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:

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; Yersinia enterocolitica; Toxoplasma gondii; Salmonella enterica subsp. enterica serovar Typhimurium; Mammarenavirus choriomeningitidis; Orthohantavirus puumalaense; Leptospira interrogans; Rickettsia typhi; Mycobacterium tuberculosis variant bovis; Mycobacterium tuberculosis; Mycobacterium tuberculosis variant microti; Mycobacterium canetti; Orthohantavirus seoulense

Type:

Methylation profiling by array

Platform:

GPL21445

4 Samples

Download data: IDAT, TXT

(Submitter supplied) Antibiotic resistance (AR) is one of the greatest threats to global health and is associated with higher treatment costs, longer hospital stays, and increased mortality. Current gold standard antibiotic susceptibility tests (AST) are dependent on organism growth rates resulting in prolonged diagnostic answers for slow growing organisms. Changes in the cellular transcriptome can be instantaneous in the presence of stressors such as antibiotic pressure. more...

Organism:

Yersinia pestis; Bacillus anthracis

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL33703 GPL29781

48 Samples

Download data: XLSX

(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) In order to study the gene expression differences of ev76 in the environment and the appropriate growth temperature of flea (21 ℃) and mouse body temperature (37 ℃), we cultured ev76 at 21 ℃ and 37 ℃ respectively, collected bacterial precipitation and sequenced the transcriptome

Organism:

Yersinia pestis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL23606

6 Samples

Download data: XLSX

(Submitter supplied) Purpose: In previous studies, we found that the fyuA gene plays an important role in the virulence and pathogenicity of Yersinia pestis strain 201. In order to globally observe which functions of the fyuA gene also affect Y. pestis, we performed RNA-seq on the Y. pestis wild strain 201-WT and mutant strains △fyuA and △fyuAGCAdel, hoping to find their differences at the transcription level, so that better elucidate the effect of fyuA gene on Y. more...

Organism:

Yersinia pestis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL29436

18 Samples

Download data: TXT

(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; Salmonella enterica; Salmonella enterica subsp. enterica serovar Typhimurium str. LT2; Escherichia coli K-12

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) The goal of this study is to determine the host and pathogen transcriptomic response during pneumonic plague infection. Mice were infected intranasally with high dose of 800,000 cfu/mouse (1500 LD50). Mice were sacrificed at 1, 24 and 48 hours post infection and dual RNA was extracted. In order to isolate high quantities of superior quality mRNA from bacteria and mice we used a novel technique, that employed infusion of an RNA preserving reagent (RNAlater) into the lungs of the animals through the trachea under deep anesthesia prior to the collection of the organs. more...

Organism:

Yersinia pestis; Mus musculus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL24247 GPL24209 GPL21103

17 Samples

Download data: XLSX

(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:

Neisseria meningitidis; Staphylococcus epidermidis; Streptococcus pyogenes; Listeria monocytogenes; Salmonella enterica; Achromobacter xylosoxidans; Helicobacter pylori; Enterococcus faecalis; Borreliella burgdorferi; Pseudomonas aeruginosa; Legionella pneumophila; Klebsiella pneumoniae; Yersinia pseudotuberculosis; Vibrio cholerae; Streptococcus suis; Streptococcus agalactiae; Streptococcus pneumoniae; Mycobacterium tuberculosis; Burkholderia pseudomallei; 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

Type:

Expression profiling by high throughput sequencing

30 related Platforms

1122 Samples

Download data: TXT

(Submitter supplied) Yunnan Province, China is thought to be the original source of biovar Orientalis of Yersinia pestis, the causative agent of the third plague pandemic that has spread globally since the end of the 19th century. Although encompassing a large area of natural plague foci, Y. pestis strains have rarely been found in live rodents during surveillance in Yunnan, and most isolates are from rodent corpses and their fleas. more...

Organism:

Yersinia pestis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL29436

4 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) Our comparative transcriptomic studies found that the cobB and yfiQ deletions resulted in differential expression of a large number of genes,we found 399 DEGs in the cobB mutant, among which 142 were down-regulated and 257 were up-regulated and there were 594 DEGs in the yfiQ mutant, among which 219 were down-regulated and 375 were up-regulated in comparison with the Yersinia pestis wild-type strain.Interestingly, expression of the virulence-related genes hmsHFRS, psaABEF were significantly lower in both ΔcobB and ΔyfiQ. more...

Organism:

Yersinia pestis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24209

6 Samples

Download data: TXT

(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) We use RNA-seq to identify Crp-regulated, Biofilm-regulated and Glucose-regulated genes in Yersinia pestis grown in planktonic and biofilm growth states.

Organism:

Yersinia pestis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL27001

6 Samples

Download data: XLSX

(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