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Items: 1 to 20 of 14015

1.

Laboratory Evolution Experiments Help Identify a Predominant Site of ΔrnhA-dnaA Constitutive Stable DNA Replication Initiation

(Submitter supplied) The study evaluated the effect of cSDR on gene expression by comparing the gene expression states in ΔrnhA-dnaA and evolved suppressor mutants
Organism:
Escherichia coli str. K-12 substr. MG1655
Type:
Expression profiling by high throughput sequencing
Platform:
GPL18956
10 Samples
Download data: TXT
Series
Accession:
GSE135706
ID:
200135706
2.

Microbial metabolic reprogramming regulates intraspecific competition of Enterobacteriaceae in the inflamed gut

(Submitter supplied) Imbalance in beneficial and harmful bacteria underlies gastrointestinal diseases, such as inflammatory bowel disease. Here, we demonstrated that certain E. coli strains, specifically adherent-invasive E. coli (AIEC), utilize a serine metabolism pathway to outcompete other E. coli strains in the inflamed gut. In contrast, amino acid metabolism has a minimal effect on their competitive fitness in the healthy gut. more...
Organism:
Escherichia coli LF82
Type:
Expression profiling by high throughput sequencing
Platform:
GPL20215
8 Samples
Download data: TXT
Series
Accession:
GSE106412
ID:
200106412
3.

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
4.

Dts-seq: a simple method of library preparation for a highly reproducible characterization of the tRNA epitranscriptome by deep sequencing

(Submitter supplied) High-throughput sequencing of cellular tRNAs is severely hindered by the presence of base modifications. These modifications impair the reverse transcription (RT) enzyme and prevent a large fraction of transcripts to be converted into cDNA in conventional sequence library preparation. Recent attempts to circumvent this issue made use of enzymatic treatments to remove methyl groups (Cozen et al. 2015; Zeng et al. more...
Organism:
Escherichia coli str. K-12 substr. MG1655
Type:
Non-coding RNA profiling by high throughput sequencing
Platform:
GPL18956
15 Samples
Download data: TXT
Series
Accession:
GSE135937
ID:
200135937
5.

Impact of heavy atmospheric pollution on the transcriptome of Escherichia coli BW25113 and the adapted E. coli strain T56-1

(Submitter supplied) Expression profile of E. coli BW25113 grown under standard laboratory atmosphere with a fine particulate matter (PM2.5) concentration of 17 mg m-3, under urban polluted atmosphere with a PM2.5 of 230 mg m-3 or under diesel exhaust atmosphere with a PM2.5 of 613 mg m-3. Expression profile of the diesel exhaust atmosphere-adapted E. coli strain T56-1 grown under diesel exhaust atmosphere.
Organism:
Escherichia coli BW25113
Type:
Expression profiling by high throughput sequencing
Platform:
GPL25146
12 Samples
Download data: TXT
Series
Accession:
GSE115330
ID:
200115330
6.

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
7.

Engineering orthogonal signaling pathways reveals the sparse distribtion of protein protein interactions in sequence space

(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:
GPL21117
55 Samples
Download data
Series
Accession:
GSE120789
ID:
200120789
8.

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
Download data
Series
Accession:
GSE135211
ID:
200135211
9.

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
10.

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
11.

Engineering orthogonal signaling pathways reveals the sparse distribtion of protein protein interactions in sequence space [combinatorial_library_sort_seq]

(Submitter supplied) The cross compatibility of functional PhoQ-PhoP mutants with altered specificity residues was analyzed by sort seq. We cloned and combinatorially combined 79 PhoQ* and 71 PhoP* variants, producing a library with a theoretical diversity of 5,609. The library was then subjected to Sort-Seq, using fluorescence-activated cell sorting (FACS) and deep sequencing to quantify the signal responsiveness of variants in the library. more...
Organism:
Escherichia coli str. K-12 substr. MG1655
Type:
Other
Platform:
GPL21117
55 Samples
Download data: CSV
Series
Accession:
GSE120786
ID:
200120786
12.

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
13.

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
14.

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
15.

Polynucleotide phosphorylase promotes the stability and function of Hfq-binding sRNAs by degrading target mRNA-derived fragments

(Submitter supplied) In many gram-negative and some gram-positive bacteria small regulatory RNAs (sRNAs) that bind the RNA chaperone Hfq have a pivotal role in modulating virulence, stress responses, metabolism, and biofilm formation. These sRNAs recognize transcripts through base-pairing, and sRNA-mRNA annealing consequently alters the translation and/or stability of transcripts leading to changes in gene expression. We have previously found that the highly conserved 3'-to-5' exoribonuclease polynucleotide phosphorylase (PNPase) has an indispensable role in paradoxically stabilizing Hfq-bound sRNAs and promoting their function in gene regulation in Escherichia coli. more...
Organism:
Escherichia coli str. K-12 substr. MG1655
Type:
Expression profiling by high throughput sequencing; Other
Platform:
GPL15010
12 Samples
Download data: TXT, XLSX
Series
Accession:
GSE125368
ID:
200125368
16.

Multifaceted stoichiometry control of bacterial operons revealed by data-independent acquisition mass spectrometry

(Submitter supplied) More than half of the protein-coding genes in bacteria are organized in polycistronic operons composed of two or more genes. Whether the operon organization maintains the stoichiometric expression of the genes within an operon remain under debate. In this study, we performed a label-free data-independent acquisition hyper reaction monitoring mass-spectrometry (HRM-MS) experiment to quantify the Escherichia coli proteome in exponential phase and quantified 93.6% of the cytosolic proteins, covering 67.9% and 56.0% of the translating polycistronic operons in BW25113 and MG1655 strains, respectively. more...
Organism:
Escherichia coli BW25113
Type:
Expression profiling by high throughput sequencing
Platforms:
GPL25852 GPL25851
4 Samples
Download data: TXT
Series
Accession:
GSE122971
ID:
200122971
17.

Coordinate regulation of expression of SdsR toxin and its downstream pphA gene by RyeA antitoxin expression in Escherichia coli

(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
Series
Accession:
GSE122921
ID:
200122921
18.

RNA-seq of Escherichia coli K-12 MG1655 and Stx2 phage lysogens

(Submitter supplied) Here, we investigated the impact of Stx2 phage carriage on Escherichia coli (E. coli) K-12 MG1655 host gene expression. Using quantitative RNA-seq analysis, we compared the transcriptome of naïve MG1655 and the lysogens carrying the Stx2 phage of the 2011 E. coli O104:H4 outbreak strain or of the E. coli O157:H7 strain PA8, which share high degree of sequence similarity.
Organism:
Escherichia coli K-12
Type:
Expression profiling by high throughput sequencing
Platform:
GPL26204
9 Samples
Download data: CSV
Series
Accession:
GSE126710
ID:
200126710
19.

Expression data of enterohemorrhagic E. coli (EHEC) dicF mutant

(Submitter supplied) sRNAs play important roles in regulating gene expression post-transcriptionally. Here, we used RNA-seq to compare gene expression in a WT strain and a dicF1-4 deletion strain.
Organism:
Escherichia coli O157:H7 str. EDL933
Type:
Expression profiling by high throughput sequencing
Platform:
GPL24005
6 Samples
Download data: TXT
Series
Accession:
GSE123248
ID:
200123248
20.

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
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