

Platform:

GPL28356

6 Samples

Download data: XLSX

(Submitter supplied) In this study we used RNA co-immunoprecipitation followed by RNA-sequencing to identify Hfq-binding RNAs in C. crescentus.

Organism:

Caulobacter vibrioides

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21016

4 Samples

Download data: XLSX

(Submitter supplied) We used high-throughput methods to discover the Salmonella RNAs that are targeted by the bacterial Sm-like protein, Hfq. Our generic approach, using chromosomal epitope tagging and coIP-on-chip will also be useful to identify the post-transcriptional regulons of many other RNA-binding proteins. Keywords: coIP-chip

Organism:

Salmonella enterica; Salmonella enterica subsp. enterica serovar Typhimurium

Type:

Other

Platform:

GPL5791

4 Samples

Download data: TXT

(Submitter supplied) The expression profile of an S. Typhimurium hfq mutant-strain was compared to the parental strain under 2 different growth conditions; early stationary phase and SPI-1 (Salmonella pathogenicity island 1) inducing condition. Keywords: Genetic modification

Organism:

Salmonella enterica

Type:

Expression profiling by array

Platform:

GPL5780

12 Samples

Download data: TXT

(Submitter supplied) Characterization of bacterial behavior in the microgravity environment of spaceflight is of importance towards risk assessment and prevention of infectious disease during long-term missions. Further, this research field unveils new insights into connections between low fluid-shear regions encountered by pathogens during their natural infection process in vivo, and bacterial virulence. This study is the first to characterize the global transcriptomic and proteomic response of an opportunistic pathogen that is actually found in the space habitat, Pseudomonas aeruginosa. more...

Organism:

Pseudomonas aeruginosa; Pseudomonas aeruginosa PAO1

Type:

Expression profiling by array

Platform:

GPL84

8 Samples

Download data: CEL

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

Organism:

Vibrio cholerae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25180

14 Samples

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