Comparison of the QuantiGene and qPCR methods as used for assessing the inhibitory effect of flavopiridol. A &B. Transcription reactions in the presence of α-amanitin or flavopiridol were set up using the standard DNA template HS-DNA and performed following the standardized protocol as described in the Additional file 3. C &D. A 98 pb longer DNA template, HS-DNA_long, was used to set up transcription reactions in the presence of α-amanitin or flavopiridol. Reaction conditions were similar to the experiment in A &B except for a shorter incubation period of 10 min instead of 30 min in the standard setting. To quantitate the RNA synthesis yield, the optimized, standardized QG- (A & C) or qPCR-method (B & D) was applied. Residual percent RNA synthesis was calculated by relating to the RNA amount in the positive control reactions. Bars show the standard deviation of the duplicate samples.