Total RNA was extracted from laser-captured tissue microdissected from hippocampal CA1 cell body and neuropil layers from 3 adult (6–8 wk) male Amigo2-EGFP transgenic mice using the micro RNeasy kit (QIAGEN; Hilden, Germany), including on-column DNase-treatment. Total RNA samples were analysed for RNA integrity (RIN > 8.5) and concentration using the 2100 Bioanalyzer instrument (Agilent; Santa Clara, CA) and RNA 6000 Pico assay (Agilent). Stranded RNA-Seq libraries were prepared using 1–5 ng of total RNA per sample and region (1 ng for neuropil samples and 5 ng for cell body samples) with the Ovation RNA-Seq Systems 1–16 for mouse (NuGEN; San Carlos, CA), according to manufacturer instructions. Libraries were analyzed for size and concentration using the 2100 Agilent Bioanalyzer and the High Sensitivity DNA assay. Libraries were multiplexed and run on a NextSeq500 instrument (Illumina; San Diego, CA), acquiring an average of 66 ± 17 million 100 bp reads per sample. Reads were trimmed using Sickle software (https://github.com/najoshi/sickle) and only paired reads with a quality score >20 and a minimum length of 20 bp were pseudo-aligned and quantified to merged
