GEO DataSets

(Submitter supplied) In this study we determined the target spectra of the MicV and VrrA sRNAs via pulse-expression followed by RNA-sequencing.

Organism:

Vibrio cholerae C6706

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26050

9 Samples

Download data: XLSX

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

Organism:

Vibrio cholerae C6706

Type:

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

Platforms:

GPL26051 GPL26050

16 Samples

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(Submitter supplied) In this study we subjected a library of synthetic sRNAs to multiple rounds of ethanol selection and analyzed changes in sRNA variant abundance by high-throughput sequencing.

Organism:

Vibrio cholerae C6706

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL26051

7 Samples

Download data: CSV

(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) 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) 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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(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) 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) 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) In enteric bacteria, the transcription factor σE maintains membrane homeostasis by inducing expression of proteins involved in membrane repair and of two small, regulatory RNAs (sRNAs) that downregulate synthesis of abundant membrane porins. Here, we describe the discovery of a third σE-dependent sRNA, MicL, transcribed from a promoter located within the coding sequence of the cutC gene. MicL is synthesized as a 308 nt primary transcript that is processed to an 80 nt form. more...

Organism:

Escherichia coli

Type:

Expression profiling by high throughput sequencing

Platform:

GPL14548

14 Samples

Download data: WIG

(Submitter supplied) Enteric model bacteria such as Escherichia coli and Salmonella enterica express hundreds of small non-coding RNAs (sRNAs), targets for most of which are yet unknown. Some of these sRNAs are remarkably well-conserved, indicating that that they serve cellular functions that go beyond the necessities of a single organism. One of these “core sRNA” of largely unknown functions is the abundant ~100-nucleotide SdsR sRNA which accumulates in stationary phase after transcription by the general stress σ-factor, σS. more...

Organism:

Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344; Salmonella enterica

Type:

Expression profiling by array

Platform:

GPL5780

6 Samples

Download data: TXT

(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

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

Organism:

Escherichia coli K-12

Type:

Other

Platforms:

GPL19529 GPL19168

6 Samples

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(Submitter supplied) Despite the overwhelming information about sRNAs, one of the biggest challenges in the sRNA field is characterizing sRNA targetomes. Thus, we develop a novel method to identify RNAs that interact with a specific sRNA, regardless of the type of regulation (positive or negative) or targets (mRNA, tRNA, sRNA). This method is called MAPS: MS2 affinity purification coupled with RNA sequencing. As proof of principle, we identified RNAs bound to RyhB, a well-characterized E. more...

Organism:

Escherichia coli K-12

Type:

Other

Platform:

GPL19529

2 Samples

Download data: TXT

(Submitter supplied) Despite the overwhelming information about sRNAs, one of the biggest challenges in the sRNA field is characterizing sRNA targetomes. Thus, we develop a novel method to identify RNAs that interact with a specific sRNA, regardless of the type of regulation (positive or negative) or targets (mRNA, tRNA, sRNA). This method is called MAPS: MS2 affinity purification coupled with RNA sequencing. As proof of principle, we identified RNAs bound to RybB, a well-characterized E. more...

Organism:

Escherichia coli K-12

Type:

Other

Platform:

GPL19168

2 Samples

Download data: TXT

(Submitter supplied) During ribosomal and transfer RNA maturation, external transcribed spacer (ETS) and internal transcribed spacer (ITS) sequences are excised and, as non-functional by-products, are rapidly degraded. The 3’ETS of the glyW-cysT-leuZ polycistronic tRNA precursor was highly and specifically enriched by co-purification with at least two different small regulatory RNAs (sRNAs), RyhB and RybB. Both sRNAs were shown to base pair with the same region in the 3’ETS of leuZ (3’ETSleuZ). more...

Organism:

Escherichia coli K-12

Type:

Other

Platform:

GPL19168

2 Samples

Download data: TXT

(Submitter supplied) Purpose: The goals of this study are to identify the putative mRNA targets that are regulated by the 6C sRNA. We constuct an inducible vector to transiently overexpressed the 6C sRNA in M. smegmatis, and then we perform RNA-Seq to look for genes that are differicently expressed upon the over-expression of 6C sRNA, which we think these genes are the potential targets of the 6C sRNA.

Organism:

Mycolicibacterium smegmatis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25523

2 Samples

Download data: TXT

(Submitter supplied) MicF is a textbook example of a small regulatory RNA (sRNA) that acts on a trans-encoded target mRNA through imperfect base paring. The discovery of MicF as a post-transcriptional repressor of the major Escherichia coli porin OmpF established the paradigm for a meanwhile common mechanism of translational inhibition, through antisense sequestration of a ribosome binding site. However, whether MicF regulates additional genes has remained unknown for almost three decades. more...

Organism:

Salmonella enterica; Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344

Type:

Expression profiling by array

Platform:

GPL5780

6 Samples

Download data: TXT

(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