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GSE27238
Mus musculus
18 Downloadable Samples
Affymetrix Murine Genome U74A Version 2 Array (mgu74av2)
Description
Deregulated retinal angiogenesis directly cause vision loss in many ocular diseases, such as diabetic retinopathy and retinopathy of prematurity. To identify endothelial-specific genes expressed in angiogenic retinal vessels, we purified genetically labeled endothelial cells from Tie2-GFP transgenic mice and performed gene expression profiling using DNA microarray. To find out genes associated with angiogenesis, comparisons of microarray data were carried out between GFP-negative non-endothelial retinal cells and GFP-positive retinal endothelial cells in angiogenic P8 retina.
Publication Title
Sema3E-PlexinD1 signaling selectively suppresses disoriented angiogenesis in ischemic retinopathy in mice.
Sample Metadata Fields
Specimen part
View Samples- Caenorhabditis elegans
- 12 Downloadable Samples
- Affymetrix C. elegans Genome Array (celegans)
Description
C. elegans exhibits thermotaxis, where most of the animals that had been cultivated at a particular temperature ranging from 15C to 25C for a few hours with a food source and then placed on a thermal gradient for an hour migrate to the cultivation temperature. In addition, animals that were previously conditioned to migrate to a certain temperature are capable of migrating to a new cultivation temperature a few hours after the cultivation temperature was shifted to the new temperature
Publication Title
Regulation of behavioral plasticity by systemic temperature signaling in Caenorhabditis elegans.
Sample Metadata Fields
Specimen part
View Samples- Mus musculus
- 8 Downloadable Samples
- Affymetrix Mouse Gene 1.0 ST Array (mogene10st)
Description
The Hippo pathway plays a crucial in organ size control during development and tissue homeostasis in adult life. To examine a role for Hippo signaling in the intestinal epithelium, we analyzed gene expression patterns in the mouse intestinal epithelilum transfected with siRNAs or expression plasmids for shRNAs targeting the Hippo pathway effectors, YAP and TAZ.
Publication Title
Dual role of YAP and TAZ in renewal of the intestinal epithelium.
Sample Metadata Fields
Sex, Age, Specimen part, Treatment
View Samples- Homo sapiens
- 4 Downloadable Samples
Ion Torrent Proton
Description
It is unclear how the loss of TGF-b signaling components affects metastatic abilities in clear cell renal cell carcinoma (ccRCC). In this study, we identified that low TGFBR3 expression in ccRCC cells enhanced primary tumor formation and lung metastasis. In the presence of TGFBR3, TGF-b2 decreased the aldehyde dehydrogenase (ALDH)-positive ccRCC cell population, in which renal cancer-initiating cells are enriched. Loss of TGFBR3 also enhanced cell migration in cell culture and induced expression of several mesenchymal markers in a TGF-b-independent manner. Increased lamellipodium formation by FAK-PI3K signaling was observed with TGFBR3 downregulation, and this contributed to TGF-b-independent cell migration in ccRCC cells. Taken together, our findings reveal that loss of TGFBR3 endows ccRCC cells with multiple metastatic abilities through TGF-b-dependent and independent pathways. Overall design: Target genes for TGF-b2 and TGFBR3 in ccRCC cells were identified.
Publication Title
Decreased TGFBR3/betaglycan expression enhances the metastatic abilities of renal cell carcinoma cells through TGF-β-dependent and -independent mechanisms.
Sample Metadata Fields
Cell line, Subject
View Samples- Mus musculus
- 3 Downloadable Samples
- Affymetrix Mouse Gene 1.0 ST Array (mogene10st)
Description
Retinoic acid (RA) signaling regulates a variety of developmental processes through controlling the expression of numerous genes. Here, we have identified and characterized RA-responsive genes in mouse kidney development. Analysis of isolated embryonic kidneys cultured in the presence and absence of RA identified 33 candidates of RA-responsive genes. Most of these candidate genes were down-regulated by treatment with the RA receptor antagonist. Many of them have potential binding sites for Elf5, one of the RA-responsive genes, in their promoter region. Whole-mount in situ hybridization demonstrated that specific expression of Elf5 in the ureteric trunk depends on RA. RA-dependent expression in the ureteric trunk was also demonstrated for the sodium channel subunit Scnn1b, which has been shown to be the marker gene of the collecting duct. In contrast, the expression of Ecm1, Tnfsf13b and IL-33 was detected in the stromal mesenchymal cells. Both Tnfsf13b and IL-33 were previously shown to cause NF-B activation. We have demonstrated that the inhibition of NF-B signaling with specific inhibitors suppresses branching morphogenesis of the ureteric bud. Our study thus identifies and characterizes RA-dependent upregulated genes in kidney development, and suggests an involvement of NF-B signaling in the branching morphogenesis.
Publication Title
Identification and characterization of retinoic acid-responsive genes in mouse kidney development.
Sample Metadata Fields
Specimen part
View Samples- Homo sapiens
- 2 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
We investigated that gene expression profile of generated human iPS cells from cord blood cells using temperature sensitive sendai-virus vector.
Publication Title
Efficient generation of transgene-free human induced pluripotent stem cells (iPSCs) by temperature-sensitive Sendai virus vectors.
Sample Metadata Fields
Specimen part
View Samples- Caenorhabditis elegans
- 24 Downloadable Samples
- Affymetrix C. elegans Genome Array (celegans)
Description
Dietary restriction (DR) is the most effective and reproducible intervention to extend lifespan in divergent species1. In mammals, two regimens of DR, intermittent fasting (IF) and caloric restriction (CR), have proven to extend lifespan and reduce the incidence of age-related disorders2. An important characteristic of IF is that it can increase lifespan, even when there is little or no overall decrease in calorie intake2. The molecular mechanisms underlying IF-induced longevity, however, remain largely unknown. Here we establish an IF regimen that effectively extends the lifespan of Caenorhabditis elegans, and show that a nutrient-related signalling molecule, the low molecular weight GTPase Cel-Rheb, has a dual role in lifespan regulation; Cel-Rheb is required for the IF-induced longevity, whereas inhibition of Cel-Rheb mimics the CR effects. We also show that Cel-Rheb exerts its effects in part via the insulin/IGF-like signalling effector DAF-16 in IF, and that Cel-Rheb is required for fasting-induced nuclear translocation of DAF-16. We find that HSP-12.6, a DAF-16 target, functions to mediate the IF-induced longevity. Furthermore, our analyses demonstrate that most of fasting-induced upregulated genes require Cel-Rheb function for their induction, and that Cel-Rheb/Cel-TOR signalling is required for the fasting-induced downregulation of an insulin-like peptide, INS-7. These findings identify the essential role of signalling via Cel-Rheb in IF-induced longevity and gene expression changes, and suggest a molecular link between the IF-induced longevity and the insulin/IGF-like signalling pathway.
Publication Title
Signalling through RHEB-1 mediates intermittent fasting-induced longevity in C. elegans.
Sample Metadata Fields
No sample metadata fields
View Samples- Xenopus laevis
- 12 Downloadable Samples
- Affymetrix Xenopus laevis Genome 2.0 Array (xlaevis2)
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
The atypical mitogen-activated protein kinase ERK3 is essential for establishment of epithelial architecture.
Sample Metadata Fields
Specimen part, Treatment
View Samples- Caenorhabditis elegans
- 11 Downloadable Samples
- Affymetrix C. elegans Genome Array (celegans)
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
The microRNA machinery regulates fasting-induced changes in gene expression and longevity in <i>Caenorhabditis elegans</i>.
Sample Metadata Fields
No sample metadata fields
View Samples- Caenorhabditis elegans
- 8 Downloadable Samples
- Affymetrix C. elegans Genome Array (celegans)
Description
Intermittent fasting (IF), a dietary restriction regimen, extends the lifespans of C. elegans and mammals by inducing gene expression changes. How fasting induces gene expression changes and longevity remains unclear. MicroRNAs (miRNAs) are small non-coding RNAs (approximately 22 nucleotides) that repress gene expression, and the expression of several miRNAs has been reported to be altered by fasting. In this study, we examined the role of the miRNA machinery in fasting-induced transcriptional changes and longevity in C. elegans. Our miRNA array analyses revealed that the expression levels of numerous miRNAs changed in adult worms after 48 hours of fasting. In addition to these changes, miRNA-mediated silencing complex (miRISC) components, including Argonaute proteins and GW182 proteins, and the miRNA-processing enzyme Drosha/DRSH-1, were up-regulated by fasting. Our lifespan measurements demonstrated that IF-induced longevity was suppressed by knockout or knockdown of miRISC components and was completely inhibited by drsh-1 ablation. Remarkably, drsh-1 ablation inhibited the fasting-induced changes in the expression of the target genes of DAF-16, the insulin/IGF-1 signaling effector. Fasting-induced transcriptome alterations were substantially and modestly suppressed in the drsh-1 null mutant and the null mutant of ain-1, a gene encoding GW182, respectively. These results indicate that components of the miRNA machinery, especially the miRNA-processing enzyme Drosha, play an important role in mediating IF-induced longevity via the regulation of fasting-induced gene expression changes.
Publication Title
The microRNA machinery regulates fasting-induced changes in gene expression and longevity in <i>Caenorhabditis elegans</i>.
Sample Metadata Fields
No sample metadata fields
View Samples