GEO DataSets

(Submitter supplied) Induced sputum is used to sample inflammatory cells, predominantly neutrophils and macrophages, from the airways of COPD patients. Our aim was to identify candidate genes associated with the degree of airflow obstruction and the extent of emphysema by expression profiling, and then to confirm these findings for selected candidates using specific PCR and protein analysis.

Organism:

Homo sapiens

Type:

Expression profiling by array

Dataset:

GDS4265

Platform:

GPL570

143 Samples

Download data: CEL

Analysis of sputum from ex-smokers with moderate (stage 2) or severe (stages 3, 4) chronic obstructive pulmonary disease (COPD). Induced sputum contains inflammatory cells, predominantly neutrophils and macrophages. Results provide insight into molecular mechanisms underlying COPD progression.

Organism:

Homo sapiens

Type:

Expression profiling by array, count, 3 disease state sets

Platform:

GPL570

Series:

GSE22148

143 Samples

Download data: CEL

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

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL10379

1349 Samples

Download data: CEL

(Submitter supplied) We profiled genome-wide gene expression in non-tumorous human lung tissues. The overall goal of this project is to improve our molecular understanding of various lung diseases including lung cancer and chronic obstructive pulmonary disease (COPD).

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL10379

445 Samples

Download data: CEL

(Submitter supplied) We profiled genome-wide gene expression in non-tumorous human lung tissues. The overall goal of this project is to improve our molecular understanding of various lung diseases including lung cancer and chronic obstructive pulmonary disease (COPD).

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL10379

405 Samples

Download data: CEL

(Submitter supplied) We profiled genome-wide gene expression in non-tumorous human lung tissues. The overall goal of this project is to improve our molecular understanding of various lung diseases including lung cancer and chronic obstructive pulmonary disease (COPD).

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL10379

499 Samples

Download data: CEL

(Submitter supplied) Multiple gene expression studies have been performed separately in peripheral blood, lung, and airway tissues to study COPD. We performed RNA-sequencing gene expression profiling of large-airway epithelium, alveolar macrophage and peripheral blood samples from the same set of COPD cases and controls from the COPDGene study who underwent bronchoscopy at a single center. Using statistical and gene set enrichment approaches, we sought to improve the understanding of COPD by studying gene sets and pathways across these tissues, beyond the individual genomic determinants.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

63 Samples

Download data: TSV

(Submitter supplied) 70 miRNAs and 2667 mRNAs were differentially expressed between lung tissue from subjects with COPD and smokers without COPD. miRNA and mRNA expression profiles enriched for biological pathways that may be relevant to the pathogenesis of COPD including the transforming growth factor b, Wnt and focal adhesion pathways. miR-223 and miR-1274a were the most affected miRNAs in subjects with COPD compared with smokers without obstruction. more...

Organism:

Human alphaherpesvirus 1; human gammaherpesvirus 4; Betapolyomavirus macacae; Mus musculus; Human gammaherpesvirus 8; Homo sapiens; Human betaherpesvirus 5; Murid betaherpesvirus 1; Human immunodeficiency virus 1; Rattus norvegicus; JC polyomavirus; Murid gammaherpesvirus 4; Betapolyomavirus hominis

Type:

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

Platforms:

GPL7723 GPL4133

59 Samples

Download data

(Submitter supplied) In addition to analyzing whole-genome methylation, we concomitantly evaluated sputum cell gene expression in the context of chronic inflammatory lung disease. Nucleic acids were purified from sputum samples of subjects with Asthma, COPD as well as healthy controls. Gene expression was analyzed on the Agilent Human GE 4x44k v2 platform.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL13497

25 Samples

Download data: TXT

(Submitter supplied) We evaluated the applicability and usability of whole-genome methylomics of sputum samples in molecular profiling of chronic inflammatory lung diseases. Genomic DNA was purified from sputum samples of subjects with Asthma, COPD as well as healthy controls and analyzed on the Illumina Infinium HumanMethylation 450k platform.

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL13534

26 Samples

Download data: IDAT, TXT

(Submitter supplied) Chronic obstructive pulmonary disease (COPD) is a major public health problem. The aim of this study was to identify genes involved in emphysema severity in COPD patients. Gene expression profiling was performed on total RNA extracted from non-tumor lung tissue from 30 smokers with emphysema. Class comparison analysis based on gas transfer measurement was performed to identify differentially expressed genes. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL3877

30 Samples

Download data

(Submitter supplied) Gene expression profiles were generated from induced sputum samples in COPD and healthy controls. The study identified transcriptional phenotypes of COPD.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL10558

87 Samples

Download data: TXT

(Submitter supplied) Investigation of gene expression profiles among patients with COPD frequent exacerbations and to find gene targets as predictors of exacerbations

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

226 Samples

Download data: CEL

(Submitter supplied) Multiple gene expression studies have been performed in lung or airway tissues from subjects with chronic obstructive pulmonary disease (COPD). However, in comparison to genome-wide association studies (GWAS), there has been poor replication across these studies. We sought to perform gene expression profiling on a large sample of severe COPD cases and control smokers and use network methods to identify interacting genes and pathways. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL10558

151 Samples

Download data: TXT

(Submitter supplied) Whole lung tissue transcriptomic profiling studies in chronic obstructive pulmonary disease (COPD) have led to the identification of several genes associated with the severity of airflow limitation and/or the presence of emphysema, however, the cell types driving these gene expression signatures remain unidentified. T-distributed stochastic neighbor embedding and clustering of scRNA seq data revealed a total of 17 distinct populations. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

3 Samples

Download data: MTX, TSV

(Submitter supplied) Cigarette smoking is the leading cause of the respiratory diseases collectively known as chronic obstructive pulmonary disease (COPD). While the pathogenesis of COPD is complex, there is abundant evidence that alveolar macrophages (AM) play an important role. Based on the concept that COPD is a slow-progressing disorder likely involving multiple mediators released by AM activated by cigarette smoke, the present study focuses on the identification of previously unrecognized genes that may be linked to early events in the molecular pathogenesis of COPD, as opposed to factors associated with the presence of disease. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Dataset:

GDS1436

Platform:

GPL80

10 Samples

Download data: CEL, EXP

Anlaysis of alveolar macrophages of 5 phenotypically normal smokers who consume ~20 packs cigarettes/year. Smoking is the leading cause of respiratory diseases collectively known as chronic obstructive pulmonary disease (COPD). Provides insight into early events in molecular pathogenesis of COPD.

Organism:

Homo sapiens

Type:

Expression profiling by array, count, 2 stress sets

Platform:

GPL80

Series:

GSE3212

10 Samples

Download data: CEL, EXP

(Submitter supplied) Differential profiles from whole genome human expression arrays on monocytes obtained from peripheral blood in COPD was studied and compared with controls. Monocytes were isolated from Controls (Group 1) which included Control Smokers (Group 1A) and Control Never Smokers (Group 1B) and COPD (Group 2) which included COPD Smokers (Group 2A) and COPD ExSmokers (Group 2B). Differential transcriptomic expression associated with (i) Smoking, (ii) COPD, and (iii) cessation of smoking were identified.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL6480

16 Samples

Download data: TXT

(Submitter supplied) Comparison of emphysema vs non emphysema COPD lung tissue expression

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL13667

70 Samples

Download data: CEL

(Submitter supplied) Increased small airway resistance and decreased lung elasticity contribute to the airflow limitation in chronic obstructive pulmonary disease (COPD). The lesion that corresponds to loss of lung elasticity is emphysema; the small airway obstruction is due to inflammatory narrowing and obliteration. Despite their convergence in altered physiology, different mechanisms contribute to these processes. The relationships between gene expression and these specific phenotypes may be more revealing than comparison with lung function. We measured the ratio of alveolar surface area to lung volume (SA/V) in lung tissue from 43 smokers. Two samples from 21 subjects, in which SA/V differed by > 49 cm2/mL were profiled to select genes whose expression correlated with SA/V. The level of expression of 181 transcripts was related to SA/V ( p< 0.05). The relationship between expression of these transcripts and SA/V was tested in the 22 remaining subjects as a replication. Thirty of the 181 genes remained significantly associated with SA/V (P<0.05) and the direction of association was the same in 164/181. Pathway and network analysis revealed enrichment of genes involved in protein ubiquitination, and western blotting showed altered expression of genes involved in protein ubiquitination in obstructed individuals. These data implicate modified protein ubiquitination and degradation as a potentially important pathway in the pathogenesis of emphysema. Raw data not available for this study

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL3991

42 Samples

Download data: TXT