GEO DataSets

(Submitter supplied) Background Complex diseases are often difficult to diagnose, treat and study due to the multi-factorial nature of the underlying etiology. Large data sets are now widely available that can be used to define novel, mechanistically distinct disease subtypes (endotypes) in a completely data-driven manner. However, significant challenges exist with regard to how to segregate individuals into suitable subtypes of the disease and understand the distinct biological mechanisms of each when the goal is to maximize the discovery potential of these data sets. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Dataset:

GDS5000

Platform:

GPL570

131 Samples

Download data: CEL

Analysis of peripheral blood from asthmatic and non-asthmatic children (ages 9 to 13), participants of the MICA study conducted by the EPA from 11/2006 to 01/2007 in Detroit, MI. These results, together with clinical biomarker measurements, may help to differentiate asthmatics from non-asthmatics.

Organism:

Homo sapiens

Type:

Expression profiling by array, transformed count, 5 age, 3 disease state, 2 gender sets

Platform:

GPL570

Series:

GSE35571

131 Samples

Download data: CEL

(Submitter supplied) To investigate blood transcriptional changes induced by omalizumab treatment and to determine variations between omalizumab responders and non-responders.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL10558

239 Samples

Download data: TXT

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

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Methylation profiling by array

Platforms:

GPL11154 GPL13534

200 Samples

Download data: IDAT

(Submitter supplied) We generated genome-wide RNASeq data from freshly isolated airway epithelial cells of asthmatics and non-asthmatics. This data was paired with genome-wide genetic and methylation data from the same individuals allowing for an integrated analysis of genetic, transcriptional, and epigenetic signatures in asthma.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

85 Samples

Download data: TXT

(Submitter supplied) We generated genome-wide methylation data using the 450K from freshly isolated airway epithelial cells of asthmatics and non-asthmatics. This data was paired with genome-wide genetic and gene expression data from the same individuals allowing for an integrated analysis of genetic, transcriptional, and epigenetic signatures in asthma.

Organism:

Homo sapiens

Type:

Methylation profiling by array

Platform:

GPL13534

115 Samples

Download data: CSV, IDAT, TXT

(Submitter supplied) Recent studies have shown that group 2 innate lymphoid cells (ILC2s) can drive eosinophilic airway inflammation in mouse models of asthma. Moreover, elevated ILC2 counts and/or activity have been reported in asthmatics, together suggesting that ILC2s play an important role in asthma pathophysiology. However, many aspects of ILC2 biology are not fully understood, including the mechanisms underlying ILC2 activation, the tissue-specific functions of ILC2s during inflammation (e.g. more...

Organism:

Mus musculus; Homo sapiens

Type:

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

Platforms:

GPL19057 GPL16791 GPL18573

15 Samples

Download data: BED, TXT

(Submitter supplied) Group 2 innate lymphoid (ILC2) cells are major producers of the cytokines that drive allergic asthma and elevated levels of ILC2s have been detected in the blood and sputum of asthma patients. Asthma susceptibility has strong (epi)genetic components, but the underlying mechanisms and whether they are linked to ILC2 biology remain unclear. To reveal the molecular basis of ILC2 function in allergic airway inflammation (AAI) and assess its relevance for understanding how genetic variation affects asthma susceptibility. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL19057

10 Samples

Download data: TXT

(Submitter supplied) Evaluation of the airway transcriptome may reveal patterns of gene expression that are associated with clinical phenotypes of asthma. To define transcriptomic endotypes of asthma (TEA) we analyzed gene expression in induced sputum that correlate with phenotypes of disease. Gene expression was measured in sputum of subjects with asthma using Affymetrix HuGene ST 1.0 microarrays. Unsupervised clustering analysis of genes identified TEA clusters. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL6244

112 Samples

Download data: CEL

(Submitter supplied) Background: Although several studies link high levels of IL-6 and soluble IL-6 receptor (sIL-6R) with asthma severity and decreased lung function, the role of IL-6 trans-signaling (IL-6TS) in asthma is unclear. Objective: To explore the association between epithelial IL-6TS pathway activation and molecular and clinical phenotypes in asthma. Methods: Primary human bronchial epithelial cell (HBEC) air-liquid interface (ALI) cultures were stimulated with IL-6 and sIL-6R to establish an IL-6TS gene signature. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

24 Samples

Download data: TXT

(Submitter supplied) The host response in critically ill patients with sepsis, septic shock remains poorly defined. Considerable research has been conducted to accurately distinguish patients with sepsis from those with non-infectious causes of disease. Technological innovations have positioned systems biology at the forefront of biomarker discovery. Analysis of the whole-blood leukocyte transcriptome enables the assessment of thousands of molecular signals beyond simply measuring several proteins in plasma, which for use as biomarkers is important since combinations of biomarkers likely provide more diagnostic accuracy than the measurement of single ones or a few. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL13667

802 Samples

Download data: CEL

(Submitter supplied) Recent genome-wide association studies (GWAS) have identified a number of novel genetic associations with complex human diseases. In spite of these successes, results from GWAS generally explain only a small proportion of disease heritability, an observation termed the “missing heritability problem.” Several sources for the missing heritability have been proposed, including the contribution of many common variants with small individual effect sizes, which cannot be reliably found using the standard GWAS approach. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL6947

95 Samples

Download data: TXT