We used qPCR to validate the RNA-Seq data (Figure 1D,E). The RNA-Seq and qPCR expression levels of 47 transcripts from five neurotransmitter systems from the Saline sample showed strong agreement across the two methods (Pearson’s r = 0.75) over a greater than 1000-fold range of expression (Figure 1D). A comparison of the ratios of Cocaine/Saline measured by RNA-Seq and qPCR was also carried out (Figure 1E). Cocaine-mediated changes in gene expression estimated from the RNA-Seq data were consistently larger than the changes observed with qPCR; nevertheless, the ratios show good qualitative agreement (Pearson’s r = 0.60). Differences presumably reflect the much larger dynamic range of RNA-Seq and quantification across entire transcripts rather than between single primer pairs.
