I want to do paired-end (PE) sequencing, which kit version should I use? Can I use paired-end sequencing for QuantSeq REV libraries?

Yes, you can perform For paired-end Capital P and E?(PE) sequencing use using QuantSeq REV (Cat. No. 016). Please note QuantSeq REV requires a Custom Sequencing Primer (CSP) for Read 1 in order to generate reads that begin at the exact 3' end of the transcript.
We do not recommend paired-end PE sequencing for QuantSeq FWD (Cat. No. 015), as the quality of Read 2 would be very low due to the poly(T) stretch at the beginning of Read 2.