Which reverse transcriptase should be used to read through alkylated S4U nucleotides?

We recommend using Lexogen's QuantSeq 3' mRNA-Seq V2 (Cat. No. 191 - 196), for preparing RNA-Seq libraries from total RNA generated from SLAMseq experiments. The QuantSeq reverse transcriptase was shown to work ideally for RNA-Seq library generation by Herzog et al., "Thiol-linked alkylation of RNA to assess expression dynamics" in Nature Methods, DOI: 10.1038/nmeth.4435. Other reverse transcriptase enzymes were also evaluated in this publication.