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RNA sequencing was performed using massive analysis of cDNA ends (MACE), a 3′ RNA sequencing method, as previously described20,70. We recently demonstrated that MACE allows sequencing of FFPE samples with high accuracy71. Briefly, 20 barcoded libraries comprising unique molecule identifiers were sequenced on the NextSeq 500 (Illumina) with 1 × 75 bp. PCR bias was removed using unique molecular identifiers.
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