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An RNA-Seq Strategy to Detect the Complete Coding and Non-Coding Transcriptome Including Full-Length Imprinted Macro ncRNAs

Figure 3

Ribo-depleted RNA-Seq reliably detects expression of known protein-coding and non-coding genes.

(A) Saturation curves showing the percentage of RefSeq protein-coding genes (left) or RefSeq ncRNAs (right) with an RPKM+/−5% of the final RPKM for the combined CCE RiboMinus dataset (calculated at the maximum tag number) at different sequencing depths crated by randomly picking the indicated number of tags (M: million). The lines show three groups of genes with similar RPKM expression levels. Error bars indicate the minimum and maximum of ten random tag sets. If the curves reach a plateau before the final number of tags, this indicates that this gene group was sequenced exhaustively, as obtaining more tags does not change their RPKM. The large error bars originate from small gene numbers in the categories, where a small number of changed genes results in a large relative change. (B) As in A for the FH Ribo-Zero dataset.

Figure 3