!Citation=Zhao H, et al. (2002). BMC Genomics 3(1):31 !Title=Optimization and evaluation of T7 based RNA linear amplification protocols for cDNA microarray analysis. !PubMedID=12445333 !Name=Amplification Table 9 !ExptSetNo=1609 !Description=This experiment was designed to evaluate the effect of the amount of input total RNA on the fidelity, reproducibility, and yield of T7 based RNA linear amplification. BC2 total RNA was amplified using the Jeffrey lab protocol. Different amounts of T7 primer were used according to the quantity of input total RNA. Multiple amplifications were done for each quantity of input total RNA to minimize experimental variations. !Name=Amplification Figure 1 !ExptSetNo=1610 !Description=This experiment was designed to evaluate the effect of in vitro transcription time on the fidelity, reproducibility, and yield of T7 based linear amplification. Duplicate reactions were performed at 37 degree for 2, 3, 4, 5, and 6 hours. Two additional 5-hour incubation reactions were stored at 4 degree overnight to determine the effect of low temperature incubation on amplification. BC2 total RNA was amplified using the Jeffrey lab protocol with the G50 column cleanup step. !Name=Amplification BC2 uM !ExptSetNo=1613 !Description=This experiment was designed to assess the reproducibility of microarray hybridization using poly(A)+RNA. BC2 total RNA was isolated from which poly(A)+RNA was subsequently isolated. Three arrays were hybridized on the same day using arrays from the same batch. Two were done three months later using poly(A)+RNA freshly isolated from the same total RNA. !Name=Amplification Table 1 !ExptSetNo=1615 !Description=This experiment was designed to determine the effects of template switching (TS) primer and the type of columns used in ds cDNA cleanup on the fidelity of the T7 based RNA linear amplification. BC91 total RNA was amplified with or without TS primer and with two different ds cDNA cleanup protocols. !Name=Amplification Table 3 !ExptSetNo=1616 !Description=This experiment was designed to evaluate the effect of ligase used in the second strand cDNA synthesis on the fidelity of T7 based RNA linear amplification. BC2 total RNA was amplified with or without ligase using Affymetrix protocol. !Name=Amplification Table 4 !ExptSetNo=1617 !Description=This experiment was designed to evaluate the effect of column cleanup on the fidelity and yield of T7 based RNA linear amplification. BC2 total RNA was amplified using the Jeffrey lab protocol with or without G50 cleanup. !Name=Amplification Table 8, Figure2, Figure3 !ExptSetNo=1622 !Description=This experiment was designed to evaluate the fidelity and reproducibility of the T7 based linear amplification. Four different protocols were used to amplify BC2 total RNA. Multiple reactions were done for each protocol. !Name=Amplification Table 7 !ExptSetNo=1764 !Description=This experiment was designed to determine the correlation between expression levels of defferent tumors (BC2 and BC91) measured by poly(A)+RNA and aRNA for each tumor. Total RNA was amplified using the Jeffrey lab protocol with G50 cleanup.