One of our customers, Dr. Dominik Handler at the Institute of Molecular Biotechnology GmbH, Austria, examined the use of the Ribo-Zero (H/M/R) Kit with Drosophila RNA. He compared the amount of rRNA depletion with the Ribo-Zero kit and a competitive kit by qPCR after one and two rounds of rRNA removal.
qPCR analysis of rRNA depletion (click to enlarge figure). Total RNA samples were treated with one or two rounds of the Ribo-Zero kit (RZ) or a competitive kit (R-), and fold depletion calculated using qPCR with primers to multiple regions of the indicated rRNAs, after normalization to rp49 mRNA. Nitric oxide synthase (nos) mRNA was used as an internal control.
In Drosophila, as in many diptera, the 28S rRNA is processed into two parts (a “left” and “right” arm). After two rounds of rRNA removal, Dr. Handler observed depletion of the left arm by 31,000X and the right arm by 600X. Overall, the Ribo-Zero kit performed substantially better than the competitive kit.