Multidimensional scaling of the RNA-sequencing data demonstrated clear data clustering distinguishing selected lines and sexes (Supplementary Figure 1A and B). As indicated in the Methods, comparisons between lines for RNA-sequencing datasets were adjusted for sex. Principal component analyses of the proteomic and phosphoproteomic data sets revealed limited clustering for lines, sex, and a line by sex interaction (Supplementary Figure 1C–H). Due to the lack of clustering for sexes, subsequent network analyses of proteomic and phosphoproteomic data did not include sex as a factor. However, specific differences in differentially expressed proteins and phosphopeptides between each sex and the HAP and LAP lines may be found at https://github.com/dlhagger/AUD-Multi-Omics. Although sex effects on alcohol drinking exist in HAP and LAP mice, these sex effects are present in rodents, in general, suggesting sex is not specifically related to the divergent alcohol consumption and related phenotypes associated with HAP and LAP mice (Oberlin et al. 2011). Furthermore, our prior work assessing DS neurotransmission demonstrated relatively consistent effects across sexes for each line (Fritz et al. 2019). Volcano plots revealing distributions for the RNA-sequencing, proteomic, and phosphoproteomic analysis can be found in Supplementary Figure 2.
