GEO DataSets

(Submitter supplied) Tumor immune microenvironmental alterations occur early in multiple myeloma (MM) development. In this study, we aim to systematically characterize the tumor immune microenvironment (TME) and the tumor-immune interactions from precursor stages, i.e., monoclonal gammopathy of undetermined significance (MGUS) and smoldering MM (SMM), to newly diagnosed MM, comparing these to healthy donors. CIBERSORT analysis revealed proportions of 27 cell types, including 10 innate immune cells (monocytes, M0/M1/M2 macrophages, resting/activated dendritic cells, resting/activated mast cells, eosinophils, and neutrophils), 7 T cell subsets (CD8+ T cells, naive CD4+ T cells, resting/activated memory CD4+ T cells, follicular helper T cells, regulatory T cells, and gamma delta T cells), resting/activated NK cells, naive B cells, memory B cells, plasma cells, myeloma plasma cells, memory plasma cells, osteoblasts, osteoclasts and adipocytes. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

997 Samples

Download data: CEL

(Submitter supplied) Amplification of the epidermal growth factor receptor (EGFR, A0 for non-amplified and A1 for amplified) gene is one of the most common oncogenic alterations in glioblastoma (45%) making it a prime target for therapy. However, small molecule inhibitors of the EGFR tyrosine kinase showed disappointing efficacy in clinical trials for glioblastoma. Here we report expression data for 33 samples including 6 GBM derived xenografts (3 controls and 3 treated by tyrosine kinase inhibitor gefitinib) and 27 glioblastoma tumors (11 controls and 16 treated by tyrosine kinase inhibitor gefitinib). more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

33 Samples

Download data: CEL

(Submitter supplied) Early diagnosis of cancer has been shown to substantially improve 5-year survival rates for many cancer types. With current methodologies early diagnosis has proven difficult for cancers of deep tissues, such as the pancreas and lung. However, whole peripheral blood has been demonstrated to be a promising non-invasive surrogate tissue for the detection of many types of cancer. Blood samples were collected in EDTA blood collection tubes from 2,485 human volunteers and gene expression profiled with the goal to develop a classification model that differentiations patients with cancer from those without cancer.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

2845 Samples

Download data: CEL, CHP

(Submitter supplied) We performed transcriptome analysis using DNA microarray in JPH203-treated HUVEC to elucidate endothelial cell response to LAT1 inhibition.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

2 Samples

Download data: CEL, TAB

(Submitter supplied) TCI04 inhibits cell invasion and synergistically enhanced Paclitaxel activity in MDA-MB-231 cells. We used microarrays to detail the global programme of gene expression in MDA-MB-231 cells after treated with TCI04 and identified distinct classes of up- or down-regulated genes during this process.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

6 Samples

Download data: CEL, CHP

(Submitter supplied) Esophageal squamous cell carcinoma (ESCC) is a particularly aggressive form of cancer with high mortality. In this study, a novel 8-hydroxyquinoline derivative (91b1) was investigated for the anticancer activities in ESCC alongside the associated mechanisms. The in vitro cytotoxic effect of 91b1 were evaluated across five ESCC cell lines using MTS assay, with cisplatin serving as a comparative standard. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

2 Samples

Download data: CEL, CHP

(Submitter supplied) The RAS pathway is frequently exploited by cancer cells to sustain their proliferation and survival. ERK is the most distal kinase in the RAS signaling cascade, playing a pivotal role in signaling output. We performed a transcriptomic analysis to obtain an overview of the consequences of EI-52 (CER) treatment, an inhibitor of ERK protein-protein interaction, on the global cellular transcriptional activity. 

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL22321

6 Samples

Download data: CEL, XLSX

(Submitter supplied) Background: Acute myeloid leukaemia is a disease characterised by the accumulation of large number of aberrant, immature myeloid cells in the bone marrow and peripheral blood as a result of a variety of genetic alterations in early haematopoietic stem cells. Normal stem cells, which have the ability to renew themselves, can undergo neoplastic transformation as a result of mutations in signalling pathway genes, changes in epigenetics or gene expression levels. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

22 Samples

Download data: CEL

(Submitter supplied) Oncogenic KRAS is found in more than 25% of lung adenocarcinomas, the major histologic subtype of non–small cell lung cancer (NSCLC), and is an important target for drug development. To this end, we generated four NSCLC lines with stable knockdown selective for oncogenic KRAS. As expected, stable knockdown of oncogenic KRAS led to inhibition of in vitro and in vivo tumor growth in the KRAS-mutant NSCLC cells, but not in NSCLC cells that have wild-type KRAS (but mutant NRAS). more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

15 Samples

Download data: CEL

(Submitter supplied) To characterize organoids with each type of morphology, we performed DNA microarray analysis to identify genes expressed predominantly in each type of organoids on day35 of cortical organoid differentiation protocol (SFBEq).

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

21 Samples

Download data: CEL, TXT

(Submitter supplied) The genetic lesions that drive acute megakaryoblastic leukemia (AMKL) have not been fully elucidated. To search for AMKL gene, we subjected 9 AMKL cell lines and 39 non-AMKL acute myeloid leukemia cell lines to microarray gene expression analysis.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

48 Samples

Download data: CEL

(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:

GPL570 GPL9115

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 array

Platform:

GPL570

34 Samples

Download data: CEL, CHP

(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:

GPL570 GPL6804

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) There is evidence of pathophysiologic diversity in chronic rhinosinusitis with nasal polyps (CRSwNP), but data characterizing the molecular endotypes of CRSwNP and their association with treatment is lacking. The objective of this study was to identify gene signatures associated with CRSwNP endotypes, clinical features, and dupilumab treatment response. Two distinct transcriptional clusters (C1 and C2) were identified, both with elevated type 2 biomarkers. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

172 Samples

Download data: CEL