Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Expression data from mouse embryonic stem cells

ABSTRACT: Analysis of the transcriptome of ß-catenin flox/- mES cells in comparison with ß-catenin null mES cells or ß-catenin null mES cells stably transfected with an E-cadherin-?-catenin fusion protein. Expression assay was performed using the Affymetrix GeneChip Mouse Gene 1.0 ST array. The experiment includes ß-catenin flox/-, ß-catenin null and ß-catenin null E? mouse embryonic stem cells with three biological replicates for each sample.

ORGANISM(S): Mus musculus

SUBMITTER: Annaick Carles

PROVIDER: E-GEOD-44543 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

E-cadherin is required for the proper activation of the Lifr/Gp130 signaling pathway in mouse embryonic stem cells.

del Valle Ignacio I Rudloff Stefan S Carles Annaick A Li Yong Y Liszewska Ewa E Vogt Riana R Kemler Rolf R

Development (Cambridge, England) 20130313 8

The leukemia inhibitory factor (Lif) signaling pathway is a crucial determinant for mouse embryonic stem (mES) cell self-renewal and pluripotency. One of the hallmarks of mES cells, their compact growth morphology, results from tight cell adhesion mediated through E-cadherin, β-catenin (Ctnnb1) and α-catenin with the actin cytoskeleton. β-catenin is also involved in canonical Wnt signaling, which has also been suggested to control mES cell stemness. Here, we analyze Ctnnb1(-/-) mES cells in whic ...[more]

PMID: 23487312

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Project description:In order to identify genes regulated by VE-cadherin expression, we compared a mouse VE-cadherin null cell line (VEC null) with the same line reconstituted with VE-cadherin wild type cDNA (VEC positive). The morphological and functional properties of these cell lines were described previously [Lampugnani,M.G. et al. Contact inhibition of VEGF-induced proliferation requires vascular endothelial cadherin, beta-catenin, and the phosphatase DEP-1/CD148. J. Cell Biol. 161, 793-804 (2003)]. By Affymetrix gene expression analysis we found several genes up-regulated by VE-cadherin, among which claudin-5 reached remarkably high levels. The up-regulation of these genes required not only VE-cadherin expression but also cell confluence suggesting that VE-cadherin clustering at junctions was needed. Experiment Overall Design: VEC null or positive cells in the sparse and confluent conditions have been starved in MCDB 131 medium 1% BSA for 36 h. Next, RNA has been extracted with standard guanidinium isothiocyanate lysis buffer and cesium chloride ultracentrifugation. Synthesis of biotinylated cRNA targets, array hybridization (GeneChips MG_U74Av2 and MG_U74Bv2), staining and scanning were performed according to the Affymetrix standard protocols, starting from 15 Î¼g of total RNA. Two copies of the GeneChips were hybridized with each cRNA sample. The MAS5 algorithm was used to determine the expression levels of mRNAs; the absolute analysis was performed using default parameters and scaling factor 500. Report files were extracted for each chip, and performance of labeled target was evaluated on the basis of several values (scaling factor, background and noise values, % present calls, average signal value, etc). Gene expression levels were normalized on the median over all samples. Annotation of Probe Sets is according to Affymetrix Annotation Tables (release May 31, 2007) [Vecchi,M. et al. Gene expression analysis of early and advanced gastric cancers. Oncogene 26, 4284-4294 (2007)]. We selected the genes up-regulated by VE-cadherin expression and clustering at junctions in confluent VEC positive cells.

Dataset Information

Expression data from mouse embryonic stem cells

Publications

E-cadherin is required for the proper activation of the Lifr/Gp130 signaling pathway in mouse embryonic stem cells.

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