Transcriptomic Analysis of TRAP Samples

RNA recovered from TRAP was sequenced and has been uploaded to the Sequence Read Archive (National Center for Biotechnology Information; Accession code, PRJNA597018; Forbes et al., 2020 (link)). Briefly, sequencing libraries were prepared using the Trio RNA-Seq Library Preparation Kit (NuGen) for all samples with a RNA Integrity Number value > 7 (Bioanalyzer Pico Kit, Agilent). Paired-end reads (50 bp) were obtained using the NovaSeq 6000 System (Illumina), and trimmed with Trimmomatic (Bolger et al., 2014 (link)) according to the Library Preparation Kit protocol (NuGen). Reads were mapped to the mouse reference genome (Genome Reference Consortium Mouse Build 38, mm10) using STAR (Dobin et al., 2013 (link)), and read counts were generated using Htseq (Anders et al., 2015 (link)). Normalized read counts were generated using DESeq2 package for R (Love et al., 2014 (link)).