GEO DataSets

(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 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; Yersinia pseudotuberculosis; Rickettsia prowazekii; Bartonella quintana; Mycobacterium avium; Homo sapiens; Streptobacillus moniliformis; Bartonella henselae; Francisella tularensis subsp. tularensis; Francisella tularensis subsp. holarctica

Type:

Methylation profiling by array

Platform:

GPL21445

4 Samples

Download data: IDAT, 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) Regulons for many transcription factors have been elucidated in model strains leading to an understanding of their role in producing physiological states. Comparative analysis of a regulon and its target genes between different strains of the same species is lacking. Ferric uptake regulator (Fur), involved in iron homeostasis, is one of the most conserved TFs, and is present in a wide range of bacteria. more...

Organism:

Salmonella enterica; Escherichia coli O157:H7; Escherichia coli; Escherichia coli K-12

Type:

Expression profiling by high throughput sequencing

4 related Platforms

36 Samples

Download data: CSV

(Submitter supplied) Regulons for many transcription factors have been elucidated in model strains leading to an understanding of their role in producing physiological states. Comparative analysis of a regulon and its target genes between different strains of the same species is lacking. Ferric uptake regulator (Fur), involved in iron homeostasis, is one of the most conserved TFs, and is present in a wide range of bacteria. more...

Organism:

Escherichia coli; Escherichia coli K-12; Escherichia coli O157:H7; Salmonella enterica

Type:

Genome binding/occupancy profiling by high throughput sequencing

4 related Platforms

36 Samples

Download data: GFF

(Submitter supplied) We report the different expression level of in vivo transcriptome and DMEM cultured bacteria E.coli O157:H7 samples. After obtaining RNA from mice colon and LB cultured free living cells, RNA samples were purified using an RNeasy Mini Kit (Qiagen) and bacterial rRNAs were depleted using the Ribo-Zero rRNA Removal Kit (Epicentre; #RZNB1056). Library construction of RNA samples was carried out using a NEBNext R UltraTM Directional RNA Library Prep Kit for Illumina R (NEB, USA), following the manufacturer’s recommendations. more...

Organism:

Escherichia coli O157:H7

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26831

4 Samples

Download data: XLS

(Submitter supplied) The growth of E. coli is inhibited by millimolar concentrations of L-homoserine, which may be problematic for the industrial production of this compound or for products derived from it. In this work, an adapted laboratory evolution (ALE) was applied, which resulted in the isolation of an E. coli strain at least 10-fold more tolerant to L-homoserine than the original (MG1655) strain. Only four genomic modifications were identified after genome sequencing of this evolved strain (designed 4E), including a 49 bp truncation starting from the codon stop of thrL and leading to a modified thrL locus carrying a thrL* allele encoding a 30 amino acids polypeptide, which is 9 amino acids more than the leader peptide encoded by thrL. more...

Organism:

Escherichia coli str. K-12 substr. MG1655; Escherichia coli; Escherichia coli O157:H7 str. EDL933; Escherichia coli CFT073; Escherichia coli O157:H7 str. Sakai

Type:

Expression profiling by array

Platform:

GPL13359

24 Samples

Download data: TXT, XLSX

(Submitter supplied) The first goal of the study was to identify genes differentially regulated by MavR in EHEC strain 86-24. The second goal was to identify direct targets of MavR through the MAPS protocol.

Organism:

Escherichia coli O157:H7

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL29711 GPL28511

10 Samples

Download data: TXT

(Submitter supplied) To compare the transcriptional profiling of a FimZ-expressing strain or non-expressing strain in E. coli under stationary phase. For overexpression of fimZ gene was cloned into pBAD33 plasmid under control of the arabinose-inducible PBAD promoter, which was induced by addition of 0.2% arabinose. Goal was to determine the FimZ regulon in E. coli. Biological replicates: 2 replicates.

Organism:

Escherichia coli BW25113; Escherichia coli str. K-12 substr. MG1655; Escherichia coli CFT073; Escherichia coli O157:H7 str. Sakai; Escherichia coli O157:H7 str. EDL933

Type:

Expression profiling by array

Platform:

GPL13359

2 Samples

Download data: TXT

(Submitter supplied) To compare transcriptional profiling of a gadE-, hdeA-, or hdeD- deficient strain to wild type in E. coli under minimum medium conditions. These genes are included in the GAD cluster genes, which are involved in the glutamic acid-dependent acid resistance (GAD) in E. coli. Goal was to determine the GadE, HdeA, or HdeD regulon in E. coli. Biological replicates: 2 replicates.

Organism:

Escherichia coli str. K-12 substr. MG1655; Escherichia coli BW25113; Escherichia coli O157:H7 str. EDL933; Escherichia coli CFT073; Escherichia coli O157:H7 str. Sakai

Type:

Expression profiling by array

Platform:

GPL13359

6 Samples

Download data: TXT

(Submitter supplied) The function of cvpA, a bacterial gene predicted to encode an inner membrane protein, is largely unknown. Early studies in E. coli linked cvpA to Colicin V secretion and recent work revealed that it is required for robust intestinal colonization by diverse enteric pathogens. In enterohemorrhagic E. coli (EHEC), cvpA is required for resistance to the bile salt deoxycholate (DOC). Here, we carried out genome-scale transposon-insertion mutagenesis and spontaneous suppressor analysis to uncover cvpA’s genetic interactions and identify common pathways that rescue the sensitivity of a ∆cvpA EHEC mutant to DOC. more...

Organism:

Escherichia coli O157:H7 str. EDL933

Type:

Other

Platform:

GPL23073

6 Samples

Download data: TXT

(Submitter supplied) Enterohaemorrhagic E. coli is significant human pathogen that causes disease ranging from haemorrhagic colitis to haemolytic uremic syndrome. The later can lead to potentially fatal renal failure and is caused by the release of Shiga toxins that are encoded within lambdoid bacteriophages. The toxins are encoded within the late transcript of the phage and are regulated by anti-termination of the PR’ late promoter during lytic induction of the phage. more...

Organism:

Escherichia coli O157:H7 str. Sakai

Type:

Expression profiling by high throughput sequencing

Platform:

GPL28004

8 Samples

Download data: BEDGRAPH, SGR

(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

(Submitter supplied) The synthetic flexicate compound Λ-5b shows potent antimicrobial activity against E. coli. In this study we investigated the transcriptomic response of a clinically relevant E. coli, EHEC O157:H7, to a sublethal concentration of the compound.

Organism:

Escherichia coli O157:H7 str. Sakai

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26099

6 Samples

Download data: CSV, TXT

(Submitter supplied) Pathogens like E. coli O157:H7 are responsible for many outbreaks and can be found and survive in poor inorganic phosphate (Pi) environments. In E. coli the phosphate homeostasis is regulated by the Pst system and the two-component system PhoB/R. In a Δpst mutant, PhoB is constitutively activated and biofilm formation is increased. To understand how PhoB activation lead to biofilm increase, we compared the transcriptomes of EDL933 the WT strain and Δpst mutant both grown in MOPS Pi rich medium, using the Affymetrix GeneChip® E. more...

Organism:

Escherichia coli; Escherichia coli O157:H7 str. EDL933

Type:

Expression profiling by array

Platform:

GPL3154

6 Samples

Download data: CEL

(Submitter supplied) RNA seq experiment was perfomed in the presence and absence of 500uM indole

Organism:

Escherichia coli O157:H7

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25528

4 Samples

Download data: ASTAR, TXT

(Submitter supplied) We found that nemerous genes were up- or down regulated in ∆dnaK, including RpoS-regulated genes.

Organism:

Escherichia coli CFT073; Escherichia coli str. K-12 substr. MG1655; Escherichia coli; Escherichia coli O157:H7 str. EDL933; Escherichia coli O157:H7 str. Sakai

Type:

Expression profiling by array

Platform:

GPL13360

4 Samples

Download data: TXT

(Submitter supplied) E. coli (P1645ec: a clinical isolate) was incubated with differing concentrations of antimicrobial peptides (all at 0.5X MBC)

Organism:

Escherichia coli CFT073; Escherichia coli O157:H7 str. Sakai; Escherichia coli; Escherichia coli O157:H7 str. EDL933; Escherichia coli str. K-12 substr. MG1655

Type:

Expression profiling by array

Platform:

GPL13359

8 Samples

Download data: TXT

(Submitter supplied) Enterohaemorrhagic E. coli is a significant human pathogen that utilises a type 3 secretion system (T3S) to colonise the reservoir host, cattle, and humans. Transposon mutagenesis showed the ybeZYX-Int operon to be required for normal T3S levels. Deletion analyses identified the endoribonuclease ybeY, which was previously linked to 16S ribosomal RNA maturation and small RNA (sRNA) function. Loss of ybeY in EHEC had additional pleiotropic effects, including temperature sensitivity and reduced growth. more...

Organism:

Escherichia coli O157:H7

Type:

Other

Platform:

GPL17334

3 Samples

Download data: BEDGRAPH, GTF

(Submitter supplied) APEC cause avian colibacillosis in poultry, characterized by the systematic infection, such as septicemia, airsacculitis, and pericarditis. APEC mainly use two-component regulatory systems (TCSs) to deal with the stressing environments in host during their infection. Whereas most TCSs in E.coli are well characterized, the characterization of RstA/RstB in APEC has not been thoroughly investigated. To understand the whole picture of RstA/RstB regulation, especially its role in virulence regulation, transcriptional analysis of the effect of rstAB deletion was performed in vivo. more...

Organism:

Escherichia coli str. K-12 substr. MG1655; Escherichia coli O157:H7 str. Sakai; Escherichia coli APEC O2; Escherichia coli CFT073; Escherichia coli O157:H7 str. EDL933

Type:

Expression profiling by array

Platform:

GPL13359

6 Samples

Download data: TXT

(Submitter supplied) Enteric pathogens with low infectious doses rely on the ability to orchestrate expression of virulence and metabolism-associated genes in response to environmental cues for successful infection. Accordingly, the human pathogen enterohemorrhagic Escherichia coli (EHEC) employs a complex multifaceted regulatory network to link expression of type III secretion system (T3SS) factors to nutrient availability. more...

Organism:

Escherichia coli O157:H7 str. EDL933

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24005

6 Samples

Download data: TXT