Selective (custom) transcript depletion enables the removal of user-defined transcripts from RNA samples prior to cDNA synthesis. The depletion ribosomal RNA (rRNA) and highly abundant mRNAs (e.g., globin from blood samples), improves the sensitivity and economy of RNA-Seq, as fewer sequencing reads are associated with “unwanted” transcripts. This enables the detection of more rare transcripts and subtle fold-changes in gene expression levels between biological or experimental conditions from a given amount of sequencing. Alternatively, it allows for less sequencing to be performed to achieve experimental goals.