FFPE RNA Extraction and Quantification

Fifteen FFPE sections of 4 μm thickness from each sample were stored in tubes prior to RNA extraction, as previously described [12 (link),13 (link)]. Briefly, total RNA was isolated from FFPE samples using the Quick-RNA FFPE Kit (Zymo Research, Irvine, CA, USA). Following a DNAse I digestion using the Baseline-ZERO kit (Epicentre, Illumina, San Diego, CA, USA), the RNA concentration was measured with the Qubit RNA HS Assay Kit (Life Technologies, Carlsbad, CA, USA) on a Qubit Fluorometer (Life Technologies, Carlsbad, CA, USA). The RNA quality was determined with the RNA Pico Sensitivity Assay (PerkinElmer, Waltham, MA, USA) on a LabChip GXII Touch (PerkinElmer, Waltham, MA, USA).