Multiplexed gene expression profiling was performed using the
TruSeq1 Targeted RNA expression kit (degraded RNA protocol for
reverse transcription; dual indices) and custom target panels
(30–55 gene targets) (Illumina, San Diego, CA). Pooled libraries
were run on a MiSeq instrument (Illumina) using a MiSeq reagent
kit v3 (Illumina) with 151 cycles/read. All data was analysed using
the MSR Targeted RNA application (BaseSpace).