What method can I use to remove ribosomal RNA?

The most common method to remove RNA is poly-A selection. This technique relies on the utilization of oligo (dT) primers attached to a solid support like magnetic beads to isolate protein-coding polyadenylated RNA transcripts. Poly-A-selection relies on transcripts being intact and may over-represent 3’ regions of transcripts. PolyA selection does not work efficiently for degraded RNA samples. Ribosomal RNA can also be removed by hybridization to complementary biotinylated oligo probes, followed by extraction with streptavidin-coated magnetic beads. This form of removal is known as physical rRNA removal. rRNA removal enables detection of small RNAs and non-polyadenylated transcripts. Additionally, this method is more efficient for degraded and FFPE samples. A third method is targeted amplification, in which hexamer primers with a decreased affinity for rRNA during the first strand of cDNA synthesis are used. This method has a bias of detecting 3’ regions, and works with low inputs and degraded samples.