Figure 2

Intronic read coverage for different RNA fractions. A) RNA-seq coverage for Sample 2 across the gene NRXN1 for the four different RNA fractions, viewed in the UCSC genome browser [24]. Long neuronal genes tend to yield a high coverage in introns in conventional RNA-seq data. The figure shows that fractions except the cytoplasmic RNA show a high coverage across the entire transcript, including the introns. B) Quantitative real-time PCR (qRT-PCR) quantification of intronic and exonic expression levels in cytoplasmic and polyA+ RNA. Primers were designed within an intron and the two surrounding exons for three genes (NRXN1, CELF4 and GRID2) according to the schematic representation at the top (see Additional file 1: Table S2 for primer sequences). In all three cases, ΔCT (Intronic-Exonic) is higher in the cytoplasmic RNA compared to polyA+ RNA, while the opposite for intronic regions.