Dataset features

Specifications


Application: Gene expression microarray analysis
Number of samples: 16
Release date: Jul 6 2008
Last update date: Feb 18 2018
Access: Public
Genes: CDH5, Enhancer of terminal gene conversion, VEGFA, CTNNB1, PTPRJ, CLDN5
Taxon: Mus musculus
Dataset link Genes up-regulated by VE-cadherin expression and clustering at junctions

Experimental Protocol


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 μg 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.

Repositories


GEO

GSE11674

ArrayExpress

E-GEOD-11674

BioProject

PRJNA106073

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Contact


Elisabetta Dejana