GSM6753372: Control_S6; Homo sapiens; RNA-Seq
Fifteen FFPE sections of 4 μm thickness from each sample were stored in tubes prior to RNA extraction, as previously described 16,36. 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 on a Qubit Fluorom-eter (Life Technologies, Carlsbad, CA, USA). The RNA quality was determined with the RNA Pico Sensitivity Assay on a LabChip GXII Touch (PerkinElmer, Waltham, MA, USA). RNA sequencing was performed using massive analysis of cDNA ends (MACE), a 3' RNA sequencing method, as previously described 15,37. We recently demonstrated that MACE al-lows sequencing of FFPE samples with high accuracy, even after more than 10 years of storage 18. Briefly, 18 barcoded libraries comprising unique molecule identifiers were se-quenced on the NextSeq 500 (Illumina, San Diego, CA, USA) with 1 × 75 bp. PCR bias was removed using unique molecular identifiers.