Gene counts of EJ138 and A498

RNA-Seq reads were pre-processed using trimmomatic v0.39 with the following parameters (ILLUMINACLIP:TruSeq3-PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36) to remove contaminating sequences from adaptors and sequences with low base quality54. Reads were then aligned to the reference genome (GRCh38) using STAR v2.7.4. Trimmed reads were quantified onto discovered transcripts from gene models using SALMON with parameters ( -lib IU ) and converted to feature counts. DESeq2 was used to model raw gene counts for gene expression using a negative binomial model and identify differentially expressed genes across experimental groups with a padj of 0.05 and Log2FoldChange>157.