Optimization and evaluation of T7 based RNA linear amplification protocols for cDNA microarray analysis

BMC Genomics

Table 8 Evaluation of the reproducibility of T7 based amplification.^a,b

Protocol		Affymetrix^c	Affymetrix w/o ligase	Jeffrey lab with G-50	Jeffrey lab	poly(A)⁺ RNA
Average correlation coefficient	Same day	0.91 ± 0.04 (n = 3)	0.98 (n = 2)	0.95 ± 0.01 (n = 3)	0.97 (n = 2)	0.97 ± 0.01 (n = 3)
	Different day	0.84 ± 0.05 (n = 3)	0.88 ± 0.05 (n = 3)	0.88 ± 0.03 (n = 4)	0.90 ± 0.03 (n = 3)	0.89 ± 0.03 (n = 2)
	Overall	0.86 ± 0.05 (n = 6)	0.89 ± 0.05 (n = 5)	0.89 ± 0.03 (n = 7)	0.91 ± 0.03 (n = 5)	0.92 ± 0.05 (n = 5)

^aData were obtained from comparing expression level of 11,123 clones using the described selection criteria. ^bAmplification was done using 3 μg BC2 total RNA. ^cNote that hybridizations were performed on Stanford printed cDNA microarrays, not Affymetrix arrays.

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