Investigations of the transcriptome of Mus musculus tumour cell lines with and without mitochondrial DNA using Nanopore long reads

To determine the effect of mtDNA deletion on nuclear gene expression in a mouse tumour model, we used MinION long-read cDNA sequencing. Samples were prepared using the ONT cDNA sequencing kit, using rapid PCR barcoding to multiplexed multiple samples on MinION flow cells. Sequenced reads were then demultiplexed, oriented for strand-specific mapping, mapped to the mouse transcriptome, then summarised as transcript counts using a custom protocol. The resulting table of transcript read counts was further processed with DESeq2 in order to produce a list of transcripts that were differentially-expressed between established cell lines with and without mitochondrial DNA, and from tumours formed after injection into a host mouse.