GEO DataSets

(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) 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) 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) 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 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) In this study, we performed MAPS (MS2-affinity purification coupled with RNA sequencing) to draw the interacting map of MicF small regulatory RNA in vivo.

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) UV-crosslining of protein-RNA complexes was employed to capture sRNA-mRNA interactions occuring on the RNA degradosome protein, RNase E, in enterohaemorhaggic E. coli. Abstract from associated mansucript: In many organisms small regulatory RNAs (sRNA) play important roles in the regulation of gene expression by base-pairing to specific target mRNAs. In enterohaemorrhagic E. coli (EHEC), sRNAs are encoded by both the “core” genome and in numerous horizontally acquired pathogenicity islands. more...

Organism:

Escherichia coli O157:H7 str. Sakai

Type:

Other

Platform:

GPL21393

2 Samples

Download data: GTF, HYB

(Submitter supplied) The virulon of Staphyloccocus aureus is controlled by intricate connections between transcriptional and post-transcriptional regulators including proteins and small non coding RNAs (sRNAs). Most of the sRNAs regulate gene expression through base-pairings with mRNAs. Here, we have applied and adapted the MS2-affinity purification approach coupled to RNA sequencing (MAPS) to determine the targetome of RsaA sRNA of S. more...

Organism:

Staphylococcus aureus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19006

6 Samples

Download data: XLSX

(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) We investigated the gene expression changed in the NCM3722 wild-type and gcvB deletion strains grown in glucose minimal medium, aiming to find novel target genes controlled by small RNA GcvB. In total, five differentially expressed genes (DEGs) were identified by Illumina sequencing using a cutoff with fold change>2 and q-value<0.01. Following physiological and molecular studies identified that the physiological roles of GcvB were beyond amino acids transportation and it regulates oxdative stress response of Escherichia coli through its control of OxyR.

Organism:

Escherichia coli

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21433

4 Samples

Download data: TXT