RNA extraction, sequencing, and data processing
Total RNA was extracted from FFPE sections (Libraries were prepared from 120 ng of total RNA using the Illumina TruSeq RNA Exome Library preparation kit which allows to perform a strand-specific RNA sequencing. After individual QC, the 16 libraries were equimolarly pooled and subjected to qPCR quantification using the KAPA library quantification kit (Roche). Sequencing was carried out on the NovaSeq 6000 instrument from Illumina based on a 2 × 100 cycle mode (paired-end reads, 100 bases) to obtain around 25 million clusters (50 million raw paired-end reads) per sample. Fastq files were generated from raw sequencing data using bcl2fastq where demultiplexing was performed according to barcodes.RNA-seq data were processed using the Institut Curie RNA-seq pipeline