GEO DataSets

(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

Platform:

GPL17439

4 Samples

Download data

(Submitter supplied) DsrA regulatory RNA represses both hns and rbsD mRNAs through distinct mechanisms in Escherichia coli

Organism:

Escherichia coli str. K-12 substr. MG1655

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17439

2 Samples

Download data: TXT

(Submitter supplied) DsrA regulatory RNA represses both hns and rbsD mRNAs through distinct mechanisms in Escherichia coli

Organism:

Escherichia coli str. K-12 substr. MG1655

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17439

2 Samples

Download data: TXT

(Submitter supplied) Recently, we developed an in vivo technology to draw the interacting map of a specific small regulatory RNA (sRNA). We called it MAPS for MS2-affinity purification coupled with RNA sequencing. Using this technology, we already revealed the targetome of RyhB, RybB and DsrA, three well-characterized sRNAs in Escherichia coli. In this study, we performed MAPS with CyaR sRNA.

Organism:

Escherichia coli K-12

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19168

2 Samples

Download data: TXT

(Submitter supplied) Recently, we developed an in vivo technology to draw the interacting map of a specific small regulatory RNA (sRNA). We called it MAPS for MS2-affinity purification coupled with RNA sequencing. Using this technology, we already revealed the targetome of RyhB, RybB and DsrA, three well-characterized sRNAs in Escherichia coli. In this study, we perform MAPS with RprA sRNA.

Organism:

Escherichia coli K-12

Type:

Other

Platform:

GPL19168

2 Samples

Download data: TXT

(Submitter supplied) To elucidated the regulatory effect of DsrA on the oxidative resistance in Salmonella enterica serovar Typhimurium. RNA sample of wild-type and DsrA-deletion strain that grown in LB medium or H2O2 stress were extracted. Three biological replicates were carried out per sample. RNA sample was sequenced with Illumina HiSeq 4000 System. DESeq2 method was used to calculate the differentially expressed genes. more...

Organism:

Salmonella enterica subsp. enterica serovar Typhimurium

Type:

Expression profiling by high throughput sequencing

Platform:

GPL27471

12 Samples

Download data: XLS

(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) Recently, we developed an in vivo technology to draw the interacting map of a specific small regulatory RNA (sRNA). We called it MAPS for MS2-affinity purification coupled with RNA sequencing. Using this technology, we already revealed the targetome of RyhB, RybB and DsrA, three well-characterized sRNAs in Escherichia coli. In this study, we perform MAPS with GcvB, a sRNA involved in amino acid metabolism.

Organism:

Escherichia coli K-12

Type:

Other

Platform:

GPL19168

2 Samples

Download data: TXT

(Submitter supplied) During glyW-cysT-leuZ polycistronic tRNA maturation, the 3’external transcribed spacer (3’ETS) sequence is excised and act as a sRNA sponge (Lalaouna et al., 2015). Using MS2-affinity purification coupled with RNA sequencing (MAPS), we demonstrated that 3’ETSleuZ 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 3’ETSleuZ. more...

Organism:

Escherichia coli K-12

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19168

2 Samples

Download data: TXT

(Submitter supplied) The first goal of the study was to identify genes differentially regulated by MavR in EHEC strain 86-24. The second goal was to identify direct targets of MavR through the MAPS protocol.

Organism:

Escherichia coli O157:H7

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL29711 GPL28511

10 Samples

Download data: TXT

(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) M9 glucose minimum media were analyzed for RNA expression. We use this expression information to show that mRNA level correlate with codon efficiency (Boel et al., Nature 2015)

Organism:

Escherichia coli

Type:

Expression profiling by array

Platform:

GPL3154

1 Sample

Download data: CEL, CHP

(Submitter supplied) The fasX gene encodes a small regulatory RNA in the group A Streptococcus (GAS). To determine the FasX regulon during GAS exposure to human plasma we compared parental strain MGAS2221 with isogenic fasX mutant strain 2221ΔFasX. Gene expression was analyzed 0, 15, and 60 minutes post-plasma exposure.

Organism:

Streptococcus pyogenes

Type:

Expression profiling by array

Platform:

GPL9080

12 Samples

Download data: CEL

(Submitter supplied) Environmental stress is detrimental to cell viability and requires an adequate reprogramming of cellular activities to maximize cell survival. We present a global analysis of the response of Escherichia coli to acute heat and osmotic stress. We combine deep sequencing of total mRNA and ribosome-protected fragments to provide a genome-wide map of the stress response at transcriptional and translational level. more...

Organism:

Escherichia coli str. K-12 substr. MC4100

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20183

10 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

(Submitter supplied) In response to low levels of magnesium (Mg2+), the PhoQP two component system induces the transcription of two convergent genes, one encoding a 31-amino acid protein denoted MgtS and the second encoding a small, regulatory RNA (sRNA) denoted MgrR. Previous studies showed that the MgtS protein interacts with and stabilizes the MgtA Mg2+ importer to increase intracellular Mg2+ levels, while the MgrR sRNA base pairs with the eptB mRNA thus affecting lipopolysaccharide modification. more...

Organism:

Escherichia coli; Escherichia coli str. K-12 substr. MG1655

Type:

Expression profiling by array

Platform:

GPL3154

4 Samples

Download data: CEL, CHP