Abstract: The present disclosure provides compositions, kits and methods for sequencing double-stranded nucleic acids. The compositions, kits and methods comprise partially double-stranded identifier molecules and partially double-stranded adapter molecules. The compositions, kits and methods can be used to determine the abundance and/or identity of specific transcripts in a plurality of double-stranded nucleic acids, as well as identifying the frequency of mutations within certain transcripts in the plurality of double-stranded nucleic acids.