GEO DataSets

(Submitter supplied) Idiopathic pulmonary fibrosis (IPF) is a chronic and progressive fibrosing interstitial lung disease that is unresponsive to current therapy. While it carries a median survival of less than 3 years its rate of progression varies widely between patients. We hypothesized that studying the gene expression profiles of physiologically stable patients and those in which the disease progressed rapidly after the initial diagnosis would aid in the search for biomarkers and contribute to the understanding of disease pathogenesis.

Organism:

Homo sapiens

Type:

Expression profiling by SAGE

Platform:

GPL4

14 Samples

Download data

(Submitter supplied) Peripheral blood biomarkers are needed to identify and determine the extent of idiopathic pulmonary fibrosis (IPF). Current physiologic and radiographic prognostic indicators diagnose IPF too late in the course of disease. These results demonstrate that the peripheral blood transcriptome can distinguish normal individuals from patients with IPF, as well as extent of disease when samples were classified by percent predicted DLCO, but not FVC.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL6480

123 Samples

Download data: TXT

(Submitter supplied) Idiopathic pulmonary fibrosis (IPF) and non-specific interstitial pneumonia (NSIP) are the 2 most common forms of idiopathic interstitial pneumonia. Response to therapy and prognosis are remarkably different. The clinical-radiographic distinction between IPF and NSIP may be challenging. We sought to investigate the gene expression profile of IPF vs. NSIP We used microarray to identifiy the gene expression profiles in patients with IPF and NSIP, mixed IPF/NSIP histologic pattern and normal controls.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL6244

48 Samples

Download data: CEL

(Submitter supplied) There is microscopic spatial and temporal heterogeneity of pathologic changes in idiopathic pulmonary fibrosis (IPF) lung tissue, which may relate to heterogeneity in pathophysiological mediators of disease and clinical progression. We measured gene expression in samples from lung biopsies or explants in order to assess relationships with pathological features and systemic biomarkers.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL6480

48 Samples

Download data: TXT

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

Organism:

Homo sapiens; synthetic construct

Type:

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

Platforms:

GPL6244 GPL8786

409 Samples

Download data: CEL

(Submitter supplied) Rationale: The fibrosing idiopathic interstitial pneumonias (IIPs) are classified based on clinical, radiographic, and pathologic criteria. The separation into phenotypic subgroups is useful in predicting outcome and therapeutic strategy; however a large degree of ambiguity remains. Gene expression profiling may contribute to traditional criteria in IIPs by characterizing the dynamic biology that more accurately distinguishes subtypes of these diseases or their prognoses. more...

Organism:

synthetic construct; Homo sapiens

Type:

Non-coding RNA profiling by array

Platform:

GPL8786

192 Samples

Download data: CEL

(Submitter supplied) Rationale: The fibrosing idiopathic interstitial pneumonias (IIPs) are classified based on clinical, radiographic, and pathologic criteria. The separation into phenotypic subgroups is useful in predicting outcome and therapeutic strategy; however a large degree of ambiguity remains. Gene expression profiling may contribute to traditional criteria in IIPs by characterizing the dynamic biology that more accurately distinguishes subtypes of these diseases or their prognoses. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL6244

217 Samples

Download data: CEL

(Submitter supplied) Idiopathic pulmonary fibrosis (IPF) is a chronic progressive fibrotic lung disease associated with significant morbidity and mortality. We identified a combinatorial signature of 5 proteins that was sufficient to distinguish IPF patients from controls; of these proteins MMP7 and MMP1 exhibited significantly higher values in both peripheral blood concentrations and lung tissue gene expression, suggesting their role as true biomarkers. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL4133

46 Samples

Download data: TXT

(Submitter supplied) We aimed at characterizing disease-specific differences by comparing the transcriptomes of epithelial cells (ECs) from idiopathic pulmonary fibrosis (IPF) and non-IPF sources

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

10 Samples

Download data: CSV, RDS

(Submitter supplied) BACKGROUND: Idiopathic Pulmonary Fibrosis (IPF) is a lethal lung disease of unknown etiology. A major limitation in transcriptomic profiling of lung tissue in IPF has been a dependence on snap-frozen fresh tissues (FF). In this project we sought to determine whether RNA-Seq could be used to identify IPF expression profiles from archived Formalin-Fixed Paraffin-Embedded (FFPE) lung fibrotic tissue. RESULTS: We isolated total RNA from 7 IPF and 5 control FFPE lung tissues (median archived time 6 years) and performed 50 bp paired-end sequencing on Illumina 2000 HiSeq. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

11 Samples

Download data: TXT

(Submitter supplied) Idiopathic pulmonary fibrosis (IPF) is a progressive lethal interstitial lung disease of unkown etiology with limited effective therapies. The pathogenic mechanisms of IPF remain unkown. Emerging evidences indicate that abnormal behaviors of fibroblasts in IPF are associated with a variety of genetic alterations and aberrant reactivation of developmental signaling pathways. We compared gene expression profiles in fibrotic lung tissues from IPF patients and normal lung tissues from patients with primary spontaneous pneumothorax using cDNA microarray to examine the mechnisms involved in the pathogenesis of IPF.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL17586

8 Samples

Download data: CEL

(Submitter supplied) Idiopathic pulmonary fibrosis (IPF) is a chronic fibrosing lung disease that is difficult to diagnose and follows an unpredictable clinical course. The object of this study was to develop a predictive gene signature model of IPF from whole lung tissue. We collected whole lung samples from 11 IPF patients undergoing diagnostic surgical biopsy or transplantation. Whenever possible, samples were obtained from different lobes. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Dataset:

GDS4279

Platform:

GPL570

23 Samples

Download data: CEL

Analysis of whole lung biopsy or explant from early and advanced idiopathic pulmonary fibrosis (IPF) patients. IPF is a fatal subtype of pulmonary fibrosis difficult to diagnose. Results provide insight into developing a diagnostic model for IPF.

Organism:

Homo sapiens

Type:

Expression profiling by array, transformed count, 3 disease state, 3 gender, 3 specimen, 3 tissue sets

Platform:

GPL570

Series:

GSE24206

23 Samples

Download data: CEL

(Submitter supplied) Idiopathic pulmonary fibrosis (IPF) and lung cancer share common risk factors, epigenetic and genetic alterations, cellular and molecular aberrations, the activation of similar signaling pathways and poor survival. The aim of this study was to examine the gene expression profiles of stromal cells from patients with IPF and lung adenocarcinoma (ADC) as well as from normal lung.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL22321

12 Samples

Download data: CEL

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

Organism:

Homo sapiens

Type:

Methylation profiling by array; Expression profiling by array

Platforms:

GPL10558 GPL8490

14 Samples

Download data

(Submitter supplied) Genome wide DNA methylation profiling of normal and IPF lung samples. The Illumina human methylation 27 Beadchip was used to obtain DNA methylation profiles across approximately 27,000 CpGs samples. 2 normal samples, and 4 IPF samples

Organism:

Homo sapiens

Type:

Methylation profiling by array

Platform:

GPL8490

6 Samples

Download data: TXT

(Submitter supplied) To compare the gene expression changes in IPF and normal lung tissues.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL10558

8 Samples

Download data: TXT

(Submitter supplied) The activated fibroblast is the central effector cell for the progressive fibrotic process that characterizes idiopathic pulmonary fibrosis (IPF). An understanding of the genomic phenotype of this cell in isolation is essential to the understanding of disease pathogenesis and is integral to strategizing therapeutic trials. Employing a unique technique that minimizes cellular phenotypic alterations, we characterized the genomic phenotype of non-cultured pulmonary fibroblasts from the lungs of patients with advanced IPF. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL8903

58 Samples

Download data: GPR, MEV, TXT

(Submitter supplied) Objectives: Idiopathic pulmonary fibrosis (IPF) is a complex disease in which a multitude of proteins and networks are disrupted. Interrogation of genome-wide transcription through RNA sequencing (RNA-Seq) enables the determination of genes whose differential expression is most significant in IPF, as well as the detection of alternative splicing events which are not easily observed with traditional microarray experiments. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

15 Samples

Download data: TXT

(Submitter supplied) Global mRNA expression was compared between stable and progressive IPF using bronchoalveolar lavage derived mesenchymal stromal cells

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

8 Samples

Download data: CEL