Similar studies for GEO DataSets (Select 200102381) - GEO DataSets

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Items: 20

Select item 2001023811.

The contribution of the post-transcriptional regulator CsrA to RNA stability

(Submitter supplied) Analysis of the contribution of the post-transcriptional regulator CsrA to RNA stability during exponential growth in Escherichia coli

Organism:: Escherichia coli str. K-12 substr. MG1655

Type:: Expression profiling by high throughput sequencing

Platform:: GPL15010
20 Samples

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Series

Accession:: GSE102381

ID:: 200102381

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Select item 2001023862.

The contribution of the post-transcriptional regulator CsrA to RNA stability and translation and identification of binding partners

(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

Platform:: GPL15010
50 Samples

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Series

Accession:: GSE102386

ID:: 200102386

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Select item 2001023853.

The contribution of the post-transcriptional regulator CsrA to translation

(Submitter supplied) Analysis of the contribution of the post-transcriptional regulator CsrA to translation during exponential growth in Escherichia coli

Organism:: Escherichia coli str. K-12 substr. MG1655

Type:: Expression profiling by high throughput sequencing; Other

Platform:: GPL15010
20 Samples

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Series

Accession:: GSE102385

ID:: 200102385

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Select item 2001023804.

RNA binding partners of the post-transcriptional regulator CsrA

(Submitter supplied) Analysis of RNA binding partners of the post-transcriptional regulator CsrA to translation during exponential growth in Escherichia coli

Organism:: Escherichia coli str. K-12 substr. MG1655

Type:: Other

Platform:: GPL15010
10 Samples

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Series

Accession:: GSE102380

ID:: 200102380

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Select item 2001066335.

Global maps of ProQ binding in vivo reveal target recognition via RNA structure and stability control at mRNA 3' ends

(Submitter supplied) In this study binding sites for the RNA-binding protein ProQ was determined in Salmonella and Escherichia coli

Organism:: Escherichia coli str. K-12 substr. MG1655; Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344

Type:: Other

Platforms:: GPL21117 GPL20056
10 Samples

Download data: WIG

Series

Accession:: GSE106633

ID:: 200106633

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Select item 2000940686.

The Legionella pneumophila genome evolved to accommodate multiple regulatory mechanisms controlled by the CsrA-system

(Submitter supplied) The RNA binding protein CsrA is the master regulator of the bi-phasic life cycle of Legionella pneumophila governing virulence expression in this intracellular pathogen. The goal of the study was to use deep sequencing of RNA enriched by co-immunoprecipitation with epitope tagged CsrA to identify CsrA-associated transcripts at the genome level. We found 478 mRNAs or non-coding RNAs to be targets of CsrA. more...

Organism:: Legionella pneumophila str. Paris

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

Platform:: GPL22984
10 Samples

Download data: WIG

Series

Accession:: GSE94068

ID:: 200094068

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Select item 2001073307.

E. coli MazF does not create specialized ribosomes that translate leaderless mRNAs, but instead blocks rRNA maturation and ribosome biogenesis

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

Organism:: Escherichia coli

Type:: Expression profiling by high throughput sequencing; Other

Platforms:: GPL14548 GPL21222
19 Samples

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Series

Accession:: GSE107330

ID:: 200107330

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Select item 2001073298.

E. coli MazF does not create specialized ribosomes that translate leaderless mRNAs, but instead blocks rRNA maturation and ribosome biogenesis [5'OH-seq]

(Submitter supplied) The purpose of this experiment was to characterize MazF cleavage specificity with single-nucleotide resolution by enriching and sequencing 5’-OH ends (a 5’-OH end is generated by MazF cleavage).

Organism:: Escherichia coli

Type:: Other

Platform:: GPL14548
2 Samples

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Series

Accession:: GSE107329

ID:: 200107329

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Select item 2001073289.

E. coli MazF does not create specialized ribosomes that translate leaderless mRNAs, but instead blocks rRNA maturation and ribosome biogenesis [Ribo-Seq]

(Submitter supplied) The purpose of this experiment was to assess translation of mRNA after MazF expression to determine if cleavage events resulted in a loss in ribosome footprints.

Organism:: Escherichia coli

Type:: Other

Platform:: GPL21222
3 Samples

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Series

Accession:: GSE107328

ID:: 200107328

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Select item 20010732710.

E. coli MazF does not create specialized ribosomes that translate leaderless mRNAs, but instead blocks rRNA maturation and ribosome biogenesis [RNA-seq]

(Submitter supplied) The purpose of this experiment was to characterize MazF cleavage specificity and locations of cleavage genome-wide in E. coli and also identify any leaderless transcripts .To do this, MazF was expressed in a ΔmazF background and compared to an empty vector. rRNA-subtracted samples were used to assess cleavage in the mRNA, and total RNA samples were used to assess changes in the rRNA.

Organism:: Escherichia coli

Type:: Expression profiling by high throughput sequencing

Platform:: GPL21222
14 Samples

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Series

Accession:: GSE107327

ID:: 200107327

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Select item 20007481011.

Genomic Targets and Features of BarA-UvrY (-SirA) Signal Transduction Systems

(Submitter supplied) Using ChIP-exo, we have identified at single nucleotide resolution genomic binding sites for UvrY in E. coli and its homolog SirA in S. Typhimurium.

Organism:: Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S; Escherichia coli str. K-12 substr. MG1655

Type:: Genome binding/occupancy profiling by high throughput sequencing

Platforms:: GPL15010 GPL20046
2 Samples

Download data: TXT

Series

Accession:: GSE74810

ID:: 200074810

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Select item 20010783512.

Analysis of the contribution of the post-transcriptional regulator CsrA to RNA stability in Salmonella during growth in LB and mLPM media

(Submitter supplied) Analysis of the contribution of the post-transcriptional regulator CsrA to RNA stability in Salmonella during growth in LB and mLPM media

Organism:: Salmonella enterica subsp. enterica serovar Typhimurium

Type:: Other

Platform:: GPL17070
39 Samples

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Series

Accession:: GSE107835

ID:: 200107835

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Select item 20010783413.

Analysis of the contribution of the post-transcriptional regulator CsrA to translation during exponential growth in Escherichia coli

(Submitter supplied) Analysis of the contribution of the post-transcriptional regulator CsrA to translation during exponential growth in Escherichia coli

Organism:: Salmonella enterica subsp. enterica serovar Typhimurium

Type:: Expression profiling by high throughput sequencing; Other

Platform:: GPL17070
32 Samples

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Series

Accession:: GSE107834

ID:: 200107834

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Select item 20007442514.

Global RNA recognition patterns of post‐transcriptional regulators Hfq and CsrA revealed by UV crosslinking in vivo

(Submitter supplied) The molecular roles of many RNA‐binding proteins in bacterial post‐transcriptional gene regulation are not well understood. Approaches combining in vivo UV crosslinking with RNA deep sequencing (CLIP‐seq) have begun to revolutionize the transcriptome‐wide mapping of eukaryotic RNA‐binding protein target sites. We have applied CLIP‐seq to chart the target landscape of two major bacterial post‐transcriptional regulators, Hfq and CsrA, in the model pathogen Salmonella Typhimurium. more...

Organism:: Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344

Type:: Expression profiling by high throughput sequencing

Platform:: GPL20056
12 Samples

Download data: WIG

Series

Accession:: GSE74425

ID:: 200074425

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Select item 20015297415.

Grad-seq shines light on unrecognized RNA and protein complexes in the model bacterium Escherichia coli

(Submitter supplied) Stable protein complexes, including those formed with RNA, are major building blocks of every living cell. Escherichia coli has been the leading organism with respect to global bacterial protein-protein networks. However, there has been no global census of RNA/protein complexes in this model species of microbiology. Here, we performed Grad-seq to establish an RNA/protein complexome, reconstructing sedimentation profiles in a glycerol gradient for ~85% of all E. more...

Organism:: Escherichia coli

Type:: Expression profiling by high throughput sequencing

Platform:: GPL21222
22 Samples

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Series

Accession:: GSE152974

ID:: 200152974

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Select item 20010341516.

Metabolome and transcriptome-wide effects of the carbon storage regulator A in enteropathogenic Escherichia coli.

(Submitter supplied) The carbon storage regulator A (CsrA) is a conserved swivel of a global regulatory system known to regulate central carbon pathways, biofilm formation, motility, and pathogenicity. The aim of this study was to characterize changes in major metabolic pathways induced by CsrA in the human enteropathogenic Escherichia coli (EPEC) strain E2348/69. The EPEC strain E2348/69 and a csrA deletion mutant were grown under virulence factor inducing conditions and characterized by a combined analysis of their metabolomes and transcriptomes. more...

Organism:: Escherichia coli

Type:: Expression profiling by high throughput sequencing

Platform:: GPL18133
6 Samples

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Series

Accession:: GSE103415

ID:: 200103415

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Select item 20003133317.

Elucidation and validation of new targets of the global regulator PdhR in Escherichia coli

(Submitter supplied) The pyruvate dehydrogenase regulator protein (PdhR) of Escherichia coli acts as a transcriptional regulator in a pyruvate dependent manner to control central metabolic fluxes. However, the complete PdhR regulon has not yet been uncovered. To achieve an extended understanding of its gene regulation network, we combined large-scale network inference and experimental verification of results obtained by a systems biology approach.

Organism:: Escherichia coli str. K-12 substr. MG1655; Escherichia coli; Escherichia coli O157:H7 str. EDL933; Escherichia coli CFT073; Escherichia coli O157:H7 str. Sakai

Type:: Expression profiling by array

Platform:: GPL13359
24 Samples

Download data: TXT

Series

Accession:: GSE31333

ID:: 200031333

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Select item 20023566118.

Interrogation of RNA-protein interaction dynamics in bacterial growth

(Submitter supplied) RNA-protein interactions are fundamental for bacterial homeostasis. However, we lack a system-wide understanding of their dynamics upon environmental perturbation. In this study, we have characterised the dynamics of 91% of the Escherichia coli proteome and the RNA-interaction properties of 271 RNA-binding proteins (RBPs) at different growth phases. We find that 68% of RBPs differentially bind RNA across growth phases and reveal novel RBP functions for proteins like the chaperone HtpG, a new tRNA-binding protein. more...