GEO DataSets

(Submitter supplied) Pathogenic bacteria sense and respond to environmental fluctuations, a capability essential for establishing successful infections. The YmoA/Hha protein family are conserved transcription regulators in Enterobacteriaceae, playing a critical role in these responses. Specifically, YmoA in Yersinia adjusts the expression of virulence-associated traits upon temperature shift. Still, the molecular mechanisms transducing environmental signals through YmoA remain elusive. more...

Organism:

Yersinia pseudotuberculosis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL35020

9 Samples

Download data: TXT

(Submitter supplied) Bacterial pathogens, such as in Yersinia pseudotuberculosis, encounter temperature fluctuations during host infection and upon return to the environment. These temperature shifts impact RNA structures globally. While previous transcriptome-wide studies have focused on RNA thermometers in the 5’-untranslated region of virulence-related mRNAs, our investigation revealed temperature-driven structural rearrangements in the small RNA (sRNA) CyaR. more...

Organism:

Yersinia pseudotuberculosis YPIII

Type:

Expression profiling by high throughput sequencing

Platform:

GPL34617

24 Samples

Download data: XLSX

(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; 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; 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

Type:

Methylation profiling by array

Platform:

GPL21445

4 Samples

Download data: IDAT, TXT

(Submitter supplied) RNA degradation is an essential process that allows bacteria to regulate gene expression and has emerged as an important mechanism for controlling virulence. However, the individual contributions of RNases in this process are mostly unknown. Here, we report that of 11 tested potential RNases of the intestinal pathogen Yersinia pseudotuberculosis, two, the endoribonuclease RNase III and the exoribonuclease PNPase, repress the synthesis of the master virulence regulator LcrF. more...

Organism:

Yersinia pseudotuberculosis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL28682

30 Samples

Download data

(Submitter supplied) One milliliter of triplicate bacterial cultures in both Wild type (WT) and rpoN mutant were immediately pelleted by centrifugation at 9000 rpm at room temperature for 2 minutes after adding phenol:ethanol. The supernatant were removed and the pellets resuspended in 0.5 ml Trizol solution. For Gram-negative bacteria, the cells were homogenized in Trizol solution by pipetting up and down 15 times. For Gram-positive bacteria, culture suspensions in Trizol were transferred to previously cooled bead beater tubes containing 0.1-mm glass beads and treated with Mini-Beadbeater (Biospec Products Inc, USA) twice at a fixed speed for 45 seconds, and then cooled on ice for 1 minute between the treatments. more...

Organism:

Yersinia pseudotuberculosis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL28682

24 Samples

Download data: XLSX

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

Organism:

Escherichia coli; Klebsiella pneumoniae; Shigella flexneri; Staphylococcus aureus; Pseudomonas putida; Yersinia pseudotuberculosis; Escherichia coli K-12; Salmonella enterica; Salmonella enterica subsp. enterica serovar Typhimurium str. LT2

Type:

Genome binding/occupancy profiling by high throughput sequencing

9 related Platforms

102 Samples

Download data: GFF

(Submitter supplied) Bacterial transcription factors (TFs) regulate gene expression to adapt to changing environments; when combined, the TF’s regulatory actions comprise transcriptional regulatory networks (TRNs). The chromatin immunoprecipitation (ChIP) assay is the major contemporary method for mapping in vivo protein-DNA interactions in the genome. It enables the genome-wide study of transcription factor binding sites (TFBSs) and gene regulation. more...

Organism:

Escherichia coli; Klebsiella pneumoniae; Shigella flexneri; Yersinia pseudotuberculosis; Salmonella enterica

Type:

Genome binding/occupancy profiling by high throughput sequencing

5 related Platforms

14 Samples

Download data: GFF

(Submitter supplied) Pathogenic bacteria encounter a variety of stressful host environments during infection. Their responses to meet these challenges protect them from deadly damages and aid in adaption to harmful environments. Bacterial products critical for this protection are therefore interesting as suitable targets for new antimicrobials. To shed light on the complex array of molecular pathways involved in bacterial stress responses we challenged 32 diverse human pathogenic bacteria to 11 infection related stress conditions and catalogued their transcriptomes. more...

Organism:

Helicobacter pylori; Enterococcus faecalis; Campylobacter jejuni; Francisella tularensis; Acinetobacter baumannii; Neisseria gonorrhoeae; Escherichia coli; Shigella flexneri; Aggregatibacter actinomycetemcomitans; Haemophilus influenzae; Staphylococcus aureus subsp. aureus MRSA252; Staphylococcus aureus subsp. aureus MSSA476; Neisseria meningitidis; Staphylococcus epidermidis; Streptococcus pyogenes; Listeria monocytogenes; Salmonella enterica; Achromobacter xylosoxidans; Borreliella burgdorferi; Pseudomonas aeruginosa; Legionella pneumophila; Klebsiella pneumoniae; Yersinia pseudotuberculosis; Vibrio cholerae; Streptococcus suis; Streptococcus agalactiae; Streptococcus pneumoniae; Mycobacterium tuberculosis; Burkholderia pseudomallei

Type:

Expression profiling by high throughput sequencing

30 related Platforms

1122 Samples

Download data: TXT

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

Organism:

Yersinia pseudotuberculosis

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL28960 GPL27774

20 Samples

Download data: WIG

(Submitter supplied) We combined phenotypic and genomic assays to provide insight into its role in this pathogen. RpoN was essential for Y. pseudotuberculosis virulence in mice, and in vitro functional assays showed that it controls biofilm formation and motility. Mapping of genome-wide associations of Y. pseudotuberculosis RpoN identified an RpoN-binding motif at 103 inter- and intragenic sites located on both the sense and anti-sense strands Transcriptomic analysis of bacteria lacking rpoN showed a large impact on gene expression, including down-regulation of genes encoding proteins involved in flagellar assembly, chemotaxis, and quorum sensing There were also clear indications of cross talk with other sigma factors, together with indirect effects due to altered expression of other regulators. more...

Organism:

Yersinia pseudotuberculosis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL28960

12 Samples

Download data: XLSX

(Submitter supplied) We combined phenotypic and genomic assays to provide insight into its role in this pathogen. RpoN was essential for Y. pseudotuberculosis virulence in mice, and in vitro functional assays showed that it controls biofilm formation and motility. Mapping of genome-wide associations of Y. pseudotuberculosis RpoN identified an RpoN-binding motif at 103 inter- and intragenic sites located on both the sense and anti-sense strands. more...

Organism:

Yersinia pseudotuberculosis

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL27774

8 Samples

Download data: WIG, XLSX

(Submitter supplied) In vivo probing of the Yersinia pseudotuberculosis YPIII transcriptome at 25 °C and 37 °C

Organism:

Yersinia pseudotuberculosis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL27774

4 Samples

Download data: TAB

(Submitter supplied) Yersinia pseudotuberculosis is a Gram-negative bacterium capable of causing gastrointestinal infection and is closely related to the highly virulent plague bacillus Yersinia pestis. Infection by both species are currently treatable with antibiotics such as ciprofloxacin, a quinolone-class drug of major clinical importance in the treatment of many other infections. Our current understanding of the mechanism of action of ciprofloxacin is that it inhibits DNA replication by targeting DNA gyrase, and that resistance is primarily due to mutation at this target site, along with generic efflux and detoxification strategies. more...

Organism:

Yersinia pseudotuberculosis IP 32953

Type:

Other

Platform:

GPL27002

3 Samples

Download data: TXT

(Submitter supplied) Yersinia pestis, the etiologic agent of plague, emerged as a flea-borne pathogen only within the last 6,000 years. Just five simple genetic changes in the Yersinia pseudotuberculosis progenitor, which served to eliminate toxicity to fleas and to enhance survival and biofilm formation in the flea digestive tract, were key to the transition to the arthropod-borne transmission route. To gain a deeper understanding of the genetic basis for the development of a transmissible biofilm infection in the flea foregut, we evaluated additional gene differences and performed in vivo transcriptional profiling of Y. more...

Organism:

Yersinia pestis; Yersinia pseudotuberculosis; Yersinia pestis KIM10+; Yersinia pestis CO92

Type:

Expression profiling by array

Platform:

GPL25510

54 Samples

Download data: CEL, CHP

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

Organism:

Yersinia pseudotuberculosis IP 32953; Yersinia pseudotuberculosis

Type:

Expression profiling by array

Platform:

GPL15095

16 Samples

Download data: TAB, TXT

(Submitter supplied) The Twin-arginine translocation (Tat) system promotes secretion of folded proteins that in bacteria are identified via an N-terminal signal peptide. Tat systems are associated with virulence in many bacterial pathogens and our previous studies revealed that Tat deficient Yersinia pseudotuberculosis was severely attenuated for virulence. However, in silico predictions did not reveal any obvious virulence factors among the potential Tat substrates encoded by Y. more...

Organism:

Yersinia pseudotuberculosis IP 32953; Yersinia pseudotuberculosis

Type:

Expression profiling by array

Platform:

GPL15095

4 Samples

Download data: TAB, TXT

(Submitter supplied) The Twin-arginine translocation (Tat) system promotes secretion of folded proteins that in bacteria are identified via an N-terminal signal peptide. Tat systems are associated with virulence in many bacterial pathogens and our previous studies revealed that Tat deficient Yersinia pseudotuberculosis was severely attenuated for virulence. However, in silico predictions did not reveal any obvious virulence factors among the potential Tat substrates encoded by Y. more...

Organism:

Yersinia pseudotuberculosis IP 32953; Yersinia pseudotuberculosis

Type:

Expression profiling by array

Platform:

GPL15095

4 Samples

Download data: TAB, TXT

(Submitter supplied) The Twin-arginine translocation (Tat) system promotes secretion of folded proteins that in bacteria are identified via an N-terminal signal peptide. Tat systems are associated with virulence in many bacterial pathogens and our previous studies revealed that Tat deficient Yersinia pseudotuberculosis was severely attenuated for virulence. However, in silico predictions did not reveal any obvious virulence factors among the potential Tat substrates encoded by Y. more...

Organism:

Yersinia pseudotuberculosis; Yersinia pseudotuberculosis IP 32953

Type:

Expression profiling by array

Platform:

GPL15095

4 Samples

Download data: TAB, TXT

(Submitter supplied) The Twin-arginine translocation (Tat) system promotes secretion of folded proteins that in bacteria are identified via an N-terminal signal peptide. Tat systems are associated with virulence in many bacterial pathogens and our previous studies revealed that Tat deficient Yersinia pseudotuberculosis was severely attenuated for virulence. However, in silico predictions did not reveal any obvious virulence factors among the potential Tat substrates encoded by Y. more...

Organism:

Yersinia pseudotuberculosis; Yersinia pseudotuberculosis IP 32953

Type:

Expression profiling by array

Platform:

GPL15095

4 Samples

Download data: TAB, TXT

(Submitter supplied) A microarray was developed to screen rodent samples for pathogens of zoonotic importance In the work described here, a homologue to Yersinia pestis was found in rodent samples after screening with the microarray

Organism:

Campylobacter jejuni; Yersinia pestis; Mycobacterium tuberculosis variant microti; Rattus rattus; Mycobacterium canetti; Francisella tularensis subsp. mediasiatica; Mammarenavirus choriomeningitidis; Orthohantavirus puumalaense; Orthohantavirus seoulense; Yersinia enterocolitica; Rickettsia prowazekii; Rickettsia typhi; Mycobacterium tuberculosis variant bovis; Toxoplasma gondii; Apodemus sylvaticus; Salmonella enterica subsp. enterica serovar Typhimurium; Leptospira interrogans; Francisella tularensis subsp. novicida; Yersinia pseudotuberculosis; Mycobacterium avium subsp. paratuberculosis; Mycobacterium tuberculosis; Mus musculus; Streptobacillus moniliformis; Bartonella henselae; Francisella tularensis subsp. tularensis; Paslahepevirus balayani; Bartonella quintana; Staphylococcus aureus; Mycobacterium avium; Rattus norvegicus; Cowpox virus; Escherichia coli O157:H7; Francisella tularensis subsp. holarctica

Type:

Genome variation profiling by array

Platform:

GPL21445

65 Samples

Download data: TXT