GEO DataSets

(Submitter supplied) The R-loop is a common chromatin feature presented from prokaryotic to eukaryotic genomes and has been revealed to be involved in multiple cellular processes. Here, we developed a novel R-loop profiling technique, ULI-ssDRIP-seq, to decte global R-loops from a limited number of cells. Based on this method, we profiled the R-loop landscapes during parental-to-zygotic transition and early development regulatory in zebrafish, and revealed a series of important characters of R-loops.

Organism:

Arabidopsis thaliana; Danio rerio; Escherichia coli; synthetic construct

Type:

Other; Expression profiling by high throughput sequencing

4 related Platforms

60 Samples

Download data: BW

(Submitter supplied) Microbial physiology plays a pivotal role in construction of a superior microbial cell factory for efficient production of desired products. Here we identified pcnB repression through genome-scale CRISPRi modulation combining fluorescence-activated cell sorting (FACS) and next-generation sequencing (NGS), which confers improved physiology for free fatty acids (FFAs) overproduction in Escherichia coli. more...

Organism:

Escherichia coli str. K-12 substr. MG1655

Type:

Other

Platform:

GPL26592

5 Samples

Download data: XLSX

(Submitter supplied) Microbial physiology plays a pivotal role in construction of a superior microbial cell factory for efficient production of desired products. Here we identified pcnB repression through genome-scale CRISPRi modulation combining fluorescence-activated cell sorting (FACS) and next-generation sequencing (NGS), which confers improved physiology for free fatty acids (FFAs) overproduction in Escherichia coli. more...

Organism:

Escherichia coli str. K-12 substr. MG1655

Type:

Expression profiling by high throughput sequencing

Platform:

GPL34485

6 Samples

Download data: XLS

(Submitter supplied) The dataset contains small RNAs that associated with HrAgo1 during heterologous expression in E. coli. The goal of the study was to determine what type of small RNAs associate with HrAgo1 and from what RNA transcripts these small RNAs are derived

Organism:

Escherichia coli

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL25368

1 Sample

Download data: XLSX

(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

(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

(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:

Yersinia pseudotuberculosis; Rickettsia prowazekii; Bartonella quintana; Mycobacterium avium; Homo sapiens; Streptobacillus moniliformis; Bartonella henselae; Francisella tularensis subsp. tularensis; Francisella tularensis subsp. holarctica; Leptospira interrogans; Rickettsia typhi; Mycobacterium tuberculosis variant bovis; Mycobacterium tuberculosis; Mycobacterium tuberculosis variant microti; Mycobacterium canetti; Orthohantavirus seoulense; Yersinia enterocolitica; Toxoplasma gondii; Salmonella enterica subsp. enterica serovar Typhimurium; Mammarenavirus choriomeningitidis; Orthohantavirus puumalaense; 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

Type:

Methylation profiling by array

Platform:

GPL21445

4 Samples

Download data: IDAT, TXT

(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

(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

(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

(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:

GPL21222 GPL34292

8 Samples

Download data: BW

(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:

GPL21222 GPL34292

4 Samples

Download data: BW

(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

(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:

GPL17342 GPL21222

19 Samples

Download data: TXT

(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

(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

(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

(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

(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

(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