GEO DataSets

(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:

Escherichia coli; Homo sapiens

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:

Enterobacter cloacae; Escherichia coli; Enterobacter sp. BIDMC93

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 str. K-12 substr. MG1655; Escherichia coli BW25113

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

(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

(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

(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:

Pseudomonas aeruginosa PA14; Escherichia coli BW25113

Type:

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

Platforms:

GPL25344 GPL33546 GPL30881

27 Samples

Download data: CSV, FA, TXT

(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:

Homo sapiens; Escherichia coli

Type:

Other

Platforms:

GPL15520 GPL16085 GPL25368

30 Samples

Download data: TXT

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

Organism:

Escherichia coli str. K-12 substr. MG1655; Escherichia coli K-12

Type:

Expression profiling by high throughput sequencing; Other

Platforms:

GPL30519 GPL33080

102 Samples

Download data: BEDGRAPH

(Submitter supplied) How biomolecules condense to organize subcellular processes is of fundamental significance. Nitrogen-starved Escherichia coli form a single condensate, which we termed Bacterial Stress Body (BSB). Its formation is triggered by long polyphosphate chains, which scaffold the RNA chaperone Hfq into high molecular weight complexes with distinct sequence-specific RNA and DNA binding properties. We show that polyP is crucial for the stabilization of select RNAs, the sequestration of translation- and RNA metabolism-associated proteins that likely stall protein synthesis, and the specific nucleoid-associated localization of BSBs. more...

Organism:

Escherichia coli str. K-12 substr. MG1655

Type:

Other

Platform:

GPL33080

42 Samples

Download data: CSV

(Submitter supplied) How biomolecules condense to organize subcellular processes is of fundamental significance. Nitrogen-starved Escherichia coli form a single condensate, which we termed Bacterial Stress Body (BSB). Its formation is triggered by long polyphosphate chains, which scaffold the RNA chaperone Hfq into high molecular weight complexes with distinct sequence-specific RNA and DNA binding properties. We show that polyP is crucial for the stabilization of select RNAs, the sequestration of translation- and RNA metabolism-associated proteins that likely stall protein synthesis, and the specific nucleoid-associated localization of BSBs. more...

Organism:

Escherichia coli str. K-12 substr. MG1655

Type:

Expression profiling by high throughput sequencing

Platform:

GPL33080

56 Samples

Download data: CSV

(Submitter supplied) How biomolecules condense to organize subcellular processes is of fundamental significance. Nitrogen-starved Escherichia coli form a single condensate, which we termed Bacterial Stress Body (BSB). Its formation is triggered by long polyphosphate chains, which scaffold the RNA chaperone Hfq into high molecular weight complexes with distinct sequence-specific RNA and DNA binding properties. We show that polyP is crucial for the stabilization of select RNAs, the sequestration of translation- and RNA metabolism-associated proteins that likely stall protein synthesis, and the specific nucleoid-associated localization of BSBs. more...

Organism:

Escherichia coli K-12

Type:

Other

Platform:

GPL30519

4 Samples

Download data: BEDGRAPH

(Submitter supplied) We report using global regulator libraries based on the CRISPR-enabled trackable genome engineering (CREATE) method to engineer tolerance against multiple inhibitors in Escherichia coli. Deep mutagenesis libraries were rationally designed, constructed, and screened to target 34,340 mutations across 23 global regulators.These libraries were divided into G1, G2, G3, G4 and G5 sub-groups according to different gene functions (such as active sites, DNA binding sites, and predicted functional sites) . more...

Organism:

Escherichia coli str. K-12 substr. MG1655

Type:

Other

Platform:

GPL21117

5 Samples

Download data: TXT

(Submitter supplied) Role of L-arabinose on gene expression in E. coli O157:H7 TUV93-0 where CTRL samples were grown in the absence of L-arabinose and ARA samples were grown in the presence of L-arabinose.

Organism:

Escherichia coli O157:H7

Type:

Expression profiling by high throughput sequencing

Platform:

GPL34321

6 Samples

Download data: TXT

(Submitter supplied) In order to systematically assess the frequency and origin of stop codon recoding events, we designed a library of reporters. We introduced premature stop codons into mScarlet that enabled high-throughput quantification of protein synthesis termination errors in E. coli using fluorescent microscopy. We found that under stress conditions, stop codon recoding may occur with a rate as high as 80%, depending on the nucleotide context, suggesting that evolution frequently samples stop codon recoding events. more...

Organism:

Escherichia coli str. K-12 substr. MG1655

Type:

Other

Platform:

GPL33229

13 Samples

Download data: BAM

(Submitter supplied) The DNA damage inducible SOS response in bacteria serves to increase survival of the species. The SOS response first initiates error-free repair which is followed by error-prone repair. Here, we have employed a multi-omics approach to elucidate the temporal coordination of the SOS response using transcriptomics, signalomics, and metabolomics. Escherichia coli was grown in batch cultivation in bioreactors to ensure highly controlled conditions. more...

Organism:

Escherichia coli str. K-12 substr. MG1655

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21117

42 Samples

Download data: CSV

(Submitter supplied) Antimicrobial exposure can potentially lead to increased antimicrobial resistance plasmid transfer. RNA sequencing data was collected from conjugal pairs of Salmonella enterica and Escherichia coli exposed or not exposed to tetracycline over a time course to determine differences in transcript numbers associated with conjugation and tetracycline exposure. The samples were sequenced on the Illumina HiSeq X10 platform with the 150-bp paired-end kit. more...

Organism:

Salmonella enterica; Escherichia coli J53

Type:

Expression profiling by high throughput sequencing

Platform:

GPL34283

24 Samples

Download data: XLSX

(Submitter supplied) Recent studies have combined DNA methyltransferase footprinting of genomic DNA in nuclei with long-read sequencing, resulting in detailed chromatin maps for multi-kilobase stretches of genomic DNA from one cell. Nucleosome footprints and nucleosome-depleted regions can be identified, yielding unprecedented information concerning their degree of correlation within the same cell. The enzyme of choice is M.EcoGII, which methylates adenines in any sequence context, potentially resulting in very high resolution. more...

Organism:

Saccharomyces cerevisiae; Escherichia coli

Type:

Other

Platforms:

GPL32099 GPL29643

12 Samples

Download data: BAM, BED, BIGWIG