Macro ncRNAs are more efficiently detected in RiboMinus and Ribo-Zero RNA-Seq.

Different ncRNAs annotated in the RefSeq database (http://genome.ucsc.edu/, mm9, RefSeq identifier given in brackets) are shown with their respective RPKM values in two polyA and one RiboMinus RNA-Seq dataset from adult brain (Mortazavi et al., Cui et al., details see text) and the Ribo-Zero as well as the RiboMinus FH datasets presented here. Note that the ncRNAs with unknown function (asterisks) show a reliable RPKM level (>3) in the Cui et al. polyA RNA-Seq datasets and in all the ribosomal RNA depleted datasets. The functional Airn and Kcnq1ot1 macro ncRNAs (bold) that are expressed in mouse brain are only detected in the FH datasets (RPKM>3, details see text).