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) 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:

Bacillus anthracis; Yersinia pestis

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL33703 GPL29781

48 Samples

Download data: XLSX

(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) 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:

GPL21103 GPL24247 GPL24209

17 Samples

Download data: XLSX

(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) 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) 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) Hfq is a ubiquitous Sm-like RNA-binding protein in bacteria involved in physiological fitness and pathogenesis, while its in vivo binding nature remains elusive. Here we reported genome-wide Hfq-bound RNAs in Yersinia pestis, a causative agent of plague, by using cross-linking immunoprecipitation coupled with deep sequencing (CLIP-seq) approach. We show that the Hfq binding density is enriched in more than 80% mRNAs of Y. more...

Organism:

Yersinia pestis

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL21403

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

Type:

Expression profiling by array

Platform:

GPL25510

54 Samples

Download data: CEL, CHP

(Submitter supplied) The pathogenic spirochete Borrelia burgdorferi senses and responds to diverse environmental challenges, including changes in nutrient availability, throughout its natural infectious cycle in Ixodes spp. ticks and mammalian hosts. This study examined the role of the putative DnaK suppressor protein (DksA) in the transcriptional response of B. burgdorferi to starvation. Wild-type and dksA-deficient B. more...

Organism:

Yersinia pestis; Coxiella burnetii; Streptococcus pyogenes; Borreliella burgdorferi; Chlamydia trachomatis; Staphylococcus aureus

Type:

Expression profiling by array

Platform:

GPL2129

12 Samples

Download data: CEL, CHP

(Submitter supplied) Several methicillin resistance (SCCmec) clusters characteristic of hospital-associated methicillin-resistant Staphylococcus aureus (MRSA) strains harbor the psm-mec locus. In addition to encoding the cytolysin, phenol-soluble modulin (PSM) mec, this locus has been attributed gene regulatory functions. Here we employed genome-wide transcriptional profiling to define the regulatory function of the psm-mec locus. more...

Organism:

Borreliella burgdorferi; Chlamydia trachomatis; Staphylococcus aureus; Yersinia pestis; Streptococcus pyogenes; Coxiella burnetii

Type:

Expression profiling by array

Platform:

GPL2129

12 Samples

Download data: CEL, CHP

(Submitter supplied) Cultures of Y. pestis Kimberley53 (Kim53) virulent strain and Kim53∆nlpD were grown in heart infusion broth supplemented with 0.2% xylose and 2.5 mM CaCl2 for 5 h at 37°C, 200rpm. Total RNA samples were extructed and used for cRNA synthesis and labelling (using Cy3-CTP and Cy5-CTP). cRNA of two independent samples from each strain were labeled and hybridized to custom made Agilent 8x15K slide. Goal: Identifing alterations in gene expression profile between the wild-type Kim53 virulent strain and Kim53∆nlpD. more...

Organism:

Yersinia pestis

Type:

Expression profiling by array

Platform:

GPL21664

4 Samples

Download data: TXT

(Submitter supplied) Using a library of over 1 million Y. pestis CO92 random mutants and transposon-directed insertion site sequencing, we identified 530 essential genes when the bacteria were cultured at 28oC. When the library of mutants was subsequently cultured at 37oC we identified 19 genes that were essential at 37oC but not at 28oC, including genes which encode proteins that play a role in enabling functioning of the type III secretion and in DNA replication and maintenance.

Organism:

Yersinia pestis

Type:

Other

Platform:

GPL23606

7 Samples

Download data: RD

(Submitter supplied) The Yersinia pestis PhoPQ gene regulatory system is induced during infection of the flea digestive tract and is required to produce adherent biofilm in the foregut, which greatly enhances bacterial transmission during a flea bite. To understand the in vivo context of PhoPQ induction and to determine PhoP-regulated targets in the flea, we undertook whole genome comparative transcriptional profiling of Y. more...

Organism:

Coxiella burnetii; Chlamydia trachomatis; Streptococcus pyogenes; Yersinia pestis; Borreliella burgdorferi; Staphylococcus aureus

Type:

Expression profiling by array

Platform:

GPL2129

40 Samples

Download data: CEL, CHP

(Submitter supplied) Cultures of Y. pestis Kimberley53 virulent strain were exposed to different concentrations of ciprofloxacin (including 0.016 µg/ml representing the strains' MIC value) for various time periods. Total RNA samples were extructed and used for cRNA synthesis and labelling (using Cy3-CTP for the treated samples and Cy5-CTP for the non-treated sample in one biological experiment and dye swap for the 2nd replicate of independent biological experiment). more...

Organism:

Yersinia pestis

Type:

Expression profiling by array

Platform:

GPL21664

8 Samples

Download data: 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:

Bartonella quintana; Staphylococcus aureus; Mycobacterium avium; Rattus norvegicus; Cowpox virus; Escherichia coli O157:H7; Francisella tularensis subsp. holarctica; 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; 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

Type:

Genome variation profiling by array

Platform:

GPL21445

65 Samples

Download data: TXT

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

Organism:

Yersinia pestis; Yersinia pestis CO92

Type:

Expression profiling by array

Platforms:

GPL10439 GPL9009

48 Samples

Download data: TXT

(Submitter supplied) The etiologic agent of bubonic plague, Yersinia pestis, senses cell density-dependent chemical signals to synchronize transcription between cells of the population in a process named quorum sensing. Though the closely related enteric pathogen Y. pseudotuberculosis uses quorum sensing system to regulate motility, the role of YpeIR quorum sensing in Y. pestis has been unclear. YpeIR is one of the AHL quorum sensing system in Y. more...

Organism:

Yersinia pestis

Type:

Expression profiling by array

Platform:

GPL10439

6 Samples

Download data: TXT

(Submitter supplied) Temperature is a key environmental factor for facultative pathogens during the host adaptation response. To assess the functional role of temperature in Yersinia pestis, a microarray study was conducted comparing the Δpgm (pigmentation-negative) R88 strain grown at 37°C or 30°C.

Organism:

Yersinia pestis

Type:

Expression profiling by array

Platform:

GPL10439

6 Samples

Download data: TXT