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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Transcription profiling of rat insulinoma (INS-1 derived) cell lines that vary in their glucose responsiveness

ABSTRACT: The aim of this study was to identify the gene expression changes associated with glucose responsiveness in Rat INS-1 derived cell lines. RNA was prepared from cell lines which were shown to be highly glucose responsive and also lines which were shown to be poorly glucose responsive. Dr. Chris Newgard's lab quantified the RNA and sent it frozen in water. 3 biological replicates per condition were sent for the following conditions: (i) 832/13 and 833/15, robust glucose responsiveness; (ii)832/1 and 832/2 showed poor glucose responsiveness.

ORGANISM(S): Rattus norvegicus

SUBMITTER: John Brestelli

PROVIDER: E-CBIL-35 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Functional genomics of the beta-cell: short-chain 3-hydroxyacyl-coenzyme A dehydrogenase regulates insulin secretion independent of K+ currents.

Hardy Olga T OT Hohmeier Hans E HE Becker Thomas C TC Manduchi Elisabetta E Doliba Nicolai M NM Gupta Rana K RK White Peter P Stoeckert Christian J CJ Matschinsky Franz M FM Newgard Christopher B CB Kaestner Klaus H KH

Molecular endocrinology (Baltimore, Md.) 20061221 3

Recent advances in functional genomics afford the opportunity to interrogate the expression profiles of thousands of genes simultaneously and examine the function of these genes in a high-throughput manner. In this study, we describe a rational and efficient approach to identifying novel regulators of insulin secretion by the pancreatic beta-cell. Computational analysis of expression profiles of several mouse and cellular models of impaired insulin secretion identified 373 candidate genes involv ...[more]

PMID: 17185391

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Transcription profiling of rat insulinoma (INS-1 derived) cells grown in lipid culture

Project description:This experiment was designed to study the effects of lipid culture on INS-1 derived glucose-responsive 832/13 cells. After 48-hr culture with lipids, a dramatic decrease in glucose-responsiveness is observed. In order to detect some earlier changes, RNA was also collected at earlier time points (12 hr and 24 hr). To compensate for any changes associated with cell density, control cells (1%BSA culture) were included for each time point. RNA was prepared from INS-1 cells in Dr. Chris Newgard's lab, quantified and sent frozen in water. Six biological replicates were sent for the following conditions: (i) 1%BSA (12, 24, and 48 hours) (ii) 1mM-Oleate/Palmitate (12, 24, and 48 hours).

2007-09-11 | E-CBIL-34 | biostudies-arrayexpress

Cytotoxicity Study of Rat INS1 cell lines

Project description:Cytokines IL-1 and IFN-gamma have been shown to be the primary effectors of beta-cell destruction during the immune response. The aim of this study was to identify the gene expression changes that are associated with resistance of beta cells to cytokines. INS-1 rat insulinoma cells were grown in increasing doses of cytokines until a resistance phenotype had developed. RNA was prepared from these cytokine resistant sublines as well as the original, cytokine-sensitive parental INS-1 cells in Dr. Chris Newgard's lab, quantified and sent frozen in water. 3-7 biological replicates per condition were sent for the following three conditions: (i) 834/40, Cytokine-sensitive (CS), (ii) 833/15 and 833/117, Cytokine resistant grown in the absence of cytokines (CRu), (iii) 833/15C and 833/117C: Cytokine Resistant Grown in the Presence of Cytokines (CRt)

2014-07-22 | E-MTAB-2776 | biostudies-arrayexpress

Transcription profiling of wild type and Foxa2 knock out mouse mature beta cells

Project description:The winged helix transcription factor Foxa2 regulates Pdx1 gene expression and fetal endocrine pancreas development. We show here by inducible gene ablation that Foxa2 inactivation in mature beta-cells induces hyperinsulinemic hypoglycemia in Foxa2loxP/loxP, Pdx1-CreERT2 adult mice. Mutant beta-cells exhibited a markedly increased pool of docked insulin granules, some of which were engaged in sequential or compound exocytosis, consistent with an increased first phase glucose-stimulated insulin secretion. Expression of multiple genes involved in vesicular trafficking, membrane targeting and fuel-secretion pathways is dependent on Foxa2. In addition, impaired cytosolic Ca2+ oscillations and elevated intracellular cAMP production accompanied this secretory defect, and were likely contributors to the sensitization of the exocytotic machinery. Thus, in the absence of Foxa2, alterations in intracellular second messenger signaling redistribute the insulin granules into the readily releasable pool. We conclude that Foxa2 is required both for the fetal pancreas development and for the function of mature beta-cells.

2007-09-22 | E-CBIL-39 | biostudies-arrayexpress

Transcription profiling of HNF4 alpha null mice to investigate the phenotype of dis-regulated insulin secretion and abnormal beta cell growth

Project description:The aim of this experiment was to use microarray analysis to examine the phenotype of dis-regulated insulin secretion and abnormal beta cell growth in HNF4 alpha null mice. These mice show impaired glucose tolerance and elevated fasting and fed plasma insulin levels. Rana Gupta from Klaus Kaestner's Lab extracted RNA from isolated islets. Three controls and five mutants were provided for the study.

2006-09-05 | E-CBIL-6 | biostudies-arrayexpress

Transcription profiling of Foxa2 knock-outs in mice to better define the role of this gene in glucose homeostasis

Project description:Study to further characterize the genetic and functional consequence of the beta cell-specific ablation of Foxa2 (hepatocyte nuclear factor 3 beta, HNF-3b) in mice to better define the role of this gene in glucose homeostasis. The study involved 8 two-channel assays on UPenn Mouse PancChip 4.0, each consisting of a competitive mutant vs control hybridization. 4 control and 4 Foxa2loxP/loxP;Ins.CRE RNA samples were hybridized to the array using a dye-swap design. (The results from one of these assays had to be discarded from the analyses, so 7 assays were used.)

2006-06-30 | E-CBIL-13 | biostudies-arrayexpress

Transcription profiling of wild type and foxA1 null mice

Project description:The aim of this experiment was to use microarray analysis to examine the phenotype of the foxA1 (HNF3alpha) null mouse. foxA1 has a central role in the regulatory control of islet genes essential for glucose homeostasis in vivo. Previous studies have shown that the foxA1 null mouse demonstrates severe postnatal growth retardation followed by death between P2 and P12. These mutant mice are hypoglycemic despite unchanged expression of foxA1 target genes involved in hepatic gluconeogenesis. foxA1 is known to bind to and transactivate the proglucagon gene promoter and mice null for this gene have a 70% reduction in pancreatic proglucagon gene expression and plasma glucagon levels are reduced markedly. Marco Vatamaniuk from Klaus Kaestner Lab extracted RNA from isolated islets. Three biological replicates were provided for both the WT and Null.

2007-09-12 | E-CBIL-37 | biostudies-arrayexpress

Chromatin immunoprecipitation and transcription of mouse liver in the presence or absence of exogenous glucocorticoid to identify direct targets of the glucocorticoid receptor

Project description:The purpose of this study was to identify direct targets of the glucocorticoid receptor (GR) using an orthogonal analysis. An expression study of mouse livers in the presence or absence of exogenous glucocorticoid complemented a genome-wide location analysis on chromatin from the same livers. These were hybridized to the BCBC Mouse PancChip 5.0 and the Mouse PromoterChip BCBC-3.0 respectively.

2007-09-14 | E-CBIL-38 | biostudies-arrayexpress

Chromatin immunoprecipitation of wild type and Foxa2 knock-out mouse liver using anti-HNF6 anitbodies to test whether Foxa2 inhibits HNF6-mediated transcription in the liver

Project description:The aim of this study was to test, in vivo, if Foxa2 inhibits HNF6-mediated transcription in the liver. We utilized hepatocyte-specific gene ablation of Foxa2 and the Mouse PromoterChip BCBC 3.0 and Mouse PancChip 5.0 cDNA microarrays to investigate HNF6 binding to its target promoters in vivo in the presence or absence of Foxa2. For the mouse promoter microarray analysis, chromatin immunoprecipitation using anti-HNF6 antibodies was performed on chromatin isolated from Foxa2loxP/loxP Alfp.Cre and control mouse livers. Along with sheared genomic DNA (common reference), the immunoprecipitated DNA was amplified, labeled and hybridized to the Mouse PromoterChip BCBC 3.0. For microarray analysis of gene expression, liver RNAs were isolated from three Foxa2loxP/loxP Alfp.Cre and three control mice. RNAs were reverse transcribed, labeled, and hybridized to the Mouse PancChip 5.0. Overall, our studies demonstrate that HNF6 binds to and regulates its target promoters in vivo in the presence and absence of Foxa2 and that the expression levels of HNF6 targets are not influenced by Foxa2.

2007-09-14 | E-CBIL-36 | biostudies-arrayexpress

Gene expression profiling of MafA, MafB, and MafA/MafB Mutants in E18.5 pancreas

Project description:MafA and MafB transcription factors have been shown to be key regulators of insulin and glucagon transcription. MafB is essential for alpha and beta cell differentiation, as MafB deficient mice produced fewer insulin+ and glucagon+ cells during development, with MafA expressed in remaining insulin+ cells. In contrast, beta cell development was reported to be normal in a total MafA knock out, although the animals developed beta cell dysfunction and diabetes as adults. However, we have found that MafB expression is elevated during development and retained in adult insulin+ cells after conditional removal of MafA in the pancreas. These studies will evaluate the broader significance of these insulin and glucagon regulators in alpha and beta cell development and function. Our efforts will focus on determining if the concerted actions of MafA and MafB factors are significant to beta cell formation, and we specifically plan to: Determine how alpha and beta cell differentiation is affected in MafA/MafB compound mutant mice during pancreas development. cDNA microarray studies (pancchip 6.0) with wild type, MafAKO, MafB-/-, and MafAKOMafB-/- mutant E18.5 pancreata will be performed to comprehensively identify genes controlled by MafA and MafB in developing alpha and beta cells.

2014-11-04 | E-MTAB-3070 | biostudies-arrayexpress

Transcription profiling of mouse islet growth after partial pancreatectomy and exendin-4 Treatment

Project description:Diabetes mellitus results from an inadequately functioning beta-cell mass. In the adult pancreas, beta-cell mass is dynamic, increasing to meet metabolic demands and decreasing with metabolic or injury insults. Exendin-4 (Ex-4) is a glucagon-like peptide-1 receptor agonist that augments beta-cell mass by increasing beta-cell neogenesis and proliferation and by reducing apoptosis. We utilized a cDNA microarray approach to identify genes that are differentially regulated during islet growth after Ex-4 treatment or a partial pancreatectomy (Ppx). Mice underwent 50% Ppx or sham operation and received Ex-4 or vehicle every 24 hours. cDNA prepared from total pancreatic RNA isolated at 12, 24 and 48 hrs after surgery was hybridized to the PancChip 4.0 microarray.

2005-12-01 | E-CBIL-5 | biostudies-arrayexpress

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