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Items: 1 to 20 of 26012

1.

RNAP stalling-derived genome instability underlies ribosomal antibiotics efficacy and resistance evolution (ChIP-seq data)

(Submitter supplied) Bacteria often evolve antibiotic resistance through mutagenesis. However, the processes causing the mutagenesis have not been fully resolved. Here we found that a broad range of ribosome-targeting antibiotics caused mutations through an underexplored pathway. Focusing on the clinically important aminoglycoside gentamicin, we found that the translation inhibitor caused genome-wide premature stalling of RNA polymerase (RNAP) in a loci-dependent manner. more...
Organism:
Escherichia coli
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL25368
12 Samples
Download data: BED, TXT
Series
Accession:
GSE267245
ID:
200267245
2.

RNA Post-transcriptional Modifications of an Early-Stage Large Subunit Ribosomal Intermediate

(Submitter supplied) Protein production by the ribosomes is fundamental to life and proper assembly of the ribosome is required for protein production. The RNA, which is post-transcriptionally modified, provides the platform for ribosome assembly. Thus, a complete understanding of ribosome assembly requires the determination of the RNA post-transcriptional modifications in all the ribosome assembly intermediates and on each pathway. more...
Organism:
Escherichia coli
Type:
Other
Platform:
GPL16085
3 Samples
Download data: CSV
Series
Accession:
GSE232539
ID:
200232539
3.

Spermine-induced DNA methylation change in human macrophages

(Submitter supplied) Polyamines, crucial molecules involved in cell proliferation and growth, play a pivotal role in cancer development and progression. Within the tumor microenvironment, macrophages, key components of the immune system, exhibit a complex relationship with polyamines. Evidence suggests that polyamines can modulate macrophage polarization, influencing their functional phenotypes. Here, we detected the gene DNA methylation changes in spermine-stimulated human macrophages isolated from PBMCs and TAMs.
Organism:
Leptospira interrogans; Rickettsia typhi; Mycobacterium tuberculosis variant bovis; Mycobacterium tuberculosis; Mycobacterium tuberculosis variant microti; Mycobacterium canetti; Orthohantavirus seoulense; Yersinia pseudotuberculosis; Rickettsia prowazekii; Bartonella quintana; Mycobacterium avium; Homo sapiens; Streptobacillus moniliformis; Bartonella henselae; Francisella tularensis subsp. tularensis; Francisella tularensis subsp. holarctica; Campylobacter jejuni; Francisella tularensis subsp. novicida; Yersinia pestis; Staphylococcus aureus; Mycobacterium avium subsp. paratuberculosis; Cowpox virus; Escherichia coli O157:H7; Francisella tularensis subsp. mediasiatica; Paslahepevirus balayani; Yersinia enterocolitica; Toxoplasma gondii; Salmonella enterica subsp. enterica serovar Typhimurium; Mammarenavirus choriomeningitidis; Orthohantavirus puumalaense
Type:
Methylation profiling by array
Platform:
GPL21445
4 Samples
Download data: IDAT, TXT
Series
Accession:
GSE267014
ID:
200267014
4.

Bacteria conjugate ubiquitin-like proteins to interfere with phage assembly

(Submitter supplied) Multiple immune pathways in humans conjugate ubiquitin-like proteins to virus and host molecules as a means of antiviral defense. Here we studied an anti-phage defense system in bacteria, comprising a ubiquitin-like protein, ubiquitin-conjugating enzymes E1 and E2, and a deubiquitinase. We show that during phage infection, this system specifically conjugates the ubiquitin-like protein to the phage central tail fiber, a protein at the tip of the tail that is essential for tail assembly as well as for recognition of the target host receptor. more...
Organism:
Escherichia coli; Caulobacter sp. Root343
Type:
Expression profiling by high throughput sequencing
Platforms:
GPL34341 GPL32081
12 Samples
Download data: XLSX
Series
Accession:
GSE262579
ID:
200262579
5.

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...
Organism:
Escherichia coli
Type:
Other
Platform:
GPL16085
8 Samples
Download data: BEDGRAPH
Series
Accession:
GSE235661
ID:
200235661
6.

Transcriptome analysis of Escherichia coli TO114 under salt stress

(Submitter supplied) Here, we treated Escherichia coli strain TO114 expressing a halotolerant cyanobacterium Halothece sp. PCC7418-derived NhaC Na+/H+ antiporter (H2569) with salt stress (0.4 M NaCl) and performed RNA sequencing analysis.
Organism:
Escherichia coli
Type:
Expression profiling by high throughput sequencing
Platform:
GPL25368
3 Samples
Download data: XLSX
Series
Accession:
GSE264731
ID:
200264731
7.

Antagonistic conflict between transposon-encoded introns and guide RNAs

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Escherichia coli; Clostridium senegalense
Type:
Other; Expression profiling by high throughput sequencing
Platforms:
GPL34292 GPL21222
8 Samples
Download data: BW
Series
Accession:
GSE261344
ID:
200261344
8.

Antagonistic conflict between transposon-encoded introns and guide RNAs (RNA-Seq)

(Submitter supplied) TnpB nucleases represent the evolutionary precursors to CRISPR-Cas12 and are widespread in all domains of life. IS605-family TnpB homologs function in bacteria as programmable RNA-guided homing endonucleases driving transposon maintenance through DSB-stimulated homologous recombination. Here we uncover molecular mechanisms of transposition lifecycle of IS607-family elements that, remarkably, also encode group I introns. more...
Organism:
Escherichia coli; Clostridium senegalense
Type:
Expression profiling by high throughput sequencing
Platforms:
GPL34292 GPL21222
4 Samples
Download data: BW
Series
Accession:
GSE261343
ID:
200261343
9.

Antagonistic conflict between transposon-encoded introns and guide RNAs (RIP-Seq)

(Submitter supplied) TnpB nucleases represent the evolutionary precursors to CRISPR-Cas12 and are widespread in all domains of life. IS605-family TnpB homologs function in bacteria as programmable RNA-guided homing endonucleases driving transposon maintenance through DSB-stimulated homologous recombination. Here we uncover molecular mechanisms of transposition lifecycle of IS607-family elements that, remarkably, also encode group I introns. more...
Organism:
Escherichia coli
Type:
Other
Platform:
GPL21222
4 Samples
Download data: BW
Series
Accession:
GSE261342
ID:
200261342
10.

The genetic architecture of protein interaction affinity and specificity

(Submitter supplied) Proteins function in crowded cellular environments in which they must bind to specific target proteins but also avoid binding to many other off-target proteins. In large protein families this task is particularly challenging because many off-target proteins have very similar structures. How this specificity of physical protein-protein interactions in cellular networks is encoded and evolves is not very well understood. more...
Organism:
Escherichia coli; Saccharomyces cerevisiae
Type:
Other
Platforms:
GPL21222 GPL17342
19 Samples
Download data: TXT
Series
Accession:
GSE245326
ID:
200245326
11.

Functional CRISPR-Cas9 knockout screening of the genetic determinants of human fibroblast migration propensity

(Submitter supplied) Directional cell migration plays a central role in a wide range of physiological and pathological conditions, such as inflammation and cancer. Steps involved in cell migration include cell polarization, formation of membrane protrusions at the cell front side and adhesion disassembly at the rear side, and a general cytoskeletal rearrangement. However, there are cell-specific and context-specific molecular events acting in the process. more...
Organism:
Homo sapiens; Escherichia coli
Type:
Other
Platforms:
GPL11154 GPL14548
11 Samples
Download data: TXT
Series
Accession:
GSE266226
ID:
200266226
12.

Adenine effect on Enterohemorraghic E.coli

(Submitter supplied) Previous experiments have shown that E. feacalis increases EHEC virulence by secreting adenine, this RNAseq aims to understand the molecular mechanism underlaying adenine role on EHEC
Organism:
Escherichia coli
Type:
Expression profiling by high throughput sequencing
Platform:
GPL25368
20 Samples
Download data: TXT
Series
Accession:
GSE244178
ID:
200244178
13.

TnpB homologs exapted from transposons are RNA-guided transcription factors

(Submitter supplied) Transposon-encoded tnpB and iscB genes encode RNA-guided DNA nucleases that promote their own selfish spread through targeted DNA cleavage and homologous recombination. These widespread gene families were repeatedly domesticated over evolutionary timescales, leading to the emergence of diverse CRISPR-associated nucleases including Cas9 and Cas12. We set out to test the hypothesis that TnpB nucleases may have also been repurposed for novel, unexpected functions other than CRISPR-Cas. more...
Organism:
Escherichia coli; Enterobacter sp. BIDMC93; Enterobacter cloacae
Type:
Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing; Other
4 related Platforms
51 Samples
Download data: BED, BW, XLSX
Series
Accession:
GSE245749
ID:
200245749
14.

Robust Host Engineering: Enhancing Escherichia coli´s Abiotic Stress Resistance through Ornithine Lipid Membrane Modification

(Submitter supplied) Transcriptome analysis revealed that strains had differentially expressed stress and membrane-related genes compared to the control strain
Organism:
Escherichia coli
Type:
Expression profiling by high throughput sequencing
Platform:
GPL25368
8 Samples
Download data: TXT, XLSX
Series
Accession:
GSE233657
ID:
200233657
15.

Motility-activating mutations upstream of flhDC reduce acid shock survival of Escherichia coli

(Submitter supplied) Many neutralophilic bacterial species try to evade acid stress with an escape strategy, which is reflected in the increased expression of genes coding for flagellar components. Extremely acid-tolerant bacteria, such as Escherichia coli, survive the strong acid stress, e.g. in the stomach of vertebrates. Recently, we were able to show that the induction of motility genes in E. coli is strictly dependent on the degree of acid stress, i.e. more...
Organism:
Escherichia coli BW25113; Escherichia coli str. K-12 substr. MG1655
Type:
Expression profiling by high throughput sequencing
Platforms:
GPL32899 GPL34252
12 Samples
Download data: XLSX
Series
Accession:
GSE260455
ID:
200260455
16.

A new reagent for in vivo structure probing of RNA G and U residues that improves RNA structure prediction alone and combined with DMS

(Submitter supplied) A key to understanding the roles of RNA in regulating gene expression is knowing their structures in vivo. One way to obtain this information is through probing structures of RNA with chemicals. To probe RNA structure directly in cells, membrane-permeable reagents that modify the Watson-Crick (WC) face of unpaired nucleotides can be used. While dimethyl sulfate (DMS) has led to substantial insight into RNA structure, it has limited nucleotide specificity in vivo, with WC face reactivity only at Adenine (A) and Cytosine (C) at neutral pH. more...
Organism:
Escherichia coli
Type:
Other
Platform:
GPL32081
33 Samples
Download data: TXT
Series
Accession:
GSE254895
ID:
200254895
17.

A cell-free pipeline for recreating methylation patterns radically enhances DNA transformation in bacteria

(Submitter supplied) The bacterial world offers diverse strains for understanding medical and environmental processes and for engineering synthetic-biology chasses. However, genetically manipulating these strains has faced a long-standing bottleneck: how to efficiently transform DNA. Here we report IMPRINT, a generalized, rapid and scalable approach to overcome DNA restriction, a prominent barrier to transformation. IMPRINT utilizes cell-free systems to express DNA methyltransferases from the bacterial host’s restriction-modification systems. more...
Organism:
Escherichia coli; Bifidobacterium breve
Type:
Other
Platforms:
GPL25368 GPL33564
7 Samples
Download data: TSV
Series
Accession:
GSE240651
ID:
200240651
18.

RpoS acts as a global repressor of virulence gene expression in Escherichia coli O104:H4 and enteroaggregative E. coli

(Submitter supplied) In 2011, in Germany, Escherichia coli O104:H4 caused the enterohemorrhagic E. coli (EHEC) outbreak with the highest incidence rate of hemolytic uremic syndrome. This pathogen carries an exceptionally potent combination of EHEC- and enteroaggregative E. coli (EAEC)-specific virulence factors. Here, we identified an E. coli O104:H4 isolate that carried a single nucleotide polymorphism (SNP) in the start codon (ATG>ATA) of rpoS, encoding the alternative sigma factor S. more...
Organism:
Escherichia coli
Type:
Expression profiling by high throughput sequencing
Platform:
GPL21222
12 Samples
Download data: CSV
Series
Accession:
GSE243699
ID:
200243699
19.

The modification landscape of P. aeruginosa tRNAs

(Submitter supplied) RNA modifications have a substantial impact on tRNA function. While modifications in the anticodon loop play an important role in translational fidelity, modifications in the tRNA core influence tRNA structural stability. In bacteria, tRNA modifications play important roles in the stress response and expression of virulence factors. While tRNA modifications are well characterized in a few model organisms, our knowledge of tRNA modifications in human pathogens, such as Pseudomonas aeruginosa is lacking. more...
Organism:
Escherichia coli BW25113; Pseudomonas aeruginosa PA14
Type:
Non-coding RNA profiling by high throughput sequencing; Expression profiling by high throughput sequencing
Platforms:
GPL25344 GPL30881 GPL33546
27 Samples
Download data: CSV, FA, TXT
Series
Accession:
GSE236676
ID:
200236676
20.

Dual Barcode is Essential for the Specificity of DSB Repair Capture

(Submitter supplied) We discovered that PCR-mediated template switching poses a significant challenge in ensemble tagged PCR, particularly in the template sequences with high similarities, which we successfully addressed by introducing a dual barcode. Template switching presents in repair sequencing (repair seq) and severely interfere the interpretation of the association between repair outcomes and the sgRNA in the vicinity. more...
Organism:
Escherichia coli; Homo sapiens
Type:
Other
Platforms:
GPL15520 GPL25368 GPL16085
30 Samples
Download data: TXT
Series
Accession:
GSE253191
ID:
200253191
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