There are some limitations to this work that must be considered. It is important to bear in mind that this analysis used tissue from the entire DS while our previous study examined the two major subregions of the DS (the dorsolateral and dorsomedial striatum). It is therefore possible that subregion-specific effects may have been obscured. Although, subregions could have been used for RNA-sequencing, the lack of total tissue available from these subregions in each animal prevented us from completing subregion specific proteomics and phosphoproteomics which require more tissue to accurately quantify protein abundance. Additionally, we cannot be confident that the results from our analyses are unique to the DS or if similar enrichments in GO or pathways are observed in other brain regions relevant to AUD. For the present study, HAP and LAPs from replicate 2 were used. Although behavioral phenotypes (Oberlin et al. 2011) and electrophysiological measures in the DS between replicates two and three are quite similar (Fritz et al. 2019), it remains possible that different replicates may not contain identical gene-sets which may limit the generalizability of
