Epigenetically-controlled tumor antigens derived from splice junctions between exons and transposable elements [RNA-seq]

To study the expression of junctions between exons and transposable elements (TEs), we generated paired-end RNAseq from various mouse tumor cell lines, with several biological replicates (cultures from different days). To analyse regulation of JET expression, we generated Setdb1-deficient B16F10 and B16OVA cells, using lentivirus-based CRISPR/Cas9. Ctrl and KO cells lines were used to generate paired-end RNAseq, with several biological replicates (cultures on different days). We generated paired-end RNAseq from healthy female mouse tissues, to compare JET expression in healthy and tumor cells. We performed gene, TE and JET expression analyses on these datasets.