Filters
Technology
Platform
GSE56396
Homo sapiens
112 Downloadable Samples
Affymetrix Human Gene 1.0 ST Array (hugene10st)
Description
Evaluation of the airway transcriptome may reveal patterns of gene expression that are associated with clinical phenotypes of asthma. To define transcriptomic endotypes of asthma (TEA) we analyzed gene expression in induced sputum that correlate with phenotypes of disease. Gene expression was measured in sputum of subjects with asthma using Affymetrix HuGene ST 1.0 microarrays. Unsupervised clustering analysis of genes identified TEA clusters. Clinical characteristics were compared.
Publication Title
Noninvasive Analysis of the Sputum Transcriptome Discriminates Clinical Phenotypes of Asthma.
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 4 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
Under various pathophysiological muscle-wasting conditions like diabetes and starvation, a family of ubiquitin ligases, including MuRF1 (Muscle specific RING-Finger protein 1), are induced to target muscle proteins for degradation via ubiquitination. In an attempt to identify the in vivo targets of MuRF1 we have generated transgenic mouse lines overexpressing MuRF1 in a skeletal muscle specific fashion. MuRF1-TG lines were viable and had normal fertility. Characterization of their skeletal muscles did not reveal evidence for muscle wasting at 10 weeks of age. In this experiment we compared the skeletal muscle transcriptome of transgenic mice with wildtypes.
Publication Title
MuRF1-dependent regulation of systemic carbohydrate metabolism as revealed from transgenic mouse studies.
Sample Metadata Fields
Sex, Age, Specimen part
View Samples- Mus musculus
- 16 Downloadable Samples
Illumina HiSeq 2500
Description
Overconsumption of high-fat diet (HFD) and sugar-sweetened beverages are risk factors for development of obesity, insulin resistance and fatty liver disease. To dissect mechanisms underlying this association, mice were fed chow or HFD with or without addition of fructose- or glucose-supplemented water. There were no physiological differences in mice supplemented with fructose or glucose on chow diet. Despite similar caloric intake, mice on HFD supplemented with fructose developed more pronounced obesity, glucose intolerance and hepatomegaly than glucose-supplemented mice. While both sugars increased Chrebp-?, fructose supplementation uniquely increased Srebp1c and downstream fatty acid synthesis genes resulting in reduced liver insulin signaling, whereas glucose enhanced total Chrebp expression and triglyceride synthesis but was associated with improved hepatic insulin signaling. Metabolomic and RNA sequence analysis confirmed dichotomous effects of fructose and glucose supplementation on liver metabolism in spite of inducing similar amount of hepatic lipid accumulation. Ketohexokinase, the first enzyme of fructose metabolism, was increased in fructose-fed mice and in obese adolescents with steatohepatitis. Knockdown of ketohexokinase-C in liver improved hepatic steatosis and glucose tolerance in fructose-supplemented mice. Thus, fructose is a component of dietary sugar that is uniquely associated with poor metabolic outcomes, while increased glucose intake may be protective.
Publication Title
No associated publication
Sample Metadata Fields
Sex, Age, Specimen part, Cell line
View Samples- Mus musculus
- 12 Downloadable Samples
- Illumina HiSeq 2500
Description
By using DREADD technology, we found that activating Gi signaling in hepatocytes promotes hepatic glucose production. While we demonstrated that intact JNK signaling is required for maximal glucose output after stimulation of hepatic Gi signaling, other pathways may also contribute to this response. To obtain information about such non-JNK-dependent pathways, we studied changes in hepatic gene expression in an unbiased fashion using RNA-seq analysis. In this study, we used a viral delivery strategy to selectivity express a Gi-coupled DREADD (full name: hM4Di) in mouse hepatocytes (Hep-Di mice). We prepared liver RNA from Hep-Di mice 30 min after injection with either CNO (10 mg/kg i.p.) or saline (control) and then subjected these RNA samples to RNA-seq analysis.
Publication Title
No associated publication
Sample Metadata Fields
Sex, Age, Specimen part, Cell line
View Samples- Homo sapiens
- 8 Downloadable Samples
- Affymetrix Human Genome U133A Array (hgu133a)
Description
Among the dendritic cell (DC) subsets, plasmacytoid DCs are thought to be important in both generating antiviral and antitumor responses. These cells may be useful in developing dendritic cell-based tumor vaccines, however, the rarity of these cells in the peripheral blood have hampered attempts to understand their biology. To provide better insight into the biology of plasmacytoid DCs, we isolated these cells from the peripheral blood of healthy donors in order to further characterize their gene expression. Using gene array technology we compared the genetic profiles of these cells to those of CD14+ monocytes isolated from the same donors and found several immune related genes upregulated in this cell population. Understanding the genetic profiles of this dendritic cell subtype as well as others such as the BDCA-1 expressing myeloid DCs may enable us to manipulate these cells ex-vivo to generate enhanced DC-based tumor vaccines inducing more robust antitumor responses.
Publication Title
Genetic profiles of plasmacytoid (BDCA-4 expressing) DC subtypes-clues to DC subtype function in vivo.
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 4 Downloadable Samples
- Affymetrix Mouse Expression 430A Array (moe430a)
Description
RNa extracted from Brca1 presence/absence mice livers and processed on Mouse Expression 430A chips and processed by the NIDDK microarray facility
Publication Title
No associated publication
Sample Metadata Fields
Age, Specimen part, Disease, Disease stage, Subject, Time
View Samples- Homo sapiens
- 27 Downloadable Samples
- IlluminaHiSeq2500
Description
Tick-borne flaviviruses (TBFVs) are ss(+)RNA viruses that cause febrile illnesses, which may progress to severe encephalitis and/or death in humans globally. 30—60% of people who recover from severe acute disease continue to suffer debilitating neurological sequelae due to viral persistence, neurological cell damage incurred during infection and/or host response, or a combination of these. When TBFVs infect mammalian cells in vitro, an acute phase characterized by dramatic apoptosis ensues and kills >95% of infected cells by day 5. Upon refreshing the cell growth medium, surviving cells repopulate and become persistently infected for extended periods of time. However, molecular mechanisms responsible for the initiation and maintenance of viral persistence in vivo and in vitro remain vague. We used unbiased deep sequencing of the HEK 293T cell transcriptome to determine the profiles of acutely infected cells at selected time points as well as of persistently infected cells. Many genes were significantly differentially expressed during the course of the acute phase, but 451 genes were significantly differentially expressed uniquely in persistently infected cells. Ingenuity Pathways Analysis of these genes suggested that the oncogenes AKT2 and ERBB2, which favor cell survival were up-regulated in persistently infected cells, whereas pro-apoptotic genes, such as Bad and IFN-ß1 were down-regulated. There was also an up-regulation of genes encoding antiviral cytokines, such as CCL5, TNF-a and CXCL10 during the acute phase, but these were relatively suppressed in persistently infected cells. Exogenous induction of apoptosis in persistently infected cells with chelerythrine chloride indicated that these cells were resistant to apoptosis in a dose-dependent manner. In summary, the transcriptome profiles of acutely and persistently infected HEK 293T cells are different and evasion of apoptosis is critical for the initiation of TBFV persistence. These results provide a basis for further studying the precise molecular mechanisms of TBFV persistence.
Publication Title
No associated publication
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 6 Downloadable Samples
- Affymetrix Human Transcriptome Array 2.0 (hta20)
Description
The purpose of this study was to chacterise the effect of KDM1A knocking down on genome-wide gene expression in human NSCLC cells in vivo. Affymetrix human transcriptome array 2.0 was used to profile the transcriptome of xenograft tumors derived from PC9 cells stably expressing either ShRNA KDM1A or ShRNA control. These cells were subcutanously injected into the right axillary of the mouse, and allowd to grow for 5 weeks to form xenograft tumors. Although KDM1A is up-regulated in NSCLC, but key genes and pathways regulated by KDM1A was not well-understood in NSCLC. Using this approach, we have shown that KDM1A repressed or activated a distinctive set of pathways and key target genes in vivo.
Publication Title
No associated publication
Sample Metadata Fields
Specimen part
View Samples- Homo sapiens
- 8 Downloadable Samples
- Affymetrix Human Genome U133A Array (hgu133a)
Description
Previous data have demonstrated the attenuation of platelet-derived growth factor (PDGF)-induced hyperproliferation and migration in primary human mesangial cells by lipoxin A4. In these experiments we aimed to find out what the effect of Lipoxin A4 would be on the global genomic changes associated with PDGF. We treated cells with PDGF (10ng/ml) ± LXA4 (1nM) for a 24h period and examined genomic differences, we could derive from our results that lipoxin A4 was diminishing the pro-inflammatory, pro-proliferative and pro-fibrotic responses induced by PDGF.
Publication Title
No associated publication
Sample Metadata Fields
Specimen part, Compound
View Samples- Homo sapiens
- 12 Downloadable Samples
- Illumina HiSeq 1500
Description
MDA-MB-231 and T47D human breast cancer cells were chronically treated with the novel STAT3/5 inhibitor SH-4-54 for 60 and 30 days, respectively. Surviving treatment-resistant individual clones were isolated and characterized for their phosphorylated STAT3 and phosphorylated STAT5 status. 3 biological replicates of mRNA from a representative resistant clone derived from both MDA-MB-231 and T47D cells, in parallel with mRNA from their respective wild-type counterparts, was subjected to NextGeneration Sequencing to analyze changes in gene expression between untreated and resistant cells.
Publication Title
No associated publication
Sample Metadata Fields
Sex, Specimen part, Cell line, Treatment
View Samples