GEO DataSets

(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) 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) 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) Rationale: Respiratory syncytial virus (RSV) is the leading cause of acute lower respiratory tract infections and hospitalizations in infants worldwide. Known risk factors, however, incompletely explain the variability of RSV disease severity among children. We postulate that severity of RSV infection is influenced in part by modulation of the host immune response by the local microbial ecosystem at the time of infection. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL10558

104 Samples

Download data: TXT

(Submitter supplied) high throughput sequencing of the metagenome of mexican children

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

8 Samples

Download data: FASTA, TXT

(Submitter supplied) The impact of viral infections, on host microbiota composition and dynamics is poorly understood. Influenza A viruses (IAV) are common respiratory pathogens causing acute infections. In this study, we show dynamic changes in respiratory and intestinal microbiota over the course of a sublethal IAV infection in a mouse model. Using a combination of 16S rRNA gene specific next generation sequencing and qPCR as well as culturing of bacterial organ content, we found body site specific and transient microbiota responses to influenza infection. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17021

14 Samples

Download data: TXT

(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) A pressing clinical challenge is identifying the etiologic basis of acute respiratory illness. Without reliable diagnostics, the uncertainty associated with this clinical entity leads to a significant, inappropriate use of antibacterials. Use of host peripheral blood gene expression data to classify individuals with bacterial infection, viral infection, or non-infection represents a complementary diagnostic approach. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL571

280 Samples

Download data: CEL

(Submitter supplied) Goals: Study responses in peripheral blood of patients infected with influenza virus and compare to healthy control. Results: Strong differential host reponse after infection was observed.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

41 Samples

Download data: TXT

(Submitter supplied) Gene expression changes in the blood was studied by RNAseq Results: Strong differential host reponse after infection with influenza virus compared to healthy controls project SIG_2020

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20301

69 Samples

Download data: TXT

(Submitter supplied) Gene expression changes in the blood was studied by RNAseq; project SIG-2018 Results: Strong differential host reponse after infection with influenza virus compared to healthy controls

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20301

74 Samples

Download data: TXT

(Submitter supplied) Gene expression changes in the blood was studied by RNAseq; project SIG-2019 Results: Strong differential host reponse after infection with influenza virus compared to healthy controls

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20301

79 Samples

Download data: TXT

(Submitter supplied) BACKGROUND. Lower respiratory tract infection (LRTI) is a leading cause of death in children worldwide. LRTI diagnosis is challenging since non-infectious respiratory illnesses appear clinically similar and existing microbiologic tests are often falsely negative or detect incidentally-carried microbes common in children. These challenges result in antimicrobial overuse and adverse patient outcomes. Lower airway metagenomics has the potential to detect host and microbial signatures of LRTI. Whether it can be applied at scale and in a pediatric population to enable improved diagnosis and precision treatment remains unclear. METHODS. We used tracheal aspirate RNA-sequencing to profile host gene expression and respiratory microbiota in 261 children with acute respiratory failure. We developed a random forest gene expression classifier for LRTI by training on patients with an established diagnosis of LRTI (n=117) or of non-infectious respiratory failure (n=50). We then developed a classifier that integrates the: i) host LRTI probability, ii) abundance of respiratory viruses, and iii) dominance in the lung microbiome of bacteria/fungi considered pathogenic by a rules-based algorithm. RESULTS. The host classifier achieved a median AUC of 0.967 by 5-fold cross-validation, driven by activation markers of T cells, alveolar macrophages and the interferon response. The integrated classifier achieved a median AUC of 0.986 and significantly increased the confidence of patient classifications. When applied to patients with an uncertain diagnosis (n=94), the integrated classifier indicated LRTI in 52% of cases and nominated likely causal pathogens in 98% of those. CONCLUSIONS. Lower airway metagenomics enables accurate LRTI diagnosis and pathogen identification in a heterogeneous cohort of critically ill children through integration of host, pathogen, and microbiome features.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL24676

261 Samples

Download data: CSV