Normalization with genes encoding ribosomal proteins but not GAPDH provides an accurate quantification of gene expressions in neuronal differentiation of PC12 cells

Table 1 Selection of candidate reference genes from microarray data

Gene symbol	Definition	Mean	geNorm	NormFinder
RPL29	Ribosomal protein L29	14.04	1	1
RPL10a	Ribosomal protein L10A	12.49	2	2
LOC292640	Vps20-associated 1 homolog	10.87	3	3
LOC498143	Similar to ribosomal protein L15	13.71	4	4
LOC317275	Similar to ribosomal protein L7-like 1	11.88	7	5
RPS15	Ribosomal protein S15	12.97	5	6
ARBP	Acidic ribosomal phosphoprotein P0	14.27	6	7
RPL14	Ribosomal protein L14	13.89	9	8
EEF1A1	Eukaryotic translation elongation factor 1 alpha 1	14.17	8	9
RPS15A	Ribosomal protein S15a	13.93	10	10
RPL18	Ribosomal protein L18	13.58	11	11
REPS1 (P)	RalBP1 associated Eps domain containing protein (predicted)	10.73	12	12
LOC363720	chromatin modifying protein 2B	10.61	14	13
CNOT8	CCR4-NOT transcription complex, subunit 8	11.00	15	14
RTCD1	RNA terminal phosphate cyclase domain 1	10.48	17	15
RPL19	Ribosomal protein L19	13.74	13	16
NDUFB6 (P)	NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 6,	10.43	16	17
RPL9	Ribosomal protein L9	13.74	18	18
LOC499803	Similar to 40S ribosomal protein S3	13.76	19	19
RPL3	Ribosomal protein L3	14.03	20	20
ACTB	Actin, beta	13.85
GAPDH	Glyceraldehyde-3-phosphate dehydrogenase	12.88

Microarray analysis of the expression profiles of 21,910 genes in naïve PC12 cells and those treated with NGF or GDNF for 0.5 h and 72 h. Twenty candidate reference genes were selected based on pairwise comparison (geNorm) and model based variation (NormFinder) analysis of the top 100 genes with the lowest CV. The log2 transformed values of the average signal intensities among the 24 arrays were shown as Mean. Thirteen of the twenty genes were Ribosomal Protein Genes (Bold). Both ACTB and GAPDH were included for comparison but were not among the top 100 genes recommended by either statistical analysis.

ISSN: 1471-2164