GEO DataSets

(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) RNA-seq analysis of cells with pulsed overexpression of SdsR Most small noncoding RNAs (sRNAs) are known to base pair with target mRNAs and regulate their stability or translation with the help of Hfq to trigger various changes in cell metabolism. SdsR (also known as RyeB), which is a member of the RpoS regulon, was reported as an abundant sRNA that represses tolC and mutS in E. coli. It is known to be specific to the stationary phase and is not expressed during the exponential phase, but no previous study had examined the importance of this growth phase-dependent regulation for cell growth and survival. more...

Organism:

Escherichia coli str. K-12 substr. MG1655

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18956

3 Samples

Download data: TXT

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

Type:

Expression profiling by array

Platform:

GPL5780

6 Samples

Download data: TXT

(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 C6706

Type:

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

Platforms:

GPL26051 GPL26050

16 Samples

Download data

(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) 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) The control of amino acid synthesis and transport in bacteria has been well-investigated at the transcriptional level. The discovery of a small Hfq-dependent regulatory RNA, GcvB, added another layer of gene expression control at the post-transcriptional level. GcvB RNA has been shown to directly regulate multiple ABC transporters for amino acids in E. coli and Salmonella using a highly conserved G/U-rich domain, R1. more...

Organism:

Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344

Type:

Expression profiling by array

Platform:

GPL11416

8 Samples

Download data: TXT

(Submitter supplied) Investigation of whole genome gene expression level changes in Listeria monocytogenes LO28 delta-lhrC1-5 mutant, compared to the wild type strain. The lhrC1-5 genes encode the regulatory sRNAs LhrC1-5. The microarray studied the gene expression of unstressed cells and cells exposed to cefuroxime for 30 min. The lhrC1-5 mutant employed in this study is further described in Sievers et al. (2014) A multicopy sRNA of Listeria monocytogenes regulates expression of the virulence adhesin LapB. more...

Organism:

Listeria monocytogenes LO28; Listeria monocytogenes

Type:

Expression profiling by array

Platform:

GPL18538

12 Samples

Download data: PAIR

(Submitter supplied) Understanding RNA processing and turnover requires knowledge of cleavages by major endoribonucleases within a living cell. We have employed TIER-Seq (transiently inactivating an endoribonuclease followed by RNA-Seq) to profile cleavage products of the essential endoribonuclease RNase E in Salmonella enterica. A dominating cleavage signature is the location of a uridine two nucleotides downstream in a single-stranded segment, which we rationalize structurally as a key recognition determinant that may favor RNase E catalysis. more...

Organism:

Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19729

8 Samples

Download data: WIG

(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) RNA-seq analysis of cells with an ryeA or sdsR promoter mutation In Escherichia coli, SdsR and RyeA, a unique pair of mutually cis-encoded sRNAs, act as toxin and antitoxin, respectively. They are located in the same intergenic region, but transcribed in bidirectional way. Expression of SdsR is reciprocally related to that of RyeA; however, it remains unclear how their syntheses are regulated by each other. more...

Organism:

Escherichia coli str. K-12 substr. MG1655

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18956

8 Samples

Download data: TXT

(Submitter supplied) The alternative subunit of RNA polymerase RpoS/σS controls a global adaptive response allowing many Gram-negative bacteria to survive nutrient deprivation and various stresses and contributes to biofilm formation and virulence of Salmonella enterica serovar Typhimurium. We have addressed an important but poorly understood aspect of σS-dependent control; that of a repressor. The general assumption is that negative regulation of gene expression by σS is mainly a passive phenomenon, due to competition between σS and other sigma factors for binding to a limited amount of core RNA polymerase (RNAP). more...

Organism:

Salmonella enterica subsp. enterica serovar Typhimurium

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17070

9 Samples

Download data: XLS

(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) We have deep sequenced the small transcriptome of Escherichia coli growing in LB and in MOPS, in exponential and stationary phase, and analyzed the resulting reads by a novel pipeline STARPA (Stable RNA Processing Product Analyzer). Our analysis reveals over 14,000 small transcripts enriched during both growth stages. RNA samples were collected from total RNA pools or from crude ribosome pools and then size selected by electrophoresis to limit the products to 20-300nt.

Organism:

Escherichia coli str. K-12 substr. MG1655

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL15010

16 Samples

Download data: 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) This SuperSeries is composed of the SubSeries listed below.

Organism:

Escherichia coli K-12

Type:

Other

Platforms:

GPL19168 GPL19529

6 Samples

Download data

(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