RNA-seq of CA010 cells
RNA was extracted from samples using the MagMax Pathogen DNA/RNA kit (Thermo) using 300 l as the sample input volume. Extracts were treated with Turbo DNase (Thermo). Libraries were prepared using the NEBNext Ultra II Directional RNA Library Prep kit for Illumina (New England Biolabs) following the FFPE/degraded RNA protocols. Ribodepletion was performed using the NEBNext rRNA Depletion kit (New England Biolabs). Libraries were quantified prior to sequencing, and had a mean yield of 183 ng/l. Libraries were sequenced using a NextSeq 550 2 x 75 bp kit (Illumina).