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Homo sapiens
4 Downloadable Samples
Illumina HumanHT-12 V4.0 expression beadchip
Description
Wnt signaling contributes to the reprogramming and maintenance of cancer stem cell (CSC) states that is activated by the epithelial-mesenchymal transition (EMT) program. However, the mechanistic relationship between the EMT and Wnt pathway in CSCs remains unclear. Chromatin immunoprecipitation with high-throughput sequencing (ChIP-seq) indicated that EMT induces a switch from the -catenin/E-cadherin/Sox15 complex to the -catenin/Twist1/TCF4 complex, which then binds to CSC-related gene promoters. In tandem co-IP and re-ChIP experiments using epithelial-type cells, Sox15 associated with the -catenin/E-cadherin complex and then bound to the proximal promoter region of CASP3, consequently resulting in Twist1 cleavage and negatively regulating the -cateninelicited promotion of the CSC phenotype. During the EMT, Twist1 in complex with -catenin enhanced -catenin/TCF4 transcriptional activity, which includes binding to the proximal promoter region of ABCG2, a marker of CSCs. For clinical application, the five-gene signature nuclear -cateninHigh/nuclear Twist1High/E-cadherinLow/Sox15Low/CD133High may be a valuable prognostic marker in patients with human lung cancer.
Publication Title
Diverse Targets of β-Catenin during the Epithelial-Mesenchymal Transition Define Cancer Stem Cells and Predict Disease Relapse.
Sample Metadata Fields
Specimen part, Cell line
View Samples- Homo sapiens
- 2 Downloadable Samples
- Affymetrix Human Gene 2.0 ST Array (hugene20st)
Description
KDM4B, an important epigenetic regulator of cell proliferation, metastasis and genome stability, is often overexpressed in gastric cancer. Notably, elevated expression of KDM4B is associated with a poor clinical outcome. A global transcriptomic analysis between KDM4B control and KDM4B-knockdown AGS cells without or with Helicobacter pylori challenge reveals differentially expressed genes involved in response to virus, multi-organism process, and response to stimulus, suggesting KDM4B as an inducible epigenetic factor under H. pylori challenge.
Publication Title
KDM4B is a coactivator of c-Jun and involved in gastric carcinogenesis.
Sample Metadata Fields
Specimen part, Cell line, Treatment
View Samples- Caenorhabditis elegans
- 2 Downloadable Samples
- Affymetrix C. elegans Genome Array (celegans)
Description
The nematode C. elegans was exposed to TiO2 nanoparticles (NPs) to evaluate the ecotoxicity of TiO2 nanoparticles.
Publication Title
No associated publication
Sample Metadata Fields
No sample metadata fields
View Samples
GSE40381- Rattus norvegicus
- 6 Downloadable Samples
- Affymetrix Rat Genome 230 2.0 Array (rat2302)
Description
Hepatic stellate cells (HSCs) experience phenotypic transformation, from the quiescent phenotype to the activated one, after different etiologies of liver injury. Liver fibrosis is then occurred upon the activation of HSCs. miR-16 deficiency is identified to be an important characteristic of HSCs activation. We used Affymetrix rat 230 2.0 arrays (Affymetrix, Santa Clara, U.S.A.) to uncover the global alternations of transcriptome under miR-16 restoration.
Publication Title
No associated publication
Sample Metadata Fields
Sex
View Samples- Rattus norvegicus
- 6 Downloadable Samples
- Affymetrix Rat Genome 230 2.0 Array (rat2302)
Description
Developmental Origins of Health and Disease Hypothesis (DOHaD) all emphasized that maternal nutrition plays an important role on the growth and development of offspring. More and more attention has been paid on the effect of maternal high fat diet and overnutrition during pregnancy on the susceptibility of offspring metabolic diseases. So we aim to build the rat model of maternal high fat diet which may induce steatohepatitis and change of lipid metabolism in the early life of offspring, and explore their possible mechannisms.And then to investigate the influence of maternal high fat diet on the expression of hepatic metabolic genes in the early life of offspring.
Publication Title
No associated publication
Sample Metadata Fields
Age, Specimen part
View Samples- Mus musculus
- 91 Downloadable Samples
- Illumina MouseWG-6 v2.0 expression beadchip
Description
Time-course analysis of adipocyte gene expression profiles response to high fat diet. The hypothesis tested in the present study was that in diet-induced obesity, early activation of TLR-mediated inflammatory signaling cascades by CD antigen genes, leads to increased expression of pro-inflammatory cytokines and chemokines, resulting in chronic low-grade inflammation. Early changes in collagen genes may trigger the accumulation of ECM components, promoting fibrosis in the later stages of diet-induced obesity. New therapeutic approaches targeting visceral adipose tissue genes altered early by HFD feeding may help ameliorate the deleterious effects of a diet-induced obesity.
Publication Title
Time-course microarrays reveal early activation of the immune transcriptome and adipokine dysregulation leads to fibrosis in visceral adipose depots during diet-induced obesity.
Sample Metadata Fields
Age, Specimen part, Treatment, Time
View Samples- Homo sapiens
- 69 Downloadable Samples
- Affymetrix Human Gene 1.0 ST Array (hugene10st)
Description
The treatment strategy of rectal cancer has substantially changed in recent decades. Historically postoperative chemoradiotherapy (CRT) was considered to be the first-line therapy for stage II and III rectal cancers. However, the preoperative CRT is now considered to be the optimal therapy regimen for locally advanced rectal ancer due to its improved local control, reduced toxicity, and increased rate of sphincter preservation. Our study established a clinically practical multi-class prediction model by adopting a novel strategy that applies two separate prediction models (MI and TO predictor) sequentially to a patient to predict the response. For promising clinical practice, we validated our model in a published dataset, which is completely independent dataset from ours. This study suggests a clinically plausible prediction model that correctly infers the preoperative CRT response of patients with high accuracy based on 163 gene signatures we identified.
Publication Title
No associated publication
Sample Metadata Fields
Sex, Age
View Samples- Rattus norvegicus
- 63 Downloadable Samples
- Affymetrix Rat Genome 230 2.0 Array (rat2302)
Description
Drug-induced alterations in transcriptional regulation play a central role in establishing the persistent neuroplasticities that occur during drug addiction. Additionally, changes in gene expression associated with drug administration provide valuable insight into the molecular basis of drug abuse. The molecular mechanisms that underlie susceptibility to psychostimulant addiction remain unknown. Identifying the common gene transcriptional responses to psychostimulants can provide a mechanistic insight to elucidate the molecular nature of drug dependence.
Publication Title
Neuronal development genes are key elements mediating the reinforcing effects of methamphetamine, amphetamine, and methylphenidate.
Sample Metadata Fields
Specimen part
View Samples- Homo sapiens
- 3 Downloadable Samples
- Illumina HumanHT-12 V4.0 expression beadchip
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
Methylome analysis reveals alterations in DNA methylation in the regulatory regions of left ventricle development genes in human dilated cardiomyopathy.
Sample Metadata Fields
Sex, Specimen part
View Samples- Mus musculus
- 51 Downloadable Samples
- Illumina MouseWG-6 v2.0 expression beadchip
Description
Core diet-induced obesity networks were constructed using Ingenuity pathway analysis (IPA) based on 332 high-fat diet responsive genes identified in liver by time-course microarray analysis (8 time-points over 24 weeks) of high-fat diet fed mice compared to normal diet fed mice. IPA identified five core diet-induced obesity networks with time-dependent gene expression changes in liver. When we merged core diet-induced obesity networks, Tlr2, Cd14 and Ccnd1 emerged as hub genes associated with both liver steatosis and inflammation and were altered in a time-dependent manner. Further protein-protein interaction network analysis revealed Tlr2, Cd14 and Ccnd1 were inter-related through the ErbB/insulin signaling pathway. Dynamic changes occur in molecular networks underlying diet-induced obesity. Tlr2, Cd14 and Ccnd1 appear to be hub genes integrating molecular interactions associated with the development of NASH. Therapeutics targeting hub genes and core diet-induced obesity networks may help ameliorate diet-induced obesity and NASH.
Publication Title
Time-dependent network analysis reveals molecular targets underlying the development of diet-induced obesity and non-alcoholic steatohepatitis.
Sample Metadata Fields
Age, Specimen part
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