GEO DataSets

(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) 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 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) RNA-based regulation of gene expression is substantially contributing to the ability of bacteria to rapidly adapt to changing environmental conditions. This study employs RNAseq to define the transcriptome of Caulobacter in response to treatment with the DNA-crosslinking agent mitomycin C. We identify a small, regulatory RNA ChvR synthesized under the control of the conserved ChvIG two-component system which represses production of a TonB-dependent receptor, ChvT, in Caulobacter crescentus. more...

Organism:

Caulobacter vibrioides NA1000

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21317

6 Samples

Download data: WIG

(Submitter supplied) In many gram-negative and some gram-positive bacteria small regulatory RNAs (sRNAs) that bind the RNA chaperone Hfq have a pivotal role in modulating virulence, stress responses, metabolism, and biofilm formation. These sRNAs recognize transcripts through base-pairing, and sRNA-mRNA annealing consequently alters the translation and/or stability of transcripts leading to changes in gene expression. We have previously found that the highly conserved 3'-to-5' exoribonuclease polynucleotide phosphorylase (PNPase) has an indispensable role in paradoxically stabilizing Hfq-bound sRNAs and promoting their function in gene regulation in Escherichia coli. more...

Organism:

Escherichia coli str. K-12 substr. MG1655

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL15010

12 Samples

Download data: TXT, XLSX

(Submitter supplied) Hfq, a bacterial RNA chaperone, stabilizes small regulatory RNAs (sRNAs) and facilitates sRNA base-pairing with target mRNAs. Hfq has a conserved N-terminal domain and a poorly conserved disordered C-terminal domain (CTD). In a transcriptome-wide examination of the effects of a chromosomal CTD deletion (Hfq1-65), the Escherichia coli mutant was most defective for the accumulation of sRNAs that bind the proximal and distal faces of Hfq (Class II sRNAs), but other sRNAs also were affected. more...

Organism:

Escherichia coli K-12

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24570

8 Samples

Download data: TXT

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

Organism:

Escherichia coli str. K-12 substr. MG1655

Type:

Expression profiling by high throughput sequencing; Other

Platforms:

GPL24659 GPL26592

30 Samples

Download data: FA, GTF

(Submitter supplied) By shaping gene expression profiles, small RNAs (sRNAs) enable bacteria to efficiently adapt to changes in their environment. To better understand how Escherichia coli acclimatizes to nutrient availability, we performed UV cross-linking, ligation and sequencing of hybrids (CLASH) to uncover Hfq-associated RNA-RNA interactions at specific growth stages. We demonstrate that Hfq CLASH robustly captures bona fide RNA-RNA interactions identified hundreds of novel sRNA base-pairing interactions, including many sRNA-sRNA interactions and involving 3’UTR-derived sRNAs. more...

Organism:

Escherichia coli str. K-12 substr. MG1655

Type:

Other

Platform:

GPL24659

16 Samples

Download data: TXT

(Submitter supplied) By shaping gene expression profiles, small RNAs (sRNAs) enable bacteria to efficiently adapt to changes in their environment. To better understand how Escherichia coli acclimatizes to nutrient availability, we performed UV cross-linking, ligation and sequencing of hybrids (CLASH) to uncover Hfq-associated RNA-RNA interactions at specific growth stages. We demonstrate that Hfq CLASH robustly captures bona fide RNA-RNA interactions identified hundreds of novel sRNA base-pairing interactions, including many sRNA-sRNA interactions and involving 3’UTR-derived sRNAs. more...

Organism:

Escherichia coli str. K-12 substr. MG1655

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26592

14 Samples

Download data: XLSX

(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) RNA-seq analysis was performed to examine the sRNA transcripts in wild type E. amylovora 1189 and in the deletion mutant of hfq, at 6 and 12 hours of culture in hrp-inducing minimal medium.

Organism:

Erwinia amylovora

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL18131

12 Samples

Download data: GTF, TXT

(Submitter supplied) Bacterial small regulatory RNAs (sRNAs) regulate gene expression by base-pairing to their target mRNAs. In Escherichia coli and many other bacteria, this process is dependent on the RNA chaperone Hfq, which binds sRNAs and mRNAs on different faces. YhbS (renamed here as HqbA), a putative Gcn5-related N-acetyltransferase (GNAT), was identified as a novel silencer of sRNA signaling in a genomic library screen. more...

Organism:

Escherichia coli str. K-12 substr. MG1655

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18956

24 Samples

Download data: XLSX

(Submitter supplied) We sought to define the transcriptional regulon of the ChvI response regulator in Caulobacter crescentus. This study compares gene expression between ∆chvI cells and cells overexpressing the constitutively-active chvI(D52E) mutant. Our work provides a global view of the genes directly and indirectly regulated by the ChvGI two-component system in C. crescentus.

Organism:

Caulobacter vibrioides

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24555

12 Samples

Download data: TXT

(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 subsp. enterica serovar Typhimurium; Salmonella enterica

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) 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; Pseudomonas aeruginosa PAO1

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