Total RNA was treated with TURBO DNase (Thermo Fisher Scientific) and purified using the RNeasy Micro kit (Qiagen). Integrity of RNA was assessed using the Agilent 2100 Bioanalyzer. RNA-Seq libraries were prepared using 1 μg of purified total RNA and the TruSeq Stranded Total RNA Library Prep kit (Illumina), depleting ribosomal RNA using the Ribo-Zero Gold reagent (Illumina), and modifying the RNA fragmentation times for lower RIN samples (< 7) according to manufacturer instructions. Library size was assessed using High Sensitivity DNA Analysis kits (Agilent) on the Agilent 2100 Bioanalyzer and libraries quantified using KAPA Library Quantification Kits (KAPA Biosystems) prior to pooling. Libraries were sequenced on the Illumina HiSeq 2500 or HiSeq 4000 systems, generating at least 50 million read pairs (100 million reads) per sample.
