GEO DataSets

(Submitter supplied) We have completed the Human lncRNA microarray analysis of the 4 samples that you submitted. Total RNA from each sample was quantified using the Nanodrop 1000 and the RNA integrity was assessed by Agilent 2100 Bioanalyzer. About 5 μg total RNA of each sample was used for labeling and array hybridization as the following steps: 1) Reverse transcription with invitrogen Superscript ds-cDNA synthesis kit; 2) ds-cDNA labeling with Nimblegen one-color DNA labeling kit; 3) Array hybridization using the NimbleGen Hybridization System and followed by washing with the Nimblegen wash buffer kit. more...

Organism:

Homo sapiens

Type:

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

Platform:

GPL35135

4 Samples

Download data: CALLS, PAIR, XLS

(Submitter supplied) Cigarette smoke has been demonstrated to stimulate the growth of existing bladder tumors by enhancing the survival and proliferation of cancer cells through the action of carcinogens present in smoke. Concurrently, Fatty Acid Synthase (FASN), a key enzyme in fatty acid synthesis crucial for lipid metabolism, exhibits dysregulation in various cancer types, often correlating with aggressive phenotypes. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL24676

3 Samples

Download data: BIGWIG, NARROWPEAK

(Submitter supplied) RNA seq was applied to the lung and liver tissues from mice with different treatment regimen to evaluate the potential effects on global transcription.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24247

29 Samples

Download data: CSV

(Submitter supplied) Emphysema is a major pathological phenotype of chronic obstructive pulmonary disease (COPD) that is characterized by progressive and irreversible alveolar tissue destruction caused by several stressors, such as tobacco smoke and air pollution. It remains incurable in part due to an incomplete understanding of cellular and molecular mechanisms underlying the failure of tissue repair. Here, we have generated a single cell RNA sequencing dataset of enriched epithelial cells from emphysematous parenchymal lung tissue of COPD patients and from healthy controls. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24247

5 Samples

Download data: CSV, MTX, TSV

(Submitter supplied) Purpose: Localized diseases are affected by and affect the systemic environment via blood circulation. In our studies, we explored the differences in different types of circulating serum RNAs between wet age-related macular degeneration (wAMD) patients and controls. Methods: Blood samples were obtained from 60 Finnish wAMD patients and 64 controls. After serum preparation and RNA sequencing, the count data was examined for differentially expressed genes (DEGs) and further checked for enriched molecular pathways and ontology terms as well as links to clinical data. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

124 Samples

Download data: TXT

(Submitter supplied) In the lungs of chronic obstructive pulmonary disease (COPD) patients, numerous cell types interact in a structurally abnormal and inflammatory microenvironment. Assessing gene expression in individual cells by single-cell RNA sequencing (scRNA-seq) allows for a deeper understanding of cell types within a complex sample, like the COPD distal lung. ScRNA-seq data can be combined with cell-cell communication prediction tools to predict cellular interactions within a given sample; indeed, this approach was previously used to show evidence for increased endothelial CXCL signaling in COPD. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

6 Samples

Download data: MTX, TSV

(Submitter supplied) The prevalence of lung adenocarcinoma (LUAD) has increased sharply in East Asia. Early diagnosis leads to better survival rates, but this requires an improved understanding of the molecular changes during early tumorigenesis, particularly in non-smokers. We performed whole exome-sequencing and RNA-sequencing of samples from 94 East Asian patients with precancerous lesions (25 with atypical adenomatous hyperplasia [AAH]; 69 with adenocarcinoma in situ [AIS]) and 73 patients with early invasive lesions (minimally invasive adenocarcinoma [MIA]). more...

Organism:

Homo sapiens

Type:

Other

Platform:

GPL24676

2 Samples

Download data: H5

(Submitter supplied) We established an immortalized term placenta-derived trophoblast cell line and demonstrated functional and transcriptomic differences against chorion trophoblasts and BeWo cells.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

31 Samples

Download data: TXT

(Submitter supplied) Copper (Cu) is an essential trace element required for mitochondrial respiration. We show that Cu drives coordinated metabolic remodeling of bioenergy, biosynthesis and redox homeostasis and promotes tumor growth and progression of clear cell renal cell carcinoma (ccRCC). Late-stage ccRCCs accumulate Cu and allocate it to cytochrome c oxidase stimulating bioenergy production. Cu induces TCA cycle-dependent oxidation of glucose and its utilization for biosynthesis of a glutathione pool that protects against H2O2 generated during mitochondrial respiration, therefore coordinating bioenergy production with redox protection. more...

Organism:

Homo sapiens

Type:

Other

Platform:

GPL24676

5 Samples

Download data: CSV, H5, JPG, JSON, MTX, PNG, TSV

(Submitter supplied) Transcriptomic analyses have advanced the understanding of complex disease pathophysiology including chronic obstructive pulmonary disease (COPD). However, identifying relevant biologic causative factors has been limited by the integration of high dimensionality data. COPD is characterized by lung destruction and inflammation with smoke exposure being a major risk factor. To define previously unknown biological mechanisms in COPD, we utilized unsupervised and supervised interpretable machine learning analyses of single cell-RNA sequencing data from the gold standard mouse smoke exposure model to identify significant latent factors (context-specific co-expression modules) impacting pathophysiology. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19057

8 Samples

Download data: MTX, TSV

(Submitter supplied) Phthalates are ubiquitous pollutants in the environment; however, the mechanisms of phthalate-associated reproductive disorders in men are not fully understood. The aim of this study is to investigate associations between urinary phthalate metabolite concentrations and sperm DNA methylation. The study was conducted on 697 men from three prospective pregnancy cohorts: Longitudinal Investigation of Fertility and the Environment (LIFE) Study, Sperm Environmental Epigenetics and Development Study (SEEDS), and Environment and Reproductive Health (EARTH) Study.

Organism:

Homo sapiens

Type:

Methylation profiling by array

Platform:

GPL29753

697 Samples

Download data: IDAT, TXT

(Submitter supplied) COPD patients are largely asymptomatic until later stages when prognosis is generally poor. Here, by shifting the focus forward to pre-COPD and smoking stages, we found the peak of reactive oxygen species (ROS) level and hypoxia character are enriched in pre-COPD samples, and hypoxia inducible factor (HIF)-3α is the key factor. Smoking induced regional tissue hypoxia and emphysema have been found in COPD patients. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

36 Samples

Download data: TXT

(Submitter supplied) Increase in frequency and size of wildfire raises a significant public health concern due to rapid climate change. Epidemiological studies have shown that wildfire smoke exposure can increase the risk of neurological disorders. Our study aims to understand how wildfire smoke particles affect brain endothelial cells using both primary human brain microvascular endothelial cells (HBMEC) and an immortalized human cerebral microvascular endothelial cell line (hCMEC/D3). more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

48 Samples

Download data: TXT

(Submitter supplied) Mild cold acclimation increases insulin sensitivity and previous studies indicate that some level of muscle contraction is essential for provoking this effect. Here, 15 adults with overweight or obesity, the majority of which had impaired glucose tolerance (n=9), were intermittently cold exposed for 10 consecutive days to induce 1 hour of shivering per day. Cold acclimation with shivering improved oral glucose tolerance, blood pressure, fasting glucose, triglyceride, and non-esterified free-fatty acid concentrations, and may thus represent a novel lifestyle approach for the prevention and treatment of obesity-related metabolic disorders.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL23227

30 Samples

Download data

(Submitter supplied) Glioblastoma is immunologically “cold” and resistant to single-agent immune-checkpoint inhibitors (ICI). Our previous study of neoadjuvant pembrolizumab in surgically-accessible recurrent glioblastoma identified a molecular signature of response to ICI and suggested that neoadjuvant pembrolizumab may improve survival. To increase the power of this observation, we performed bulk-RNA seq on resected tumor tissue in an additional 25 patients with surgically-accessible recurrent glioblastoma. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21290

20 Samples

Download data: XLSX

(Submitter supplied) Lung cancer remains a major contributor to cancer fatalities, with cigarette smoking known to be responsible for up to 80% of cases. Based on the ability of cigarette smoke to induce inflammation in the lungs and increased lung cancer incidence in smokers with inflammatory conditions such as COPD, we hypothesized that inflammation plays an important role in carcinogenicity of cigarette smoke. In order to test this hypothesis, we performed multi-omic analyses of Type II pneumocytes of A/J mice exposed to cigarette smoke for various time periods. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing; Methylation profiling by high throughput sequencing

Platforms:

GPL21626 GPL17021 GPL24247

72 Samples

Download data: BED, CSV, TXT

(Submitter supplied) Laryngeal squamous cell carcinoma (LSCC) is a common form of head and neck cancer with poor prognosis. However, the mechanism underlying the pathogenesis of LSCC remains unclear. We performed high throughout sequencing to identify miRNA that associated with LSCC progression.Small RNA libraries were constructed followed by sequencing on a cohort of LSCC tissues (50 samples) and paired adjacent normal mucosa tissues (50 samples).

Organism:

Homo sapiens

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL11154

100 Samples

Download data: TXT

(Submitter supplied) The interplay between metabolism and gene expression is primarily known through epigenetic modifications which use metabolites such as acetyl-CoA. Glucose and glutamine are critical for the synthesis of these metabolites but the concentrations of these two major nutrients are not standardized in conventional tissue culture media. The aim of this study was to investigate the transcriptomic effect of TGF-B1 after 24 hours in primary human lung fibroblasts (pHLFs) growing in DMEM with glucose and glutamine set at physiological concentrations (5 and 0.7 mM, respectively). more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

6 Samples

Download data: TXT

(Submitter supplied) The tubal ectopic pregnancy (TEP) is a severe pregnancy complication accounted for 10-15% pregnancy-related deaths owing to the implantation and growth of embryos in fallopian tubes. Placental villi from TEP exhibit significant difference compared with that from intrauterine pregnancy (IP) in total volumes, trophoblast differentiation and intravillous vascularization. To investigate the difference in expression profiles of placental villi from IP and TEP, placental villi were collected from each phenotype, separated from maternal tissues and analyzed by high-throughput sequencing. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20301

9 Samples

Download data: TXT

(Submitter supplied) By modeling interaction of cigarette smoke and hypercholesterolemia, we provide experimental evidence that atherosclerotic disease directly contributes to AAA formation and rupture; AAA progression is mediated by inflammatory Mφ residing within associated atherosclerotic plaque.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

8 Samples

Download data: MTX, TSV