GEO DataSets

(Submitter supplied) Background. Circular RNAs (circRNAs) play an important role in the occurrence and development of diseases. However, the role of circRNAs in male smokers with chronic obstructive pulmonary disease (COPD) remains unclear. Methods. Stable COPD patients and healthy controls were recruited. Peripheral blood mononuclear cells (PBMCs) were extracted. After high-throughput RNA sequencing (RNA-Seq) of PBMCs, a bioinformatics method was used to analyse differentially expressed (DE) circRNAs (DEcircRNAs) and mRNAs (DEmRNAs). more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing

Platform:

GPL20301

10 Samples

Download data: FA, FASTA, GTF, TXT

(Submitter supplied) Humans can be exposed to per- and polyfluoroalkyl substances (PFASs) via many exposure routes, including diet, which may lead to several adverse health effects. So far, little is known about PFAS transport across the human intestinal barrier. In the current study, we aimed to assess the transport of 5 PFASs (PFOS, PFOA, PFNA, PFHxS and HFPO-DA) in a human induced pluripotent stem cell (hiPSC)-derived intestinal epithelial cell (IEC) model. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

12 Samples

Download data: TXT

(Submitter supplied) Background Kabuki syndrome (KS) is a genetic disorder caused by DNA mutations in KMT2D, a lysine methyltransferase that methylates histones and other proteins, and therefore modifies chromatin structure and subsequent gene expression. Ketones, derived from the ketogenic diet, are histone deacetylase inhibitors that can ‘open’ chromatin and encourage gene expression. Preclinical studies have shown that the ketogenic diet rescues hippocampal memory neurogenesis in mice with KS via the epigenetic effects of ketones. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20301

5 Samples

Download data: MTX, TSV

(Submitter supplied) Electronic nicotine delivery system (ENDs) use among youth and young adults is increasing at a rapid pace and represents a growing public health threat.1 Newer generation devices heat e-liquids to higher temperatures and can achieve higher serum nicotine concentrations than older devices.1 Interleukin-6 (IL-6) is a cytokine that mediates atherogenesis and independently predicts future atherosclerotic cardiovascular disease events.2 Previous in vitro studies have demonstrated increased IL-6 production by human alveolar macrophages exposed to ENDs condensate.3 Although there has been considerable focus on the effects of ENDs use on airway inflammation, there are a paucity of data on the effects of ENDS on arterial inflammation. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL30173

18 Samples

Download data: TSV

(Submitter supplied) Club (“Clara”) cells, dome shaped cells with disease cytoplasmic granules and microvilli, are the major secretory cell of the human small (>6 generation) airways. Little is known regarding the biology of club cells in the human airway, nor of the ontogeny of this cell type. Taking advantage of the SCGB1A1 as the marker for club cells and our ability to sample the normal small airway epithelium by bronchoscopy and brushing healthy volunteers, we defined the transcriptome of the normal human airway club cell using single cell transcriptome sequencing. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

157 Samples

Download data: CSV

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

Organism:

Homo sapiens

Type:

Expression profiling by array; Expression profiling by high throughput sequencing

Platforms:

GPL9115 GPL570

42 Samples

Download data: CEL, CHP

(Submitter supplied) Matrix metalloproteinase-9 (MMP-9) expression is up-regulated in alveolar macrophages (AM) of HIV1+ smokers who develop emphysema. Based on the knowledge that lung epithelial lining fluid (ELF) of HIV1+ smokers has increased levels of inflammatory cytokines compared to HIV1- smokers, we hypothesized up-regulation of lung cytokines in HIV1+ smokers may be functionally related to increased MMP-9 expression. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL9115

8 Samples

Download data: TXT

(Submitter supplied) Matrix metalloproteinase-9 (MMP-9) expression is up-regulated in alveolar macrophages (AM) of HIV1+ smokers who develop emphysema. Based on the knowledge that lung epithelial lining fluid (ELF) of HIV1+ smokers has increased levels of inflammatory cytokines compared to HIV1- smokers, we hypothesized up-regulation of lung cytokines in HIV1+ smokers may be functionally related to increased MMP-9 expression. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

34 Samples

Download data: CEL, CHP

(Submitter supplied) Human airway basal cells (BC) are the stem/progenitor population of the airway epithelium, and play a central role in anchoring the epithelium to the basement membrane. The anatomic position of BC allows for potential paracrine signaling between BC and the underlying non-epithelial stromal cells. In support of this, we previously demonstrated endothelial cells (EC) support growth of BC during co-culture via vascular endothelial growth factor A (VEGFA)-mediated signaling. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

10 Samples

Download data: FPKM_TRACKING

(Submitter supplied) Background: Vitamin D is associated with lung health in epidemiologi studies, but mechanisms mediating observed associations are poorly understood. This study explores mechanisms for an effect of vitamin D in lung through an in vivo gene expression study, an expression quantitative trait loci (eQTL) analysis in lung tissue, and a population-based cohort study of sequence variants. Methods: Microarray analysis investigated the association of gene expression in small airway epithelial cell with serum 25[OH]D in adult nonsmokers. more...

Organism:

Homo sapiens

Type:

Expression profiling by array; SNP genotyping by SNP array; Genome variation profiling by SNP array

Platforms:

GPL6804 GPL570

142 Samples

Download data: CEL, CHP

(Submitter supplied) Motivation: Computational inference methods that make use of graphical models to extract regulatory networks from gene expression data can have difficulty reconstructing dense regions of a network, a consequence of both computational complexity and unreliable parameter estimation when sample size is small. As a result, identification of hub genes is of special difficulty for these methods.Methods: We present a new algorithm, Empirical Light Mutual Min (ELMM), for large network reconstruction that has properties well suited for dense graph recovery. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

270 Samples

Download data: CEL, CHP

(Submitter supplied) In the context that HOX mutant mice have profound deficits in airway branching morphogenesis, we asked whether the positional identity of HOX genes is maintained in the epithelium of the adult human tracheobronchial tree and if so, whether these positional differences are embedded in the stem/progenitor population derived from nonbranching vs branching airways. We found that 10 of 39 HOX genes are expressed in varying degrees in the nonbranching (trachea) or branching (large and small airways) human airway epithelium. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

60 Samples

Download data: CEL, CHP

(Submitter supplied) Background: Cases where genotype-phenotype relationships depend on environmental factors have been quantified for many complex diseases. Such genotype-environment interactions (GEI or GxE) may also affect expression Quantitative Trait Loci (eQTL) present in tissues critical for the manifestation of disease. To assess this hypothesis, we performed an analysis of eQTL-GEI resulting from an individual's smoking environment in the lung small airway epithelium (SAE). more...

Organism:

Homo sapiens

Type:

Expression profiling by array; SNP genotyping by SNP array

Platforms:

GPL570 GPL6804

180 Samples

Download data: CEL, CHP

(Submitter supplied) CXCL14, a recently described chemokine constitutively expressed in various epithelia, has multiple putative roles in inflammation and carcinogenesis. Based on the knowledge that cigarette smoking and the smoking-induced disorders, such as chronic obstructive pulmonary disease (COPD) and lung cancer, are associated with inflammation, we hypothesized that the airway epithelium, the primary site of smoking-induced pathologic changes in COPD and adenocarcinoma, responds to cigarette smoking with an altered CXCL14 gene expression as a part of disease-relevant molecular phenotype. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

135 Samples

Download data: CEL, CHP

(Submitter supplied) Testican 3 (coded for by SPOCK3), is an extracellular matrix heparan/chondroitin sulphate proteoglycan that possesses serine and cysteine protease inhibitor-like domains Based on the knowledge that serine proteases contribute to the destruction of the lung in cigarette smokers, but that only a fraction of smokers develop smoking-induced lung disease, we hypothesized that smokers expressed SPOCK3 at lower levels in the small airway epithelium, the initial site of smoking-induced disease, and further, that genetic variability modulates the expression of SPOCK3 in the airway epithelium. more...

Organism:

Homo sapiens

Type:

Expression profiling by array; SNP genotyping by SNP array; Genome variation profiling by SNP array

Platforms:

GPL570 GPL6804

212 Samples

Download data: CEL, CHP

(Submitter supplied) Since the primary effect of the ketogenic diet is to establish a glucose-deprived condition in vivo, we, therefore, used glucose starvation in vitro to mimic the effects of the keto diet. In our endeavor to comprehend the influence of glucose starvation on pro-metastatic genes associated with BACH1, we performed RNA-Seq analysis on MDA-MB-231 ctrl cells and BACH1 knockout cells.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

10 Samples

Download data: XLSX

(Submitter supplied) The Recombinant human bone morphogenetic protein 2 (rhBMP-2) and the human bone marrow mesenchymal stromal cells (hBM-MSCs) have been thoroughly studied with research and translational bone regenerative purposes. rhBMP-2 induces in vivo the endochondral ossification and bone formation processes, while hBM-MSCs are considered its target, bone forming cells. The in vitro ability of rhBMP-2 to induce hBM-MSC osteogenic differentiation has been previously tested. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

6 Samples

Download data: TAB

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

Organism:

Homo sapiens; Mus musculus

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL29480 GPL28330

43 Samples

Download data: BIGWIG, BW, CSV, RESULTS

(Submitter supplied) Obesity is a risk factor for developing severe COVID-19. However, the mechanism underlying obesity-accelerated COVID-19 remains unclear. Here, we report results from a study in which K18-hACE2 mice were fed an obesity-inducing western diet (WD) for over 3 months before intranasal infection with SARS-CoV2. After infection, the WD-fed K18-hACE2 mice lost more body weight and had more severe lung inflammation than normal chow (NC)-fed mice. more...

Organism:

Mus musculus; Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL30173 GPL30172

24 Samples

Download data: TXT

(Submitter supplied) The aim of this work is to demonstrate the correlation of Oral Squamous Cell Carcinoma (OSCC) tumor inflammation and stromal density with patient demographics and with the differential gene expression (DGE) analysis of 8 OSCC tumor tissue. Using the IO-360 nanoString platform, we showed that at a transcriptional level, decreased cytokine signaling and activation of oncogenic pathways were observed in immune excluded tumors and absence of peritumoral stromal inflammation. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL27956

8 Samples

Download data: RCC