The workflow for using Nanopore direct RNA sequencing and proteomics to study human cell and virus interactions.
The A459 cell line was cultivated and divided into two groups; one group was treated with Sindbis virus. The cell cultures were collected to extract RNA for Nanopore direct RNA sequencing, as well as IVT data. Protein was also extracted for proteomics. Each culture included three biological replicates.
- Nanopore data: Transcripts annotation & abundance, m6A modification, PolyA length, and alternative splicing (Number and type of isoform).
- Proteomics data: Protein annotation & abundance, PTM: Oxidation, Acetyl, Methyl, Phospho, Phospho Uridine, Phosphoadenosine.
