Strand-specific RNA sequencing protocol

Strand-specific RNA sequencing libraries were constructed from rRNA-depleted RNA using the ScriptSeq V2 Kit according to the manufacturer’s instructions (Epicentre). The libraries were sequenced using a Hiseq2000/2500 instrument (Illumina), 50 bp paired-end, with the exception of one sample (ALL_707) that was sequenced on a MiSeq instrument, 83 bp paired-end. Raw sequence reads were trimmed using Cutadapt 1.2.1 [20 ] and mapped to the human 1000 Genomes build 37 (GRCh37) using Tophat 2 (2.0.4) [21 (link)]. Quality control of RNA sequencing data was performed with RNA-SeQC [22 (link)] (Additional file 1: Table S2). Detailed information of RNA sequencing and computational analysis is provided in Additional file 2.