These protocols describe two methods for the enrichment of polyadenylated RNA molecules from extracted total RNA by: removal of rRNA using the RiboMinus™ Eukaryotic Kit v2, or selectively isolating poly(A) molecules using the DYNAL™ Dynabeads TM mRNA Purification Kit. To demonstrate the performance, RNA was extracted from Saccharomyces cerevisiae cells (S288c) and GM12878 cells using TRIzol based methods: sequencing libraries were prepared from 1000 ng total RNA or 500 ng poly(A)-enriched RNA using the Direct RNA Sequencing Kit and run on MinION.