E-GEOD-2450 - Transcription profiling of human primary HUVECs and an immortalized HUVEC cell line treated with atorvastatin and/or mevalonate

Status
Submitted on 25 March 2005, released on 21 August 2007, last updated on 27 March 2012
Organism
Homo sapiens
Samples (16)
Array (1)
Protocols (2)
Description
Rationale: Immortalized cells may exhibit important differences relative to their primary cell counterparts. Microarrays were used compare primary human umbilical vein endothelial cells (HUVECs) and the immortalized HUVEC cell line EA.hy926, in their response to inhibition of the mevalonate pathway by a HMG-CoA reductase inhibitor (atorvastatin). The effects of atorvastatin were reversed by the addition of mevalonate, to subtract non-specific changes in gene expression. Methods: Confluent cell cultures of HUVECs and EA.hy926 cells (two independent experiments in each cell type) were incubated with 1) statin-free media; 2) 10 microM atorvastatin; 3) 500 microM mevalonate; or 4) a combination of 10 microM atorvastatin and 500 microM mevalonate. All cells were harvested at 24 h. Total RNA was isolated using Trizol reagent (Invitrogen). cDNA was prepared from 10 microgram total RNA using a double-stranded cDNA synthesis kit (Life Technologies) with a T7-dT24 primer for first-strand synthesis. cRNA was synthesized from cDNA and biotinylated using the BioArray High Yield RNA Transcript Labeling Kit (Enzo Diagnostics). Twenty microgram of cRNA was fragmented by heating at 94°C for 35 min in fragmentation buffer, containing 40 mM Tris-acetate, pH 8.1, 125 mM KOAc, 30 mM MgOAc. Fifteen micrgram of fragmented cRNA, together with control cRNAs and grid alignment oligonucleotides, were hybridized overnight to GeneChip Human Genome U133A 2.0 arrays (Affymetrix) at 45°C under constant rotation. Arrays were washed and incubated with an anti-streptavidin antibody. Fluorescent signals were measured using an Agilent Gene Array Laser Scanner and analyzed with MicroArray Suite 5.0 (Affymetrix). Microarrays were scaled using default settings.
Experiment types
transcription profiling by array, cell type comparison, co-expression, compound treatment
Contact
Citation
Comparative expression profiling in primary and immortalized endothelial cells: changes in gene expression in response to hydroxy methylglutaryl-coenzyme A reductase inhibition. Marjan Boerma, Gregory R Burton, Junru Wang, Louis M Fink, Robert E McGehee, Martin Hauer-Jensen. Blood Coagul Fibrinolysis 17(3):173-80 (2006)
MIAME
PlatformsProtocolsVariablesProcessedRaw
Files
Investigation descriptionE-GEOD-2450.idf.txt
Sample and data relationshipE-GEOD-2450.sdrf.txt
Raw data (1)E-GEOD-2450.raw.1.zip
Processed data (1)E-GEOD-2450.processed.1.zip
Array designA-AFFY-33.adf.txt
R ExpressionSetE-GEOD-2450.eSet.r
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