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) Francisella tularensis, the etiological agnet of Tularemia is a Category A select agent. Preparedness means for prompt proper antibiotic treatment are of need to prevent morbidity and mortality. While standard antimicrobial susceptibility tests are time consuming, the quantification of the changes in the expression levlels of specific mRNA markers folowing antibiotic exposure may enable a rapid determination of antimicrobial susceptibility. more...

Organism:

Francisella tularensis subsp. tularensis SCHU S4

Type:

Expression profiling by high throughput sequencing

Platform:

GPL32560

12 Samples

Download data: TXT

(Submitter supplied) To assess which F. tularensis LVS transcripts are impacted by loss of bS21-2, we generated cells lacking the gene encoding bS21-2 (LVS ∆rpsU2). We then grew wild-type cells containing an empty vector (LVS pF), cells lacking bS21-2 with empty vector (LVS ∆rpsU2 pF), and cells lacking the native bS21-2 but ectopically expressing bS21-2 from a plasmid (LVS ∆rpsU2 pF-rpsU2-V). We isolated RNA from mid-log phase cells and analyzed by RNA-Seq.

Organism:

Francisella tularensis subsp. holarctica LVS

Type:

Expression profiling by high throughput sequencing

Platform:

GPL32555

7 Samples

Download data: TXT

(Submitter supplied) Francisella tularensis is a highly infectious zoonotic pathogen with as few as 10 organisms causing tularemia, a disease that is fatal if untreated. Although F. tularensis subspecies tularensis (type A) and subspecies holarctica (type B) share over 99.5% average nucleotide identity, notable differences exist in genomic organization and pathogenicity. The type A clade has been further divided into subtypes A.I and A.II, with A.I strains being recognized as some of the most virulent bacterial pathogens known. more...

Organism:

Francisella tularensis subsp. holarctica; Francisella tularensis subsp. tularensis

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL32256 GPL32255

96 Samples

Download data: FPKM_TRACKING

(Submitter supplied) To understand differences of gene expression profiles between Francisella strains RNA profiles of Francisella strains were generated by deep sequencing, in triplicate, using NovaSeq6000. qRT–PCR validation was performed using SYBR Green assays. Our study represents the first detailed differential transcriptomic analysis of Francisella strains , with biologic replicates, generated by RNA-seq technology.

Organism:

Francisella tularensis subsp. tularensis SCHU S4; Francisella tularensis subsp. novicida U112

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL30175 GPL30176

9 Samples

Download data: TXT

(Submitter supplied) Liver fibrosis is the excessive accumulation of extracellular matrix that can progress to cirrhosis and failure if untreated. The mechanisms of fibrogenesis are multi-faceted and remain elusive with no approved antifibrotic treatments available. Here we use single-cell RNA sequencing (scRNA-seq) of the adult zebrafish liver to study the molecular and cellular dynamics of the liver at a single-cell level and demonstrate the value of the adult zebrafish as a model for studying liver fibrosis. more...

Organism:

Danio rerio; Francisella tularensis subsp. tularensis SCHU S4

Type:

Expression profiling by high throughput sequencing; Third-party reanalysis

Platform:

GPL20828

6 Samples

Download data: MTX, RDS, TSV, TXT, XLSX

(Submitter supplied) Francisella tularensis is a Gram-negative bacterium that causes a fatal human disease known as tularemia. The Centers for Disease Control have classified F. tularensis as Category A Tier-1 Select Agent. The virulence mechanisms of Francisella are not entirely understood. Francisella possesses very few transcription regulators, and most of these regulate the expression of genes involved in intracellular survival and virulence. more...

Organism:

Francisella tularensis subsp. holarctica LVS

Type:

Expression profiling by high throughput sequencing

Platform:

GPL23586

12 Samples

Download data: XLS

(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; 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; Borreliella burgdorferi; Pseudomonas aeruginosa; Legionella pneumophila; Klebsiella pneumoniae; Yersinia pseudotuberculosis; Vibrio cholerae; Streptococcus suis; Streptococcus agalactiae; Streptococcus pneumoniae; Mycobacterium tuberculosis; Burkholderia pseudomallei; Helicobacter pylori; Enterococcus faecalis

Type:

Expression profiling by high throughput sequencing

30 related Platforms

1122 Samples

Download data: TXT

(Submitter supplied) The bacterium, Francisella tularensis (Ft), is one of the most infectious agents known and classified as a category A bioweapon. Ft virulence is controlled by a unique set of transcription regulators, the MglA-SspA heterodimer, PigR, and the stress signal, ppGpp. These factors activate Francisella pathogenicity island (FPI) gene expression, which is required for virulence. MglA-SspA is expressed during infection and constitutively associates with the σ70 associated RNAP holoenzyme (RNAPσ70), indicating that RNAPσ70-(MglA-SspA) is a virulence specific polymerase. more...

Organism:

Francisella tularensis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL28561

3 Samples

Download data: BW

(Submitter supplied) The facultative intracellular bacterial pathogen Francisella tularensis is the causative agent of tularemia in humans and animals. Gram negative bacteria utilize two-component regulatory systems (TCS) to sense and respond to their changing environment. No classical, tandemly arranged sensor kinase and response regulator TCS genes exist in the human virulent Francisella tularensis subsp. tularensis, but orphaned members are present. more...

Organism:

Francisella tularensis; Francisella tularensis subsp. novicida

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL28891 GPL28890

16 Samples

Download data: CSV, XLSX

(Submitter supplied) We used transposon insertion sequencing (Tn-Seq) to identify the genes that are required for in vitro growth and intramacrophage growth of the live vaccine strain of F. tularensis (LVS).

Organism:

Francisella tularensis subsp. holarctica LVS

Type:

Other

Platform:

GPL27588

5 Samples

Download data: WIG

(Submitter supplied) Francisellosis outbreaks have been reported in the literature as occurring seasonally when water temperature is below 24°C. The aim of this study was to quantify the median lethal doses (LD50) of FNO in experimental challenges at 28°C and 22°C, and to investigate the impact of temperature changes in whole genome expression using microarray technology. The LD50 for Nile tilapia at 28°C was ~105.7, whereas at 22°C, the LD50 was ~102.2, showing that the decrease in temperature enhanced pathogen virulence. more...

Organism:

Francisella orientalis

Type:

Expression profiling by array

Platform:

GPL26043

8 Samples

Download data: TXT

(Submitter supplied) The goal of this study is to compare transcriptomics between wild type LVS vs AR-13 isogenic resistant mutant

Organism:

Francisella tularensis subsp. holarctica LVS

Type:

Expression profiling by high throughput sequencing

Platform:

GPL23586

10 Samples

Download data: XLSX

(Submitter supplied) Francisella tularensis, is an extremely virulent bacterium that can be transmitted naturally by blood sucking arthropods. During mammalian infection, F. tularensis infects numerous types of host cells, including erythrocytes. As erythrocytes do not undergo phagocytosis or endocytosis, it remains unknown how F. tularensis invades these cells. Furthermore, the consequence of inhabiting the intracellular space of red blood cells has not been determined. more...

Organism:

Francisella tularensis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL22893

10 Samples

Download data: TXT

(Submitter supplied) These samples are part of an experiment comparing the expression profiles of Francisella tularensis novicida grown in chemically defined medium and bacteria isolated 24 hours post infection of J774 macrophages to identify virulence factors

Organism:

Francisella; Francisella tularensis subsp. novicida U112

Type:

Expression profiling by array

Platform:

GPL20119

3 Samples

Download data: CEL

(Submitter supplied) As vector-borne pathogens transit between the arthropod and vertebrate, adaptation is key for survival as each host varies and initiates unique defense mechanisms. An environmental signal that relapsing fever (RF) and Lyme causing spirochetes detect is the change of temperature between vector and mammal, yet incomplete genomes have hindered progress in understanding the genetic constituents expressed during tick colonization. more...

Organism:

Coxiella burnetii; Rickettsia prowazekii; Brucella suis; Francisella tularensis; Borrelia hermsii; Burkholderia mallei; Borrelia turicatae 91E135

Type:

Expression profiling by array

Platform:

GPL7246

9 Samples

Download data: CEL, CHP

(Submitter supplied) In this work, we analyzed recognized PAM sequences from four CRISPR-Cas systems: E. coli I-E, B. halodurans I-C, S. thermophilus CR1 II-A, and F. novicida V. Cells containing functional PAMs were sorted using FACS and subsequently sequenced.

Organism:

Escherichia coli; Francisella tularensis subsp. novicida; Streptococcus thermophilus; Halalkalibacterium halodurans

Type:

Other

4 related Platforms

14 Samples

Download data: XLSX

(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; 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; Campylobacter jejuni; Yersinia pestis; Mycobacterium tuberculosis variant microti; Rattus rattus; Mycobacterium canetti; Francisella tularensis subsp. mediasiatica; Mammarenavirus choriomeningitidis; Orthohantavirus puumalaense; Orthohantavirus seoulense

Type:

Genome variation profiling by array

Platform:

GPL21445

65 Samples

Download data: TXT

(Submitter supplied) In many bacteria, the ability to modulate biofilm production relies on specific signaling molecules that are either self-produced or made by neighboring microbes within the ecological niche. We analyzed the potential interspecies signaling effect of the Burkholderia diffusible signal factor (BDSF) on Francisella novicida, a model organism for Francisella tularensis, and demon- strated that BDSF both inhibits the formation and causes the dispersion of Francisella biofilm. more...

Organism:

Francisella tularensis subsp. novicida U112

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20815

2 Samples

Download data: TXT

(Submitter supplied) Comparison of expression profiles of strains of Francisella to identify virulence factors We used custom microarrays to detail the global gene expression of four strains of Francisella (Schu4, LVS, OR960246, U112) and identified distinct classes of differentially expressed genes during this process.

Organism:

Francisella tularensis subsp. holarctica LVS; Francisella tularensis subsp. holarctica OR96246; Francisella tularensis subsp. tularensis SCHU S4; Francisella; Francisella tularensis subsp. novicida U112

Type:

Expression profiling by array

Platform:

GPL20119

12 Samples

Download data: CEL