Separate brains from 12 HAP (6 male, 6 female) and 12 LAP (6 male, 6 female) mice were rapidly harvested by a blinded researcher and the DS, as a whole, was dissected bilaterally and homogenized. Tissue collection was completed in the morning to midday and samples were deidentified until tissue was fully processed and data was prepared for analysis. RNA was isolated from brain tissue using the RNeasy Plus Universal Mini Kit (Qiagen #73404) according to the manufacturer’s protocol. The paired-end library was prepared using the Dual Indexed KAPA mRNA Hyperprep Kit (KK8581; Roche). Bulk RNA-sequencing was performed on an Illumina HiSeq4000. Reads 75bp long were generated using a HiSeq3000/4000 PE cluster/SBS kits (Illumina #PE-410–1001, #FC-410–1002). Although single cell RNA-sequencing would have provided detailed data on differential gene expression across heterogenous cell populations in the DS of HAP and LAP mice, current technical capabilities limit the performance of single cell proteomics/phosphoproteomics. As our intent with the current study was to provide a complementary and integrative multi-omic analysis of the DS, we chose to employ bulk RNA-sequencing so that our findings
