Project description:Genome wide DNA methylation profiling of Chronic Obstructive Pulmonary Disease (COPD) patients and healthy subjects. The Illumina Infinium HumanMethylation450 BeadChip was used to obtain DNA methylation profiles across in peripheral blood mononuclear cell samples. Samples included 6 normal subjects and 12 COPD patients among which 3 of them have 2nd samples from follow-up examination.
Project description:Background: CD8 cells seem to play an important role in the pathogenesis of chronic obstructive pulmonary disease (COPD). However, relatively little is known about their phenotype and function. Aims: To define the transcriptome of pulmonary CD8 cells in COPD and compare to paired circulating CD8 cells and smoker control pulmonary CD8 cells. COPD was defined according to the Global initiative for chronic Obstructive Lung Disease guidelines. Severity of disease was defined according to the patients lung function. In particular the forced evpiratroy volume in 1 second (FEV1).
Project description:Rhinovirus (RV) is the most prevalent human respiratory virus. Each year, RV infects billions of people and is responsible for at least half of all common colds, the most common illness of humans. RV infection also affects the morbidity of a range of respiratory illnesses, such as bronchiolitis, pneumonia, asthma, chronic obstructive pulmonary disease, and cystic fibrosis. Despite its biological importance and public health significance, little is known about the genetic architecture of response to RV. To address this, we obtained genome-wide genotype and gene expression data in uninfected and RV-infected peripheral blood mononuclear cells (PBMCs) from 98 individuals. We characterized gene expression differences in response to RV infection and mapped expression quantitative trait loci (eQTLs) in both uninfected and RV-infected PBMCs.
Project description:Rhinovirus (RV) is the most prevalent human respiratory virus. Each year, RV infects billions of people and is responsible for at least half of all common colds, the most common illness of humans. RV infection also affects the morbidity of a range of respiratory illnesses, such as bronchiolitis, pneumonia, asthma, chronic obstructive pulmonary disease, and cystic fibrosis. Despite its biological importance and public health significance, little is known about the genetic architecture of response to RV. To address this, we obtained genome-wide genotype and gene expression data in uninfected and RV-infected peripheral blood mononuclear cells (PBMCs) from 98 individuals. We characterized gene expression differences in response to RV infection and mapped expression quantitative trait loci (eQTLs) in both uninfected and RV-infected PBMCs. The study includes data from uninfected and rhinovirus-infected peripheral blood mononuclear cells (PBMCs) from 98 individuals. Twenty ml of blood was drawn from each participant. PBMCs were isolated from whole blood samples by Ficoll-Paque separation. From each subject, 4 million PBMCs were treated with media alone for 24 hours and 4 million PBMCs were treated with media containing RV16 for 24 hours. The multiplicity of infection was 10 plaque-forming units per cell. Total RNA was extracted after 24-hour incubation, using the RNeasy Plus Mini Kit; concentrations were measured on a Nanodrop ND-100 Spectrophotometer and quality was assessed using an Agilent 2100 Bioanalyzer. Genome wide gene expression profiling of uninfected and rhinovirus-infected PBMCs was obtained using Illumina HumanHT-12 v4 Expression BeadChip arrays at the University of Chicago Functional Genomics Core.
