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

Figure 6

The template preparation protocol determines the comparability of ribo-depleted RNA-Seq to polyA RNA-Seq.

The cDNA size distribution of genes showing more than 8× expression difference (Figure S2), in the comparison of (A) FH RiboMinus - FH-RiboZero (left) and CCE RiboMinus - CCE Ribo-Zero (right). (B) as in A for the comparisons of CCE RiboMinus-Cloonan et al. EB (left), FH RiboMinus-Cui et al. adult mouse brain polyA (middle) and FH RiboMinus-Mortazavi et al. adult mouse brain polyA (right). (C) as in A for the comparisons of CCE Ribo-Zero-Cloonan et al. EB (left), FH Ribo-Zero-Cui et al. adult mouse brain polyA (middle) and FH Ribo-Zero-Mortazavi et al. adult mouse brain polyA (right). For Cloonan et al. EB both the gene expression data from the published alignment (shown in B, C, see Materials and methods) and from an alignment done with the pipeline used here (data not shown) were used and produced the same highly significant differences. Two different size classes are shown with different bin sizes (0–2 kb, 100 bp bins and >2 kb, 500 bp bins). Genes bigger than 11.5 kb are grouped in the last bin (arrow).

Figure 6

doi: https://doi.org/10.1371/journal.pone.0027288.g006