Reference genes identified in SH-SY5Y cells using custom-made gene arrays with validation by quantitative polymerase chain reaction

Hoerndli, Frédéric J., Toigo, Marco, Schild, Andreas, Gotz, Jürgen and Day, Philip J. (2004) Reference genes identified in SH-SY5Y cells using custom-made gene arrays with validation by quantitative polymerase chain reaction. Analytical Biochemistry, 335 1: 30-41. doi:10.1016/j.ab.2004.08.028


Author Hoerndli, Frédéric J.
Toigo, Marco
Schild, Andreas
Gotz, Jürgen
Day, Philip J.
Title Reference genes identified in SH-SY5Y cells using custom-made gene arrays with validation by quantitative polymerase chain reaction
Journal name Analytical Biochemistry   Check publisher's open access policy
ISSN 0003-2697
1096-0309
Publication date 2004-12-01
Year available 2004
Sub-type Article (original research)
DOI 10.1016/j.ab.2004.08.028
Open Access Status Not Open Access
Volume 335
Issue 1
Start page 30
End page 41
Total pages 12
Place of publication Philadelphia, PA, United States
Publisher Elsevier
Language eng
Formatted abstract
Transcriptomic methods are widely used as an initial approach to gain a mechanistic insight into physiological and pathological processes. Because differences in gene regulation to be assessed by RNA screening methods (e.g., SAGE, Affymetrix GeneChips) can be very subtle, these techniques require stable reference genes for accurate normalization. It is widely known that housekeeping genes, which are routinely used for normalization, can vary significantly depending on the tissue, and experimental test. In this study, we aimed at identifying stable reference genes for a fibrillar Aβ42 peptide-treated, human tau-expressing SH-SY5Y neuroblastoma cell line derived to model aspects of Alzheimer’s disease in tissue culture. We selected genes exhibiting potential normalization characteristics from public databases to create a custom-made microarray allowing the identification of reference genes for low, intermediate, and abundant mRNAs. A subset of these candidates was subjected to quantitative real-time polymerase chain reaction and was analyzed with geNorm software. By doing so, we were able to identify GAPD, M-RIP, and POLR2F as stable and usable reference genes irrespective of differentiation status and Aβ42 treatment.
Keyword Quantitative RT-PCR
Reference genes
Housekeeping genes
Transcriptional analysis
Q-Index Code C1
Q-Index Status Provisional Code
Institutional Status Non-UQ

Document type: Journal Article
Sub-type: Article (original research)
Collections: Non HERDC
Queensland Brain Institute Publications
 
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