GEO DataSets

(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) 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:

GPL24247 GPL21626 GPL17021

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) Genome-wide association studies (GWAS) identified over fifty genomic loci associated with lung cancer risk. However, the genetic mechanisms and target genes underlying these loci are largely unknown, as most risk-associated-variants might regulate gene expression in a context-specific manner. Here, we generated a barcode-shared multiome (transcriptome and chromatin accessibility map) of 117,911 human lung cells from ever- and never-smokers to profile context-specific gene regulation. more...

Organism:

Homo sapiens

Type:

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

Platform:

GPL24676

32 Samples

Download data: H5, RDS

(Submitter supplied) DSP RNA profling using the whole transcriptome atlas kit was performed on a tissue sample perior to immunotherapy from a patient with head and neck cancer.

Organism:

Homo sapiens

Type:

Other

Platform:

GPL24676

9 Samples

Download data: CSV, PKC

(Submitter supplied) This was a case-control study conducted from August 2020 to January 2021, in which 9 ischemic stroke and 2 healthy individuals (healthy control group) attending the Guangdong Provincial People's Hospital were recruited for plasma exoLRs sequencing. The other 10 normal samples from a previous study published in the Gene Expression Omnibu (GEO) database (Accession No. GSE159657) were used as part of healthy control group to analyzed the expression profile together. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

21 Samples

Download data: TXT

(Submitter supplied) The dominant risk factor for the development of idiopathic pulmonary fibrosis (IPF) is a common variant in the promoter region of the airway mucin MUC5B, variant rs35705950. The MUC5B promoter variant enhances MUC5B expression in the terminal respiratory bronchiole, where it is normally absent. We pursued a spatial gene expression approach to understand how the MUC5B variant influences IPF in age-matched unaffected and IPF lung tissue specimens.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

310 Samples

Download data: DCC, TXT

(Submitter supplied) Despite lower rates and intensity of smoking, Black men experience a higher incidence of lung cancer compared to White men. The racial disparity in lung cancer is particularly pronounced in Chicago, a highly segregated urban city. Neighborhood conditions, particularly social stress, may play a role in lung tumorigenesis. Preliminary studies indicate that Black men residing in neighborhoods with higher rates of violent crime have significantly higher levels of hair cortisol, an indicator of stress response. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL24676

15 Samples

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

(Submitter supplied) Despite lower rates and intensity of smoking, Black men experience a higher incidence of lung cancer compared to White men. The racial disparity in lung cancer is particularly pronounced in Chicago, a highly segregated urban city. Neighborhood conditions, particularly social stress, may play a role in lung tumorigenesis. Preliminary studies indicate that Black men residing in neighborhoods with higher rates of violent crime have significantly higher levels of hair cortisol, an indicator of stress response. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL24676

55 Samples

Download data: BED, TXT

(Submitter supplied) NK cells were purified from peripheral blood of healthy controls (n = 5), individuals with latent tuberculosis infection (n = 5), and active tuberculosis patients (n = 5). Total RNA was isolated from purified NK cells using RNA Isolation Kit (Dongsheng, R1061) according to the manufacturer's instructions. RNA Sequencing was conducted using the Illumina HiSeq X Ten platform (Novogene Bioinformatics Technology Co., Ltd.) with paired-end 150-bp reads.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20795

15 Samples

Download data: TXT

(Submitter supplied) We have constructed a transcriptomic map of airways using lung tissues from three COPD (GOLD grade I) who underwent surgical resection for lung cancer. We performed 5' single-cell RNA sequencing (scRNA-seq) on three COPD and three control matched lung tissue, as well as the organoid samples.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

12 Samples

Download data: MTX, TSV

(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) 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

(Submitter supplied) Transcriptomic subtyping holds promise for personalized therapy in extensive stage small cell lung cancer (ES-SCLC). In this study, we aimed to assess intratumoral transcriptomic subtype diversity and to identify biomarkers associated with long-term chemoimmunotherapy benefit in human ES-SCLC. Our work highlights that high intratumoral heterogeneity, lack of consistent association with outcome, and unclear subtype-specific target expression are major challenges for SCLC subtype-based precision oncology. more...

Organism:

Homo sapiens

Type:

Other

Platform:

GPL30173

175 Samples

Download data: DCC, PKC, PNG, XLSX

(Submitter supplied) Transcriptomic subtyping holds promise for personalized therapy in extensive stage small cell lung cancer (ES-SCLC). In this study, we aimed to assess intratumoral transcriptomic subtype diversity and to identify biomarkers associated with long-term chemoimmunotherapy benefit in human ES-SCLC. Our work highlights that high intratumoral heterogeneity, lack of consistent association with outcome, and unclear subtype-specific target expression are major challenges for SCLC subtype-based precision oncology. more...

Organism:

Homo sapiens

Type:

Other

Platform:

GPL30173

121 Samples

Download data: DCC, PKC, PNG, XLSX

(Submitter supplied) Dysbiosis, or changes within the microbiome, is a common feature of solid tumors, however whether this dysbiosis directly contributes to tumor development is largely unknown. We previously characterized the human lung cancer microbiome and identified the Gram-negative Acidovorax temperans as enriched in tumors and associated with smoking status and TP53 mutations. To determine if A. temperans exposure could contribute to the development of lung cancer, we investigated its effect in a genetically engineered mouse model of lung adenocarcinoma driven by mutant Kras and Tp53. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL23479

45 Samples

Download data: TXT

(Submitter supplied) Precision medicine's potential to transform complex autoimmune-disease treatment is often challenged by limited data availability and inadequate sample size when compared to the number of molecular features found in high-throughput multi-omics datasets. Addressing this issue, the novel framework PRoBeNet (Predictive Response Biomarkers using Network medicine) was developed. ProBeNet operates under the hypothesis that the therapeutic effect of a drug propagates through a protein–protein interaction network to reverse disease states. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

12 Samples

Download data: CSV

(Submitter supplied) Background. The unknown tissue of origin in head and neck cancer of unknown primary (hnCUP) leads to invasive diagnostic procedures and unspecific and potentially inefficient treatment options for patients. The most common histological subtype, squamous cell carcinoma, can stem from various tumor primary sites, including the oral cavity, oropharynx, larynx, head and neck skin, lungs, and esophagus. DNA methylation profiles are highly tissue-specific and have been successfully used to classify tissue origin. We therefore developed a support vector machine (SVM) classifier trained with publicly available DNA methylation profiles of commonly cervically metastasizing squamous cell carcinomas (n = 1,103) in order to identify the primary tissue of origin of our own cohort of squamous cell hnCUP patient’s samples (n = 28). Methylation analysis was performed with Infinium MethylationEPIC v1.0 BeadChip by Illumina. Results. The SVM algorithm achieved the highest overall accuracy of tested classifiers, with 87%. Squamous cell hnCUP samples on DNA methylation level resembled squamous cell carcinomas commonly metastasizing into cervical lymph nodes. The most frequently predicted cancer localization was the oral cavity in 11 cases (39%), followed by the oropharynx and larynx (both 7, 25%), skin (2, 7%), and esophagus (1, 4%). These frequencies concord with the expected distribution of lymph node metastases in epidemiological studies. Conclusions. On DNA methylation level, hnCUP is comparable to primary tumor tissue cancer types that commonly metastasize to cervical lymph nodes. Our SVM-based classifier can accurately predict these cancers’ tissues of origin and could significantly reduce the invasiveness of hnCUP diagnostics and enable a more precise therapy after clinical validation.

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL21145

28 Samples

Download data: IDAT

(Submitter supplied) Metastases in the brain are the most severe and devastating complication of cancer. The incidence of brain metastasis is increasing. Therefore, the need of finding specific druggable targets for brain metastasis is demanding. The aim of this study was to compare the brain (immune) response to brain metastases of the most common tumor lineages, viz., lung adenocarcinoma and breast cancer. Targeted gene expression profiles of 11 brain metastasis of lung adenocarcinoma (BM-LUAD) were compared to 11 brain metastasis of breast cancer (BCBM) using NanoString nCounter PanCancer IO 360™ Panel. more...

Organism:

Homo sapiens

Type:

Other

Platform:

GPL32069

22 Samples

Download data: CSV

(Submitter supplied) This study performed genomic sequencing on a rare phenotype of HPV-positive oropharyngeal squamous cell carcinoma which was resistant to standard of care platinum based chemoradiation treatment. Tissue was collected from archival FFPE when available from pretreatment and post treamtent samples from four patients and these were batch corrected to be compared to known HPV-positive tumors without recurrent disease

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL16791 GPL24676

83 Samples

Download data: TXT