GEO DataSets

(Submitter supplied) Acute respiratory infections (ARI), which generally begin with colonization of the mucosal surfaces of the upper respiratory tract (URT), are a leading cause of morbidity and mortality with the highest rate in infants. As a common colonizer of the URT, and one of the most prevalent causes of life-threatening infections in the pediatric population, Streptococcus pneumoniae (Spn) was used as a model pathogen to investigate the effect of age during URT infection. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17021

35 Samples

Download data: BW, CSV

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

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL1261

62 Samples

Download data: CEL

(Submitter supplied) We used microarrays to detail the global programme of gene expression in response to Influenza A (PR8) infection

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL1261

12 Samples

Download data: CEL, TXT

(Submitter supplied) We used microarrays to detail the global programme of gene expression in response to Influenza A (PR8) infection

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL1261

40 Samples

Download data: CEL, TXT

(Submitter supplied) We used microarrays to detail the global programme of gene expression in response to Influenza A (PR8) infection

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL1261

10 Samples

Download data: CEL, TXT

(Submitter supplied) Influenza virus neuraminidase (NA), a type II transmembrane glycoprotein, is transported to the virus assembly site at the plasma membrane and is a major viral envelope component that plays a critical role in the release of progeny virions and in determination of host range restriction. Although signals/sequences in NA for translocation, sorting and raft association have been identified, little is known about the host factors that are involved in regulating the intracellular and cell surface transport of NA. more...

Organism:

Homo sapiens

Type:

Expression profiling by array; Non-coding RNA profiling by genome tiling array

Platform:

GPL14715

6 Samples

Download data: CALLS, PAIR

(Submitter supplied) Secondary bacterial infections (‘superinfection’) are a major reason for excessive mortality and hospitalizations during influenza virus infections. Here we present a longitudinal study of gene-expression changes in murine lungs during superinfection, with an initial influenza A virus (IAV) infection and a subsequent S. pneumonia (SP) infection. In addition to the well characterized impairment of the innate immune response, we identified superinfection-specific alterations in endothelial functions, including rapid downregulation in angiogenic activity and vascular regulators. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17021

51 Samples

Download data: CSV

(Submitter supplied) Influenza A virus (IAV) predisposes individuals to secondary infections with the bacterium Streptococcus pneumoniae (the pneumococcus). Infections may manifest as pneumonia, sepsis, meningitis or otitis media (OM). It remains controversial as to whether secondary pneumococcal disease is due to the induction of an aberrant immune response or IAV induced immunosuppression. Moreover, as the majority of studies have been performed in the context of pneumococcal pneumonia, it remains unclear how far these findings can be extrapolated to other pneumococcal disease phenotypes. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL15887

12 Samples

Download data: PAIR

(Submitter supplied) Secondary bacterial pneumonia following influenza infection is a significant cause of mortality worldwide. Upper respiratory tract pneumococcal carriage is important as both determinants of disease and population transmission. The immunological mechanisms that contain pneumococcal carriage are well-studied in mice but remain unclear in humans. Loss of this control of carriage following influenza infection is associated with secondary bacterial pneumonia during seasonal and pandemic outbreaks. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20301

96 Samples

Download data: CSV

(Submitter supplied) Using gene expression data we developed a predictive signture to discriminate between typical bacterial, atyipcal bacterial, and viral pnuemonia in murine samples and validated it against open source human datasets.

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL8321

126 Samples

Download data: CEL

(Submitter supplied) HFD feeding induces a rapid adipocyte progenitors (APs) proliferation in visceral adipose tissue (vWAT), followed by a block of differentiation. In contrast, subcutaneous adipose tissue (scWAT), in obesity, undergoes trans-differentiation of beige adipocytes to white and, consequently, a hyperplastic growth at later stages. We performed ChIP-seq to profile RNA pol II recruitment and the global epigenetic changes of H3K4me1 and H3K27Ac induced by HFD feeding.

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL17021

96 Samples

Download data: BW

(Submitter supplied) HFD feeding induces a rapid adipocyte progenitors (APs) proliferation in visceral adipose tissue (vWAT), followed by a block of differentiation. In contrast, subcutaneous adipose tissue (scWAT), in obesity, undergoes trans-differentiation of beige adipocytes to white and, consequently, a hyperplastic growth at later stages. We performed RNA-seq to investigate the global transcriptomic changes induced by HFD feeding

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17021

72 Samples

Download data: TXT

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

Organism:

human metagenome

Type:

Expression profiling by high throughput sequencing; Other

Platforms:

GPL26213 GPL26212

69 Samples

Download data

(Submitter supplied) Antibiotic resistance genes expressed in the upper respiratory tract of patients infected with influenza viruses were associated with the microbial community and microbial activities. Interactions between the host systemic responses to influenza infection and ARG expression highlight the importance of antibiotic resistance in viral-bacterial co-infection.

Organism:

human metagenome

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26213

35 Samples

Download data: TXT

(Submitter supplied) Antibiotic resistance genes expressed in the upper respiratory tract of patients infected with influenza viruses were associated with the microbial community and microbial activities. Interactions between the host systemic responses to influenza infection and ARG expression highlight the importance of antibiotic resistance in viral-bacterial co-infection.

Organism:

human metagenome

Type:

Other

Platform:

GPL26212

34 Samples

Download data: HDF5

(Submitter supplied) Antibiotic resistance genes expressed in the upper respiratory tract of patients infected with influenza viruses were associated with the microbial community and microbial activities. Interactions between the host systemic responses to influenza infection and ARG expression highlight the importance of antibiotic resistance in viral-bacterial co-infection.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

56 Samples

Download data: TSV

(Submitter supplied) D’Mello et al. detail host-pathogen interaction gene expression profiles of Streptococcus pneumoniae (Spn) and its infected host at disease relevant anatomical sites using mice as experimental models. The authors identify the core and organ-specific transcriptomes of Spn, show that bacterial and host gene expression profiles are highly distinct during asymptomatic colonization versus disease-causing infection, and demonstrate that Spn and host genes with high levels of expression contribute to pathogenesis or host defense, respectively.

Organism:

Mus musculus; Streptococcus pneumoniae

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL28625 GPL21103 GPL22283

44 Samples

Download data: TXT

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

Organism:

Homo sapiens

Type:

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

Platforms:

GPL16791 GPL17692

27 Samples

Download data: BW, CEL, NARROWPEAK

(Submitter supplied) Epithelial cells are the first point of contact for bacteria entering the respiratory tract. Streptococcus pneumoniae is an obligatory human pathobiont of the nasal mucosa, carried asymptomatically but also the cause of severe pneumoniae. The role of the epithelium in maintaining homeostatic interactions or mounting an inflammatory response to invasive S. pneumoniae is currently poorly understood. However, studies have shown that chromatin modifications, at the histone level, induced by bacterial pathogens interfere with the host transcriptional program and promote infection. In this study, we demonstrate that S. pneumoniae actively induces di-methylation of histone H3 on lysine 4 (H3K4me2), which persists for at least 9 days upon clearance of bacteria with antibiotics. We show that infection establishes a unique epigenetic program affecting the transcriptional response of epithelial cells, rendering them more permissive upon secondary infection. Our results establish H3K4me2 as a unique modification induced by infection, distinct from H3K4me3, which localizes to enhancer regions genome-wide. Therefore, this study reveals evidence that bacterial infection leaves a memory in epithelial cells after bacterial clearance, in an epigenomic mark, thereby altering cellular responses for subsequent infections.

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL16791

15 Samples

Download data: BW, NARROWPEAK

(Submitter supplied) Epithelial cells are the first point of contact for bacteria entering the respiratory tract. Streptococcus pneumoniae is an obligatory human pathobiont of the nasal mucosa, carried asymptomatically but also the cause of severe pneumoniae. The role of the epithelium in maintaining homeostatic interactions or mounting an inflammatory response to invasive S. pneumoniae is currently poorly understood. However, studies have shown that chromatin modifications, at the histone level, induced by bacterial pathogens interfere with the host transcriptional program and promote infection. In this study, we demonstrate that S. pneumoniae actively induces di-methylation of histone H3 on lysine 4 (H3K4me2), which persists for at least 9 days upon clearance of bacteria with antibiotics. We show that infection establishes a unique epigenetic program affecting the transcriptional response of epithelial cells, rendering them more permissive upon secondary infection. Our results establish H3K4me2 as a unique modification induced by infection, distinct from H3K4me3, which localizes to enhancer regions genome-wide. Therefore, this study reveals evidence that bacterial infection leaves a memory in epithelial cells after bacterial clearance, in an epigenomic mark, thereby altering cellular responses for subsequent infections. Transcriptome analysis aimed at testing whether cells respond differently in the primary (1°) and secondary (2°) infection. Differential gene expression and gene set enrichment analysis performed.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL17692

12 Samples

Download data: CEL