txid632[Organism] - GEO DataSets

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Select item 2002670141.

Spermine-induced DNA methylation change in human macrophages

(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

Series

Accession:: GSE267014

ID:: 200267014

Select item 2002414892.

Relative quantification of the recA gene for antibiotic susceptibility testing in response to ciprofloxacin for pathogens of concern

(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

Series

Accession:: GSE241489

ID:: 200241489

PubMed Full text in PMC Similar studies

Select item 2002016843.

Detection of gene expression level of Yersinia pestis vaccine strain EV76 at 21 and 37 degrees Celsius

(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

Series

Accession:: GSE201684

ID:: 200201684

Select item 2001989374.

Transcriptome differences analysis between Yersinia pestis 201 wild strain and fyuA mutant strain

(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

Series

Accession:: GSE198937

ID:: 200198937

PubMed Full text in PMC Similar studies

Select item 2001816805.

RNA-seq analysis of pathogen and host in the early stages of Plague pulmonary infection using a novel dual RNA extraction method

(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

Series

Accession:: GSE181680

ID:: 200181680

SRA Run Selector

Select item 2001618886.

New genotype of Yersinia pestis found in live rodents in Yunnan Province, China

(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

Series

Accession:: GSE161888

ID:: 200161888

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 2001123137.

Protein Acetylation Mediated by YfiQ and CobB Is Involved in the Virulence and Stress II

(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

Series

Accession:: GSE112313

ID:: 200112313

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 2001352288.

The Cyclic AMP Receptor Protein Regulates Quorum Sensig and Global Gene Expression in Yersinia pestis During Planktonic Growth and Growth in Biofilms

(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

Series

Accession:: GSE135228

ID:: 200135228

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 2000775559.

Hfq Globally Binds and Destabilizes sRNAs and mRNAs in Yersinia pestis

(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

Series

Accession:: GSE77555

ID:: 200077555

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 20011924310.

Differential gene expression patterns of Yersinia pestis and Yersinia pseudotuberculosis during infection and biofilm formation in the flea digestive tract

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

Type:: Expression profiling by array

Platform:: GPL25510
54 Samples

Download data: CEL, CHP

Series

Accession:: GSE119243

ID:: 200119243

PubMed Full text in PMC Similar studies

Select item 20011902311.

DksA controls the response of the Lyme disease spirochete Borrelia burgdorferi to starvation

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

Type:: Expression profiling by array

Platform:: GPL2129
12 Samples

Download data: CEL, CHP

Series

Accession:: GSE119023

ID:: 200119023

PubMed Full text in PMC Similar studies Analyze with GEO2R

Select item 20005136612.

Genome-wide analysis of the regulatory function mediated by the small regulatory psm-mec RNA of methicillin-resistant Staphylococcus aureus

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

Type:: Expression profiling by array

Platform:: GPL2129
12 Samples

Download data: CEL, CHP

Series

Accession:: GSE51366

ID:: 200051366

PubMed Full text in PMC Similar studies Analyze with GEO2R

Select item 20010149013.

The Yersinia pestis NlpD Lipoprotein is important for iron assimilation and is functionally linked to the twin-arginine translocation system

(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

Series

Accession:: GSE101490

ID:: 200101490

Analyze with GEO2R

Select item 20010022614.

An integrated computational-experimental approach reveals Yersinia pestis genes essential across a narrow or a broad range of environmental conditions

(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

Series

Accession:: GSE100226

ID:: 200100226

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 20006155815.

Role of the PhoP-PhoQ Gene Regulatory System in Adaptation of Yersinia pestis to Environmental Stress in the Flea Digestive Tract

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

Type:: Expression profiling by array

Platform:: GPL2129
40 Samples

Download data: CEL, CHP

Series

Accession:: GSE61558

ID:: 200061558

PubMed Full text in PMC Similar studies Analyze with GEO2R

Select item 20007968716.

Y. pestis exposed to various concentrations of ciprofloxacin for various time points (treated/nontreated analysis in each array).

(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

Series

Accession:: GSE79687

ID:: 200079687

PubMed Full text in PMC Similar studies Analyze with GEO2R

Select item 20007776517.

Detection of a Yersinia pestis homologue in rodent samples

(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:: Yersinia enterocolitica; Rickettsia prowazekii; Rickettsia typhi; Mycobacterium tuberculosis variant bovis; Toxoplasma gondii; Apodemus sylvaticus; Salmonella enterica subsp. enterica serovar Typhimurium; Campylobacter jejuni; Yersinia pestis; Mycobacterium tuberculosis variant microti; Rattus rattus; Mycobacterium canetti; Francisella tularensis subsp. mediasiatica; Mammarenavirus choriomeningitidis; Orthohantavirus puumalaense; Orthohantavirus seoulense; 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

Type:: Genome variation profiling by array

Platform:: GPL21445
65 Samples

Download data: TXT

Series

Accession:: GSE77765

ID:: 200077765

Analyze with GEO2R

Select item 20003037318.

Global gene expression analysis of *Yersinia pestis* AHL quorum sensing

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

Organism:: Yersinia pestis CO92; Yersinia pestis

Type:: Expression profiling by array

Platforms:: GPL10439 GPL9009
48 Samples

Download data: TXT

Series

Accession:: GSE30373

ID:: 200030373

Analyze with GEO2R

Select item 20003034119.

Transcriptional analysis of ypeIR mutation in Yersinia pestis at 37°C

(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

Series

Accession:: GSE30341

ID:: 200030341

Analyze with GEO2R

Select item 20003033320.

Transcriptional analysis of temperature regulation in Yersinia pestis

(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

Series

Accession:: GSE30333

ID:: 200030333

PubMed Full text in PMC Similar studies Analyze with GEO2R

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