Characterization of the effect of sample quality on high density oligonucleotide microarray data using progressively degraded rat liver RNA

Table 1 RNA metrics associated with RIN value and RNA degradation method. Average values and standard deviations are reported for metrics associated with samples in each RIN class (n = 3).

Handling condition	RIN class	RIN	28s/18s rRNA	cRNA yield	cRNA length	3'/5' GAPDH	3'/5' β-actin
F/T	9.5	9.5 ± 0.1	1.43 ± 0.15	86 ± 8	1923 ± 157	1.17 ± 0.06	1.70 ± 0.35
	8	8.1 ± 0.2	1.00 ± 0.00^a	63 ± 4^b	1398 ± 116^a	1.77 ± 0.21	1.93 ± 0.06
	7	7.0 ± 0.1	0.70 ± 0.10^a	44 ± 12^a	1136 ± 207^a	3.05 ± 0.95^b	3.62 ± 1.18^b
	6	6.2 ± 0.1	0.50 ± 0.10^a	38 ± 3^a	878 ± 62^a	5.50 ± 0.8^a	5.27 ± 0.86^a
37°C	9.5	9.5 ± 0.2	1.35 ± 0.13	74 ± 16	2294 ± 236	1.01 ± 0.02	1.34 ± 0.02
	9	9.1 ± 0.1	1.33 ± 0.06	83 ± 7	2110 ± 322	1.24 ± 0.20	1.49 ± 0.26
	8	8.2 ± 0.1	1.33 ± 0.06	61 ± 19	1834 ± 293	1.29 ± 0.18	1.60 ± 0.04
	7	7.0 ± 0.2	1.07 ± 0.15^b	42 ± 6	1210 ± 158^a	2.00 ± 0.21^a	2.12 ± 0.20^a
	6	6.1 ± 0.5	0.90 ± 0.10^a	39 ± 18^a	1244 ± 223^a	1.96 ± 0.41^a	2.29 ± 0.40^a

ISSN: 1472-6750