Methamphetamine (Meth) seeking progressively increases after withdrawal (incubation of Meth craving), but the transcriptional mechanisms that contribute to this incubation are unknown. Here we used RNA-sequencing to analyze transcriptional profiles associated with incubation of Meth craving in central amygdala (CeA) and orbitofrontal cortex (OFC), two brain areas previously implicated in relapse to drug seeking. We trained rats to self-administer either saline (control condition) or Meth (10 days; 9 h/day, 0.1 mg/kg/infusion). Next, we collected brain tissue from CeA and OFC on withdrawal day 2 (when Meth seeking is low and non-incubated) and on day 35 (when Meth seeking is high and incubated), for subsequent RNA-sequencing. In CeA, we identified 10-fold more differentially expressed genes (DEGs) on withdrawal day 35 than day 2. These genes were enriched for several biological processes, including protein ubiquitination and histone methylation. In OFC, we identified many fewer expression changes than in CeA. Interestingly, there were more DEGs on withdrawal day 2 than on day 35. Several genes in OFC showed opposing expression changes on withdrawal day 2 (increase) when compared to withdrawal day 35 (decrease), which was further validated by qPCR. Our analyses highlight the CeA as a key region of transcriptional regulation associated with incubation of Meth seeking. In contrast, transcriptional regulation in OFC may contributes to Meth seeking during early withdrawal. Overall, these findings provide a unique resource of gene expression data for future studies examining transcriptional mechanisms in CeA that mediate Meth seeking after prolonged withdrawal. Overall design: Exp. 1 Genome-wide transcriptional profiling of CeA during incubation of Meth craving We performed intravenous surgeries on two groups of rats (total n=26) and trained them to self-administer either saline (n=12) or Meth (n=14) as described above in 2 independent runs. We performed live decapitation on withdrawal days 2 and 35, and collected CeA tissue for mRNA preparation. We used the extracted mRNA for library preparation and RNA-sequencing. We pooled tissue from two rats as one biological replicate. The number of biological replicates in each group was: Day 2: Saline=3, Meth=4; Day 35: Saline=3, Meth=3. Exp. 2 Genome-wide transcriptional profiling of OFC during incubation of Meth craving As above, two groups of rats (total n=32) were trained to self-administer saline (n=16) or Meth (n=16) in 2 independent runs. We performed live decapitation on withdrawal days 2 and 35, and collected OFC tissue for mRNA preparation. We used the extracted mRNA either for library preparation and RNA-sequencing or for cDNA synthesis and qPCR. We pooled tissue from two rats as one biological replicate. The number of biological replicates in each group was: Day 2: Saline=4, Meth=4; Day 35: Saline=4, Meth=4.