txid562[Organism:noexp] - GEO DataSets

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Select item 2001359461.

K5 capsule and lipopolysaccharide are important in resistance to T4 phage attack in probiotic E. coli strain Nissle 1917

(Submitter supplied) Rapidly growing antibiotic resistance among gastrointestinal pathogens, and the ability of antibiotics to induce the virulence of these pathogens makes it increasingly difficult to rely on antibiotics to treat gastrointestinal infections. The probiotic E. coli strain Nissle 1917 (EcN) is the active component of the pharmaceutical preparation Mutaflor® and has been successfully used in the treatment of gastrointestinal disorders. more...

Organism:: Escherichia coli

Type:: Expression profiling by high throughput sequencing

Platform:: GPL21222
6 Samples

Download data: CSV, WIG

Series

Accession:: GSE135946

ID:: 200135946

SRA Run Selector

Select item 2001292852.

Evolving a new protein-DNA interface via a sequential introduction of permissive and specificity-switching mutations

(Submitter supplied) Specific interactions between proteins and DNA are essential to many biological processes. Yet it remains unclear how the diversification in DNA-binding specificity was brought about, and what were the mutational paths that led to changes in specificity. Using a pair of evolutionarily related DNA-binding proteins each with a different DNA preference (ParB and Noc: both having roles in bacterial chromosome maintenance), we show that specificity is encoded by a set of four residues at the protein-DNA interface. more...

Organism:: Escherichia coli

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

Platform:: GPL18133
30 Samples

Download data: TXT

Series

Accession:: GSE129285

ID:: 200129285

Analyze with GEO2R SRA Run Selector

Select item 2001352113.

PAIR-MaP visualizes RNA base pairing complexity in human and bacterial non-coding RNAs

(Submitter supplied) Structure probing experiments were performed on in vitro transcripts and E. coli and human cell cultures under natively extracted (cell-free) and in-cell conditions to benchmark the performance of the newly introduced PAIR-MaP correlated chemical probing strategy for detecting RNA duplexes. Multiple-hit dimethyl sulfate (DMS) probing was done using new buffer conditions that facilitate DMS modification of all four nucleotides.

Organism:: Vibrio vulnificus; Homo sapiens; Escherichia coli

Type:: Other

Platforms:: GPL16085 GPL27000 GPL15520
23 Samples

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Series

Accession:: GSE135211

ID:: 200135211

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Select item 2001342184.

Transcriptome analysis of C. glutamicum ΔaceE Δpyc versus ΔaceE

(Submitter supplied) The pyruvate dehydrogenase complex (PDHC) catalyzes the oxidative decarboxylation of pyruvate yielding acetyl-CoA and CO2. The PDHC-deficient Corynebacterium glutamicum strain ΔaceE is therefore lacking an important decarboxylation step in central metabolism. Additional inactivation of pyc, encoding pyruvate carboxylase, resulted in a >15 hour lag phase in the presence of glucose, while no growth defect was observed on gluconeogenetic substrates like acetate. more...

Organism:: Gluconobacter oxydans; Escherichia coli; Corynebacterium glutamicum; Corynebacterium glutamicum ATCC 13032; Pseudomonas putida KT2440; Bacillus subtilis subsp. subtilis str. 168

Type:: Expression profiling by array

Platform:: GPL26911
3 Samples

Download data: GPR

Series

Accession:: GSE134218

ID:: 200134218

Select item 2001262485.

Transcriptome analysis of cells carrying Type II Csp231I restriction-modification (RM) system reveal the crosstalk between two unrelated transcription factors - C protein and Rac prophage repressor

(Submitter supplied) Our transcriptome analysis supported by other in vivo and in vitro assays showed that C protein can directly silence the RacR repressor and thus affect the Rac prophage-related genes.

Organism:: Escherichia coli

Type:: Expression profiling by high throughput sequencing

Platform:: GPL18133
6 Samples

Download data: TXT

Series

Accession:: GSE126248

ID:: 200126248

SRA Run Selector

Select item 2001347926.

Molecular and immunological interrogation of a live-attenuated enterotoxigenic Escherichia coli vaccine highlights features unique to wild type infection

(Submitter supplied) Enterotoxigenic Escherichia coli (ETEC) infections are a common cause of diarrheal illness in low- and middle-income countries. The live-attenuated ACE527 vaccine, adjuvanted with double mutant LT (dmLT), affords clear but partial protection against ETEC challenge inhuman volunteers. Comparatively, initial wild-type ETEC challenge completely protects against severe diarrhea on homologous re-challenge...To investigate molecular determinants of protection, vaccine antigen content was compared to wild-type ETEC, and proteome microarrays were used to assess immune responses following vaccination and ETEC challenge... more...

Organism:: Escherichia coli; Homo sapiens

Type:: Protein profiling by protein array

Platform:: GPL26932
250 Samples

Download data: XLSX

Series

Accession:: GSE134792

ID:: 200134792

PubMed Full text in PMC Similar studies Analyze with GEO2R

Select item 2001079217.

Comparison of Corynebacterium glutamicum ATCC13032ΔftsR with ATCC13032

(Submitter supplied) In summary, we have identified and characterized FtsR as a transcriptional activator of the essential cell division protein FtsZ in C. glutamicum, providing a novel regulatory player in the process of cell division.

Organism:: Gluconobacter oxydans; Bacillus subtilis subsp. subtilis str. 168; Escherichia coli; Corynebacterium glutamicum; Corynebacterium glutamicum ATCC 13032

Type:: Expression profiling by array

Platform:: GPL16989
3 Samples

Download data: GPR

Series

Accession:: GSE107921

ID:: 200107921

PubMed Full text in PMC Similar studies Analyze with GEO2R

Select item 2001239748.

Comparison of Corynebacterium glutamicum Δsurf1 and wt

(Submitter supplied) To identify genes which are differentially expressed in Corynebacterium glutamicum in the cg2460 deletion strain, we performed DNA microarray analyses of C. glutamicum Δcg2460 compared to the WT.

Organism:: Gluconobacter oxydans; Escherichia coli; Corynebacterium glutamicum; Bacillus subtilis subsp. subtilis str. 168

Type:: Expression profiling by array

Platform:: GPL22792
4 Samples

Download data: GPR

Series

Accession:: GSE123974

ID:: 200123974

Select item 2001169429.

A systematic reassessment of N6-methyladenine in metazoan genomes

(Submitter supplied) We report the application of SMRT seqeuncing from Pacific Biosciences to study the DNA base modifications in dam-/dcm- and wild type E.coli.

Organism:: Escherichia coli

Type:: Methylation profiling by high throughput sequencing

Platform:: GPL24462
2 Samples

Download data: GFF

Series

Accession:: GSE116942

ID:: 200116942

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 20013263710.

RNAseq transcriptome analysis of K. pneumoniae MS6671 and E. coli MS8345 treated with PBT2

(Submitter supplied) The emergence of colistin resistance in carbapenem-resistant and extended-spectrum ß-lactamase (ESBL)-producing bacteria is a significant threat to human health, and new treatment strategies are urgently required. Here we investigated the ability of the safe-for-human use ionophore PBT2 to restore antibiotic sensitivity in several polymyxin-resistant, ESBL-producing, carbapenem resistant Gram-negative human pathogens. more...

Organism:: Escherichia coli; Klebsiella pneumoniae

Type:: Expression profiling by high throughput sequencing

Platforms:: GPL25164 GPL18133
12 Samples

Download data: TSV, TXT

Series

Accession:: GSE132637

ID:: 200132637

SRA Run Selector

Select item 20013199211.

Systematic identification of metabolites controlling gene expression in E. coli

(Submitter supplied) Cellular metabolism controls gene expression through allosteric interactions between metabolites and transcription factors. Methods to detect these regulatory interactions are mostly based on in vitro binding assays, but there are no methods to identify them at a genome-scale in vivo. Here we show that dynamic transcriptome and metabolome data identify metabolites that are potential effectors of transcription factors in E. more...

Organism:: Escherichia coli

Type:: Expression profiling by high throughput sequencing

Platform:: GPL26155
56 Samples

Download data: CSV

Series

Accession:: GSE131992

ID:: 200131992

SRA Run Selector

Select item 20012005212.

Bacterial RNase III cleaves long dsRNA at preferred sites

(Submitter supplied) Members of the ribonuclease (RNase) III family regulate gene expression by processing double-stranded (ds) RNA. The founding member of the family, Escherichia coli (Ec) RNase III, is the most comprehensively studied and its E38A mutant (EcE38A) is an economical reagent for the preparation of small interfering (si) RNA cocktails. Previously, it was shown that EcRNase III recognizes dsRNA with little specificity and that EcE38A mainly produces 23-nucleotide (nt) siRNAs. more...

Organism:: Escherichia coli; Aquifex aeolicus

Type:: Other

Platforms:: GPL16085 GPL25581
29 Samples

Download data: XLSX

Series

Accession:: GSE120052

ID:: 200120052

PubMed Full text in PMC Similar studies Analyze with GEO2R SRA Run Selector

Select item 20011773713.

Full-length RNA profiling reveals pervasive bidirectional transcription terminators in bacteria

(Submitter supplied) The complexity and intricacy of prokaryotic transcriptomes—once deemed well understood and simple—are increasingly being discovered and appreciated. The ability to determine full-length sequences of all transcripts in the cell is essential for understanding the gene regulatory repertoire of a species. Standard RNA-seq requires fragmentation of RNA for short-read sequencing, which automatically decouples the 5' sequence of a RNA molecule from its 3' sequence. more...

Organism:: Escherichia coli

Type:: Expression profiling by high throughput sequencing; Other; Genome binding/occupancy profiling by high throughput sequencing

Platforms:: GPL21222 GPL16085
47 Samples

Download data: WIG

Series

Accession:: GSE117737

ID:: 200117737

Select item 20012622814.

Comparison of expressed pdxJ variants on global gene expression in E. coli

(Submitter supplied) DNA microarray analyses was carried out to identify genes which are differentially expressed in E. coli when mutant variants of pdxJ are expressed that rescue growth of auxotrophic E. coli delta serB and delta serC mutants.

Organism:: Gluconobacter oxydans; Corynebacterium glutamicum; Escherichia coli BW25113; Escherichia coli; Pseudomonas putida KT2440; Bacillus subtilis subsp. subtilis str. 168

Type:: Expression profiling by array

Platform:: GPL23003
4 Samples

Download data: GPR

Series

Accession:: GSE126228

ID:: 200126228

Analyze with GEO2R

Select item 20011665515.

Comparison of Corynebacterium glutamicum ATCC 13032 + pEKEx2-malR with ATCC 13032 + pEKEx2

(Submitter supplied) Investigation of the impact of an overexpression of malR (cg3315) on gene expression under standard conditions (CGXII-Glucose)

Organism:: Escherichia coli; Corynebacterium glutamicum; Gluconobacter oxydans; Corynebacterium glutamicum ATCC 13032; Bacillus subtilis subsp. subtilis str. 168

Type:: Expression profiling by array

Platform:: GPL22561
3 Samples

Download data: GPR

Series

Accession:: GSE116655

ID:: 200116655

PubMed Full text in PMC Similar studies Analyze with GEO2R

Select item 20012228616.

In vivo analysis of Influenza A mRNA secondary structures identifies critical regulatory motifs

(Submitter supplied) The Influenza A virus (IAV) is a continuous health threat to humans as well as animals due to its high mutational rate and recurring epidemics and pandemics. The IAV genome is segmented and the eight negative-sense viral RNAs (vRNAs) are transcribed into positive sense RNAs (cRNAs) and viral messenger RNAs (vmRNAs) inside infected host cells. A role for the secondary structure of vmRNAs has been hypothesized and debated for many years, but knowledge on the structure vmRNAs adopt in vivo is currently missing. more...

Organism:: Influenza A virus; Escherichia coli

Type:: Other

Platforms:: GPL21222 GPL24947 GPL25780
20 Samples

Download data: FASTA, WIG

Series

Accession:: GSE122286

ID:: 200122286

PubMed Full text in PMC Similar studies Analyze with GEO2R SRA Run Selector

Select item 20012385417.

Transcript degradation and codon usage as gene regulation in a lytic phage

(Submitter supplied) We analyze transcript abundances of T7 over the course of an infection and find evidence for differential transcript degradation.

Organism:: Enterobacteria phage T7; Escherichia coli

Type:: Expression profiling by high throughput sequencing

Platform:: GPL25938
30 Samples

Download data: TSV

Series

Accession:: GSE123854

ID:: 200123854

SRA Run Selector

Select item 20012993618.

The extruded non-template strand determines the architecture of R-loops

(Submitter supplied) We show that these R-loop objects impose specific physical constraints on the DNA, as revealed by the presence of stereotypical angles in the surrounding DNA. Biochemical probing and mutagenesis experiments revealed that the formation of R-loop objects at Airn is dictated by the extruded non-template strand, suggesting that R-loops possess intrinsic sequence-driven properties. Consistent with this, we show that R-loops formed at the fission yeast gene sum3 do not form detectable R-loop objects. more...

Organism:: Escherichia coli

Type:: Methylation profiling by high throughput sequencing

Platform:: GPL24462
2 Samples

Download data: BED

Series

Accession:: GSE129936

ID:: 200129936

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 20012881219.

Systematic detection of amino acid substitutions in proteome reveals a mechanistic basis of ribosome errors and selection for translation fidelity

(Submitter supplied) The protein translation machinery and the genes it decodes co-evolved to achieve production throughput and accuracy. Nonetheless translation errors are frequent and they affect physiology, fitness and protein evolution. Mapping translation errors in proteomes and understanding their causes was hindered by lack of a proteome-wide experimental methodology. Here, we present the first methodology for systematic detection and quantification of errors in entire proteomes. more...

Organism:: Escherichia coli BW25113; Escherichia coli

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

Platforms:: GPL26343 GPL21222
9 Samples

Download data: CSV

Series

Accession:: GSE128812

ID:: 200128812

SRA Run Selector

Select item 20012660020.

Evolution of gene expression in one population of the Long-Term Evolution Experiment with Escherichia coli

(Submitter supplied) We used microarrays to study the changes in whole-genome expression profiles accompanying the evolution of one bacterial population propagated in glucose minimal medium for 20,000 generations.

Organism:: Escherichia coli; Escherichia coli B str. REL606

Type:: Expression profiling by array

Platform:: GPL3154
18 Samples

Download data

Series

Accession:: GSE126600

ID:: 200126600

PubMed Full text in PMC Similar studies Analyze with GEO2R

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