To evaluate enrichment and depletion of transcripts in NAc lysates prepared from mice in the Saline, Cocaine, and Withdrawal groups, we calculated the relative abundance of each mRNA in the three treatment groups, computed Z-scores across samples, and hierarchically clustered genes for visualization in a heat map. Of the 19,890 detected genes, 13,184 were expressed in at least one library at an RPKM > 1.0 and were used in downstream analyses. Several patterns of expression emerged from hierarchical clustering, including transcripts showing (i) sustained increases in both Cocaine and Withdrawal, (ii) increases only in Withdrawal, (iii) transient increases only in Cocaine, (iv) transient decreases only in Cocaine, and (v) sustained decreases in Cocaine and Withdrawal (Figure 2A). The full gene list for each cluster is available in Table S2.
