GEO DataSets

(Submitter supplied) The goal of this study was to investigate and correlate differential methylation and expression in cells from the target organ in non-infectious granulomatous lung diseases, specifically sarcoidosis and chronic beryllium disease (CBD). To that end, cells were collected from patients via bronchoalveolar lavage (BAL), and extracted nucleic acids were hybridized to genome-wide arrays. We conclude that there are many genes that are both differentially methylated and expressed in the BAL fluid of patients with granulomatous lung disease. more...

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL13534

24 Samples

Download data: IDAT

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

Organism:

Homo sapiens

Type:

Expression profiling by array; Methylation profiling by genome tiling array

Platforms:

GPL21185 GPL570 GPL13534

94 Samples

Download data: CEL, IDAT, TXT

(Submitter supplied) The goal of this study was to investigate and correlate differential methylation and expression in cells from the target organ in non-infectious granulomatous lung diseases, specifically sarcoidosis and chronic beryllium disease (CBD). To that end, cells were collected from patients via bronchoalveolar lavage (BAL), and extracted nucleic acids were hybridized to genome-wide arrays. We conclude that there are many genes that are both differentially methylated and expressed in the BAL fluid of patients with granulomatous lung disease. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

22 Samples

Download data: CEL

(Submitter supplied) The goal of this study was to investigate and correlate differential methylation and expression in cells from the target organ in non-infectious granulomatous lung diseases, specifically sarcoidosis and chronic beryllium disease (CBD). To that end, cells were collected from patients via bronchoalveolar lavage (BAL), and extracted nucleic acids were hybridized to genome-wide arrays. We conclude that there are many genes that are both differentially methylated and expressed in the BAL fluid of patients with granulomatous lung disease. more...

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL13534

24 Samples

Download data: IDAT

(Submitter supplied) The goal of this study was to investigate and correlate differential methylation and expression in cells from the target organ in non-infectious granulomatous lung diseases, specifically sarcoidosis and chronic beryllium disease (CBD). To that end, cells were collected from patients via bronchoalveolar lavage (BAL), and extracted nucleic acids were hybridized to genome-wide arrays. We conclude that there are many genes that are both differentially methylated and expressed in the BAL fluid of patients with granulomatous lung disease. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL21185

24 Samples

Download data: TXT

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

Organism:

Homo sapiens

Type:

Expression profiling by array; Methylation profiling by genome tiling array

Platforms:

GPL21145 GPL21185

144 Samples

Download data: IDAT, TXT

(Submitter supplied) We performed gene expression profiling between Chronic Beryllium Disease, beryllium-sensitized, and healthy control bronchoalveolar cells, and integration with methylation and proteomic data

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL21185

72 Samples

Download data: TXT

(Submitter supplied) We performed DNA methylation profiling between Chronic Beryllium Disease, beryllium-sensitized, and healthy control bronchoalveolar cells, and integration with gene expression and proteomic data

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL21145

72 Samples

Download data: IDAT

(Submitter supplied) Approximately 60-70% of patients with pulmonary sarcoidosis have a good outcome, with disease that resolves spontaneously. It is unclear why some patients progress to fibrotic disease, and there is currently no marker that differentiates these patients from those with self-limiting lung disease. Using the Affymetrix Human Gene 1.0 ST Array, we examined gene expression in lung tissue samples obtained using bronchoscopic transbronchial biopsy from 8 patients with active but self-limiting pulmonary sarcoidosis and 7 with active, progressive, fibrotic pulmonary disease. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Dataset:

GDS3705

Platform:

GPL6244

15 Samples

Download data: CEL

Comparison of lungs from patients with nodular self-limiting pulmonary sarcoidosis (PS) to those with progressive fibrotic PS. About 60-70% of patients with PS have disease that resolves spontaneously, the rest follow a chronic course. Results provide insight into the pathogenesis of progressive PS.

Organism:

Homo sapiens

Type:

Expression profiling by array, transformed count, 2 disease state sets

Platform:

GPL6244

Series:

GSE19976

15 Samples

Download data: CEL

(Submitter supplied) We hypothesized that tissue genome-wide gene expression analysis, coupled with gene network analyses of differentially expressed genes, would provide novel insights into the pathogenesis of pulmonary sarcoidosis. Keywords: Disease state analysis

Organism:

Homo sapiens

Type:

Expression profiling by array

Dataset:

GDS3580

Platform:

GPL570

12 Samples

Download data: CEL

Analysis of lungs from patients with pulmonary sarcoidosis (PS). PS is characterized by the granulomatous inflammation of the lung. Results provide insight into the molecular pathogenesis of PS.

Organism:

Homo sapiens

Type:

Expression profiling by array, transformed count, 2 disease state sets

Platform:

GPL570

Series:

GSE16538

12 Samples

Download data: CEL

(Submitter supplied) Gene expression profiles were performed from CD3+ T cells isolated from peripheral blood samples of untreated patients with cHL versus 2 control groups consisting of healthy donors and patients with sarcoidosis. Keywords = Hodgkin’s Lymphoma Keywords = T cell Keywords = immune regulation Keywords: repeat sample

Organism:

Homo sapiens

Type:

Expression profiling by array

Dataset:

GDS1419

Platform:

GPL8300

6 Samples

Download data

Expression profiling of CD3+ T cells isolated from peripheral blood samples of untreated patients with classical Hodgkin's lymphoma. CD3+ T cells from healthy donors and patients with sarcoidosis also examined.

Organism:

Homo sapiens

Type:

Expression profiling by array, count, 3 disease state sets

Platform:

GPL8300

Series:

GSE2657

6 Samples

Download data

(Submitter supplied) Sarcoidosis + Follow-up 6 month after Keywords = sarcoidosis Keywords = follow-up Keywords: other

Organism:

Homo sapiens

Type:

Expression profiling by array

Platforms:

GPL8300 GPL91

32 Samples

Download data: CEL

(Submitter supplied) Rationale: Despite the availability of multi-“omics” strategies, insights into the etiology and pathogenesis of sarcoidosis have been elusive. This is partly due to the lack of reliable preclinical models and a paucity of validated biomarkers. As granulomas are a key feature of sarcoidosis, we speculate that direct genomic interrogation of sarcoid tissues, may lead to identification of dysregulated gene pathways or biomarker signatures. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

31 Samples

Download data: FASTA, TSV, TXT

(Submitter supplied) Lung macrophages are major participants in the pulmonary innate immune response. In the cystic fibrosis (CF) lung, the inability of lung macrophages to successfully regulate the exaggerated inflammatory response suggests dysfunctional innate immune cell function. In this study, we aim to gain insight into innate immune cell dysfunction in CF by investigating alterations in DNA methylation in bronchoalveolar lavage (BAL) cells, composed primarily of lung macrophages of CF subjects compared with healthy controls. more...

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL21145

16 Samples

Download data: IDAT

(Submitter supplied) Rationale: A well-validated animal model of sarcoidosis can help advance our understanding of the pathobiology of this complex disease. We have developed a multiwall carbon nanotube (MWCNT) based murine model that shows marked histological and inflammatory signal similarities to human sarcoidosis. In this study, we compared the alveolar immune cell transcriptional signatures of our murine model with human sarcoidosis to comprehensively assess overlapping molecular programs. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL6887

12 Samples

Download data: TXT

(Submitter supplied) DNA methylation is an important epigenetic modification involved in many biological processes and diseases. Many studies have mapped DNA methylation changes associated with embryogenesis, cell differentiation and cancer at a genome-wide scale. Our understanding of genome-wide DNA methylation changes in a developmental or disease-related context has been steadily growing. However, the investigation of which CpGs are variably methylated in different normal cell or tissue types is still limited. more...

Organism:

Homo sapiens

Type:

Methylation profiling by high throughput sequencing; Third-party reanalysis

Platforms:

GPL9115 GPL11154

31 Samples

Download data: TXT

(Submitter supplied) Genome wide DNA methylation from peripheral white blood cells (PWBCs) from individuals from different cohorts included in the MENA project. Samples included 474 individuals (DiOGenes-UNAV n=52, OBEPALIP n=29, Food4Me-UNAV n=39, GEDYMET n=57, ICTUS n=7, NUGENOB-UNAV n=22, PREDIMED-UNAV n=116, RESMENA n=44, OBEKIT n=96, and NormoP n=12). The Illumina Infinium 450k Human DNA methylation Beadchip or Infinium MethylationEPIC Beadchip (for OBEKIT) was used to obtain DNA methylation profiles across approximately 450,000 CpGs in these samples.

Organism:

Homo sapiens

Type:

Methylation profiling by array; Methylation profiling by genome tiling array

Platforms:

GPL16304 GPL21145

474 Samples

Download data: IDAT, TXT