GEO DataSets

(Submitter supplied) Current concepts of idiopathic pulmonary fibrosis (IPF) are that microscopic injury drives alveolar epithelial cell dysregulated activation and epithelial mesenchymal transition, ensuing fibrocyte recruitment, fibroblast proliferation and ECM deposition. With the background that IPF is also characterized by chronic accumulation of activated alveolar macrophages (aMAC) in the lower respiratory tract, we assessed IPFaMAC gene expression to identify patterns of activation, by RNA-seq using Illumina platform. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

23 Samples

Download data: TXT

(Submitter supplied) Background: We got interested whether genes of airway basal cells are enriched in COPD. Methods: Bronchoscopy with bronchial brushes and bronchoalveolar lavage was performed in 28 patients with COPD and 29 healthy donors and isolated BAL cells.Transcriptome of BAL cells were studied by using Affymetrix Human Genome U133 Plus 2.0 array on an Affymetrix platform. Microarray data were normalized data were imported, log2-transformed and quantile normalized using robust multi-array average (RMA). more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

57 Samples

Download data: CEL

(Submitter supplied) Background: We got interested whether genes of airway basal cells are enriched in sarcoidosis. Methods: Bronchoscopy with bronchoalveolar lavage (BAL) was performed in 26 patients with sarcoidosis, chest-x-ray type III and IV, and 20 healthy donors and isolated BAL cells.Transcriptome of BAL cells were studied by using Affymetrix Human Affymetrix Whole-Transcript Human Gene 1.0 ST array on an Affymetrix platform. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL10739

46 Samples

Download data: CEL

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

Organism:

Homo sapiens

Type:

Expression profiling by array

4 related Platforms

321 Samples

Download data: CEL, TXT

(Submitter supplied) Background: Idiopathic pulmonary fibrosis (IPF) is a fatal disease with variable outcome. Currently, there is little information whether changes in molecular pathways in the alveolar compartment of patients with IPF are indicative of disease progression. To address this question we analyzed gene expression signatures in cells obtained from bronchoalveolar lavage (BAL) of patients with IPF. Methods: BAL cells were harvested from 212 IPF patients and 20 healthy donors at the time of diagnosis. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platforms:

GPL14550 GPL17077

196 Samples

Download data: TXT

(Submitter supplied) Background: Based on previous publication and our own data we became interested in the gene expression signature of airway basal cells. Methods: Bronchoscopy with bronchial brushes and bronchoalveolar lavage was performed in healthy donors. Airway basal cells were obtained by brushing segmental bronchi of the right lower lobe and outgrowth of cells in BEGM supplemented with growth factors according to the manufacturer’s instructions. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL14550

22 Samples

Download data: TXT

(Submitter supplied) Background: When exposed to specific stimuli, macrophages exhibit distinct activation programs, M1 and M2 polarization, that define macrophage function as inflammatory/immune effectors or anti-inflammatory/tissue remodeling cells, respectively. Due to their position on the lung epithelial surface, alveolar macrophages (AM) directly interact with environmental stimuli such as cigarette smoke, the major risk factor for the development of chronic obstructive pulmonary disease (COPD). more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

70 Samples

Download data: CEL, CHP

(Submitter supplied) Changes in the respiratory microbiome are associated with disease progression in Idiopathic pulmonary fibrosis (IPF). The role of the host response to the respiratory microbiome however remains unknown. The role of this study is to explore the host-microbial interaction in IPF. Network analysis of gene expression data identified two gene modules that strongly associate with a diagnosis of IPF, BAL bacterial burden (determined by 16S quantitative PCR) and specific microbial OTUs, as well as lavage and peripheral blood neutrophilia. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL11532

174 Samples

Download data: CEL

(Submitter supplied) Background. Animal models of elastase intratracheal instillation have shown that elastase, unopposed by α-1 antitrypsin (AAT), can induce alveolar hemorrhage with ensuing macrophage inflammation and lung damage. Aim. To identify markers of alveolar hemorrhage and damage using bronchoalveolar lavage (BAL) samples and lung tissue explants from AAT deficient (AATD) subjects. Methods. BAL samples (17 patients, 15 controls) were evaluated for free heme and iron concentrations. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21697

12 Samples

Download data: CSV, XLSX

(Submitter supplied) p300 was knockout in ATII cells of murine lung, and then treated with 4mg/kg bleomycin for 2 weeks.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21103

12 Samples

Download data: TXT

(Submitter supplied) We report the application of Chromatin immunoprecipitation sequencing technology for p300 protein in PBS- or bleomycin-treated lung of mice.

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL19057

3 Samples

Download data: BW

(Submitter supplied) Idiopathic pulmonary fibrosis (IPF) is a lethal interstitial lung disease causing alveolar remodeling, inflammation, and fibrosis. We utilized single cell RNA-sequencing (scRNA-Seq) to identify epithelial cell types and associated biological processes involved in the pathogenesis of IPF. Transcriptomic analysis of epithelial cells from normal human lung defined gene expression patterns associated with highly differentiated alveolar type 2 (AT2) cells, indicated by enrichment of RNAs critical for surfactant homeostasis. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

6 Samples

Download data: XLSX

(Submitter supplied) Idiopathic pulmonary fibrosis (IPF) is a lethal interstitial lung disease causing alveolar remodeling, inflammation, and fibrosis. We utilized single cell RNA-sequencing (scRNA-Seq) to identify epithelial cell types and associated biological processes involved in the pathogenesis of IPF. Transcriptomic analysis of epithelial cells from normal human lung defined gene expression patterns associated with highly differentiated alveolar type 2 (AT2) cells, indicated by enrichment of RNAs critical for surfactant homeostasis. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

540 Samples

Download data: TXT

(Submitter supplied) Idiopathic pulmonary fibrosis (IPF) is a chronic lethal disease in the absence of demonstrated efficacy for preventing progression. Although macrophage-mediated alveolitis is determined to participate myofibrotic transition during disease development, the paradigm of continuous macrophage polarization is still under-explored due to lack of proper animal-models. Here, by integrating 2.5 U/kg intratracheally Bleomycin administration and 10 Gray thorax irradiation at day 7, we generated a murine model with continuously alveolitis-mediated fibrosis, which mimics most of the clinical features of our involved IPF patients. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

1 Sample

Download data: MTX, TSV

(Submitter supplied) To investigate the effects of miR-33 inhibition on gene expression profile of IPF lung in an ex vivo model

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

8 Samples

Download data: TXT

(Submitter supplied) Aging is associated with progressive decline in lung function and responses to environmental stress culminating in increased incidence of lung diseases. Initial analysis of Atp8b1 (ATPase, Aminophospholipid Transporter, Class I, Type 8B, Member 1) mutant mice (on C57BL/6J background) revealed deficiency in transporter function and was associated with decreased lung function. Therefore, to further study the aging-related genes in the lungs at the molecular level, the transcriptome analysis of Atp8b1 mutant and C57BL/6J lungs were carried out at 14 M and 7_9 wks of age. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL1261

23 Samples

Download data: CEL

(Submitter supplied) Rationale: Airspace macrophages are the most abundant cell in airspaces and are viewed as a homogeneous population during health. Single cell RNA sequencing allows for examination of transcriptional heterogeneity between cells and between individuals. Understanding the conserved repertoire of airspace leukocytes during health is essential to understanding cellular programing during disease. Objective: We sought to determine the transcriptional heterogeneity of human bronchoalveolar lavage cells in healthy adults. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

10 Samples

Download data: CSV

(Submitter supplied) In a prior report, we observed two distinct lung microbiomes in healthy subjects that we termed “pneumotypes”: pneumotypeSPT, characterized by high bacterial load and supraglottic predominant taxa (SPT) such as the anaerobes Prevotella and Veillonella; and pneumotypeBPT, with low bacterial burden and background predominant taxa (BPT) found in the saline lavage and bronchoscope. Here, we determined the prevalence of these two contrasting lung microbiome types, in a multi-center study of healthy subjects. more...

Organism:

human lung metagenome

Type:

Other

Platform:

GPL21074

1 Sample

Download data: TXT

(Submitter supplied) We perform single-cell RNA-seq on Bronchoalvaolar Lavage (BAL) fluid from 4 healthy volunteers.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20301

4 Samples

Download data: H5

(Submitter supplied) In order to identify transcript changes in response to DEF , we used human macrophages with or without DEF treatment. In order to study the effect of iron chelation on LPS-polarized macrophage transcriptome, we exposed DEF-treated or control macrophages to short time exposure to LPS. We then performed whole-genome transcriptome sequencing by RNA-sequencing (RNA-seq).

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

12 Samples

Download data: CSV, TXT