Reference gene validation for qPCR in rat carotid body during postnatal development

BMC Research Notes

Table 2 Ranking of the 6 selected reference genes in rat whole carotid bodies by geNorm, NormFinder and BestKeeper

geNorm	N1+N14 (n = 16)		N14+Hyper14 (n = 14)		N14+Hypo14 (n = 14)		N1+N14+Hyper14+ Hypo14 (n = 28)
Rank	Gene	M-value	Gene	M-value	Gene	M-value	Gene	M-value
Best two genes	RPII TBP	0.26	PPIA TBP	0.20	PPIA TBP	0.29	PPIA TBP	0.26
3	PPIA	0.27	RPII	0.35	RPII	0.36	RPII	0.38
4	actin	0.34	GAPDH	0.43	GAPDH	0.45	GAPDH	0.44
5	GAPDH	0.38	actin	0.50	actin	0.50	actin	0.49
6	18s	0.40	18s	0.57	18s	0.52	18s	0.53
Norm Finder	N1+N14 (n = 16)		N14+Hyper14 (n = 14)		N14+Hypo14 (n = 14)		N1+ N14+Hyper14+ Hypo14 (n = 28)
Rank	Gene	Variability	Gene	Variability	Gene	Variability	Gene	Variability
Best two genes	TBP Actin	0.009	RPII GAPDH	0.007	RPII GAPDH	0.008	PPIA TBP	0.011
1	GAPDH	0.01	RPII	0.013	TBP	0.007	TBP	0.015
2	PPIA	0.011	GAPDH	0.013	PPIA	0.015	GAPDH	0.017
3	actin	0.014	TBP	0.014	GAPDH	0.018	18s	0.019
4	TBP	0.015	actin	0.019	RPII	0.018	PPIA	0.020
5	RPII	0.016	PPIA	0.021	18s	0.020	RPII	0.021
6	18s	0.018	18s	0.021	actin	0.021	actin	0.023
Best Keeper	N1+N14 (n = 16)		N14+ yper14 (n = 14)		N14+Hypo14 (n = 14)		N1 + N14 + Hyper14+ Hypo14 (n = 28)
Rank	Gene	Coeff. of corr.[r]	Gene	Coeff. of corr.[r]	Gene	Coeff. of corr.[r]	Gene	Coeff. of corr.[r]
1	PPIA	0.89	RPII	0.97	RPII	0.86	PPIA	0.97
2	actin	0.84	PPIA	0.96	PPIA	0.85	TBP	0.95
3	GAPDH	0.83	GAPDH	0.96	TBP	0.85	GAPDH	0.95
4	18s	0.73	TBP	0.95	actin	0.75	RPII	0.93
5	RPII	0.72	actin	0.93	GAPDH	0.69	actin	0.92
6	TBP	0.70	18s	0.87	18s	0.56	18s	0.89

The reference genes are ranked in several groups of CB as follows: N1+N14 = immature and mature CB, reared in normoxia (n = 16). N14+Hyper14 = mature normoxia and hyperoxia treated CB (n = 14). N14+Hypo14 = mature normoxia and hypoxia treated CB (n = 14). N1+N14+Hyper14+Hypo14 = immature, normoxia (N1), mature, normoxia (N14), mature, hyperoxia (Hyper14), and mature, hypoxia treated (Hypo14) CB (n = 28). Genes are ranked on their stability value calculated by each respective program: geNorm, M-value; NormFinder, Variability; and BestKeeper, Coefficient of correlation [r]. (n) = number of independent determinations.

ISSN: 1756-0500