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Open Access Research article

Suitability of endogenous reference genes for gene expression studies with human intraocular endothelial cells

Ruoxin Wei, Elizabeth Anne Stewart and Winfried M Amoaku*

Author Affiliations

University of Nottingham, Division of Ophthalmology and Visual Sciences, B Floor, Eye and ENT Building, Queen’s Medical Centre, Nottingham, NG7 2UH, UK

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BMC Research Notes 2013, 6:46  doi:10.1186/1756-0500-6-46

Published: 4 February 2013

Abstract

Background

The use of quantitative real-time reverse transcription polymerase chain reaction (qRT-PCR) has become widely applied as a method to measure transcript abundance. In order to be reflective of biological processes during health and disease this method is dependent on normalisation of data against stable endogenous controls. However, these genes can vary in their stability in different cell types. The importance of reference gene validation for a particular cell type is now well recognised and is an important step in any gene expression study.

Results

Cultured primary human choroidal and retinal endothelial cells were treated with the immunostimulant polyinosinic: polycytidylic acid or untreated. qRT-PCR was used to quantify the expression levels of 10 commonly used endogenous control genes, TBP, HPRT1, GAPDH, GUSB, PPIA, RPLP0, B2M, 18S rRNA, PGK1 and ACTB. Three different mathematical algorithms, GeNorm, NormFinder, and BestKeeper were used to analyse gene stability to give the most representative validation. In choroidal endothelial cells the most stable genes were ranked as HPRT1 and GUSB by GeNorm and NormFinder and HPRT1 and PPIA by BestKeeper. In retinal endothelial cells the most stable genes ranked were TBP and PGK1 by GeNorm and NormFinder and HPRT1 by BestKeeper. The least stable gene for both cell types was 18S with all 3 algorithms.

Conclusions

We have identified the most stable endogenous control genes in intraocular endothelial cells. It is suggested future qRT-PCR studies using these cells would benefit from adopting the genes identified in this study as the most appropriate endogenous control genes.

Keywords:
Choroid; Retina; Endothelial cells; Housekeeping gene; Endogenous control; Polymerase chain reaction