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Gene Expression in White Adipose Tissue of KSR2-/- mice compared to wild type mice

ABSTRACT: The goal of this study was to define the gene expression changes that take place in the white adipose tissue of KSR2-/- mice at 6 months of age. Three wild type mice and three KSR2-/- mice were used for total RNA extraction from white adipose tissue. The RNA from each mouse was analyzed on one Affymetrix gene chip and the differences were compared using Gene Set Enrichment Analysis.

ORGANISM(S): Mus musculus

SUBMITTER: Robert Lewis

PROVIDER: E-GEOD-17923 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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KSR2 is an essential regulator of AMP kinase, energy expenditure, and insulin sensitivity.

Costanzo-Garvey Diane L DL Pfluger Paul T PT Dougherty Michele K MK Stock Jeffery L JL Boehm Matthew M Chaika Oleg O Fernandez Mario R MR Fisher Kurt K Kortum Robert L RL Hong Eun-Gyoung EG Jun John Y JY Ko Hwi Jin HJ Schreiner Aimee A Volle Deanna J DJ Treece Tina T Swift Amy L AL Winer Mike M Chen Denise D Wu Min M Leon Lisa R LR Shaw Andrey S AS McNeish John J Kim Jason K JK Kim Jason K JK Morrison Deborah K DK Tschöp Matthias H MH Lewis Robert E RE

Cell metabolism 20091101 5

Kinase suppressors of Ras 1 and 2 (KSR1 and KSR2) function as molecular scaffolds to potently regulate the MAP kinases ERK1/2 and affect multiple cell fates. Here we show that KSR2 interacts with and modulates the activity of AMPK. KSR2 regulates AMPK-dependent glucose uptake and fatty acid oxidation in mouse embryonic fibroblasts and glycolysis in a neuronal cell line. Disruption of KSR2 in vivo impairs AMPK-regulated processes affecting fatty acid oxidation and thermogenesis to cause obesity. ...[more]

PMID: 19883615

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Expression profiling of KSR1-/- MEFs expressing KSR1 and/or H-RasV12

Project description:We engineered KSR1-/- mouse embryonic fibroblasts (MEFs) to express GFP alone, KSR1 or RasV12 and GFP, or KSR1, H-RasV12 and GFP, and performed gene expression profiling on all 4 cell lines. Each cell line was measured in triplicate: 1. GFP alone 2. H-RasV12 and GFP 3. KSR1 and GFP 4. KSR1, H-RasV12, and GFP

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The YbjN regulon in Escherichia coli

Project description:YbjN, an enterobacteria-specific protein, is a multicopy suppressor of ts9 temperature sensitivity in Escherichia coli. Microarray study revealed that the expression level of ybjN was inversely correlated with the expression of flagellar, fimbrial and acid resistance genes. Over-expression of ybjN significantly down-regulated genes involved in the citric acid cycle, glycolysis, the glyoxylate shunt, oxidative phosphorylation, and amino acid and nucleotide metabolism. On the other hand, over-expression of ybjN up-regulated toxin-antitoxin modules, the SOS responsive pathway, cold shock proteins and starvation-induced transporter genes. Our results collectively suggest that YbjN may play important roles in regulating bacterial multicellular behaviors, metabolism and survival under various stress conditions in Es. coli. A total of 8 samples were analyzed: E. coli wild type strain (2 replicates); E. coli ybjN mutant strain (3 replicates); E. coli ybjN over-expression strain (3 replicates).

2011-10-14 | E-GEOD-28630 | biostudies-arrayexpress

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The Rcs regulon in Erwinia amylovora

Project description:We conducted genome-wide microarray analyses to determine the regulons of RcsB and RcsC in liquid medium and, for the first time, on immature pear fruit. Our array analyses identified a total of 648 genes differentially regulated by the RcsCB in vitro and in vivo. Consistent with our previous findings, RcsB acts as a positive regulator in both conditions, while RcsC positively controls amylovoran biosynthetic gene expression in vivo, but negatively in vitro. Besides amylovoran biosynthesis and regulatory genes, cell wall and cell envelope (membrane) as well as regulatory genes were the major components of the RcsBC regulon, including many novel genes. In addition, we have also demonstrated that transcripts of rcsA, rcsC and rcsD genes, but not rcsB gene, were up-regulated when grown in minimal medium or after infection of pear fruits compared to LB medium. Furthermore, a hidden Markov model (HMM) has predicted 60 genes with candidate RcsB binding site in the intergenic regions of the E. amylovora ATCC 49946 genome and 18 (28) of them were identified in the microarray assay. Based on our findings, a working model has been proposed to illustrate how the Rcs phosphorelay system regulates virulence gene expression in E. amylovora. A total of 12 samples were analyzed in two conditions: For in vitro condition (MBMA medium + 1% sorbitol), Erwinia amylovora wild type strain (2 replicates); E. amylovora rcsB mutant strain (2 replicates); E. amylovora rcsC mutant strain (2 replicates): For in vivo condition (on wounded immature pear fruits), Erwinia amylovora wild type strain (2 replicates); E. amylovora rcsB mutant strain (2 replicates); E. amylovora rcsC mutant strain (2 replicates).

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2013-01-01 | E-GEOD-37064 | biostudies-arrayexpress

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Chromatin-immunoprecipitant (ChIP) for CrdR binding site analysis in whole-genome tilling array

Project description:The CrdR-ChIP profiling is comparing H. pylori gDNA without crdR interaction as control and CrdR interact with H. pylori gDNA (WT vs crdR). The goal was determine the crdR binding site on H. pylori genome, it provide possible crdR-regulated genes. 2 samples: H. pylori 26695 is control, and CrdR is experiment.

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Transcription profiling of rat liver and kidney mixtures on an Affymetrix platform to assess technical and biological variability

2008-08-12 | E-TABM-536 | biostudies-arrayexpress

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Project description:In this experiment, there are replicate measurements of gene expression in a group of similarly treated animals measured in such a way as to provide data for comparison of technical variation with biological variability. The data are twelve microarray measurements on each of six rats that were subject to the same control-group treatment. The twelve measurements encompass triplicate measures of RNA from the liver, from the kidney, and from two mixtures of both RNAs. IMPORTANT: 6C-1 and 1-6B1 are outlier because of poor cRNA yield. 4A-1 (low cRNA yield too) and 4D-1 seems to have been switched during processing. 2D1 and 5A3 were also mistake (samples picked from the wrong well in the original 96 plates) as they seems to cluster with B samples (75% liver-25% Kidney).

2008-09-18 | E-TABM-554 | biostudies-arrayexpress

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2013-01-30 | E-TABM-7 | biostudies-arrayexpress

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