Evaluation of methods for amplification of picogram amounts of total RNA for whole genome expression profiling

BMC Genomics

Table 3 cDNA yields and hybridisation quality metrics of Nugen experiments.

RNA input	Amount of amplified cDNA	Background	Present Call	β-Actin 3'/5' ratio	GAPDH 3'/5' ratio
1000 pg	10.6 μg	31.9	45.6%	8.7	1.3
	6.1 μg	29.7	52.1%	6.0	1.0
500 pg	7.6 μg	33.5	45.1%	6.6	1.1
	7.4 μg	35.7	48.6%	7.2	1.2
250 pg	6.9 μg	31.5	39.3%	6.9	0.8
	8.3 μg	32.8	45.5%	10.6	1.3
100 pg	6.1 μg	29.8	37.8%	10.5	1.4
	4.4 μg	32.4	29.4%	6.2	1.0
50 pg	3.5 μg	30.7	19.6%	23.6	1.5
	4.5 μg	30.0	25.4%	11.1	1.2
0 pg	1.8 μg	-	-	-	-

Targets were synthesised in each laboratory with the Nugen protocol at five amount of input RNA and hybridised to HG U133 Plus 2.0 array. A rapid analysis was performed with Expression Console (Affymetrix, MAS 5 normalisation).

ISSN: 1471-2164