Putative pseudouridine residues in SINV RNA derived from Drosophila cells

In this study, we infected JW18-TET cells with Sindbis virus (MOI=10) to identify putative pseudouridine residues in intracellular viral RNA collected five days post-infection. We used Psi-seq, a sequencing technique which uses a chemical called CMC to selectively modify pseudouridine in RNA, followed by a base treatment. Each sample was either treated with CMC or mock-treated (no CMC) and included an internal control molecule containing a single pseudouridine to ensure proper CMC treatment. This modification causes reverse transcription to terminate one base downstream of pseudouridine sites during Illumina library preparation, enabling the identification of putative pseudouridine residues by comparing CMC+ to CMC- libraries.