Can small miRNA-containing RNA fractions be separated from large RNAs using the miRNeasy FFPE Kit?
FAQ ID -1737

Unlike the Appendix A Protocol for the miRNeasy Mini Kit, which allows removal of larger RNAs such as mRNA and rRNA to enrich miRNA in a separate small RNA fraction, this is not practical using the miRNeasy FFPE Kit. RNA from FFPE- or other compromised materials is usually strongly fragmented already. Significant amounts of rRNA and mRNA fragments would end up in the small RNA-enriched fraction.