Figure 4.

Quantification of the expression levels of the RNAi target Smn in WT and C24 datasets is not affected by detection of reads from the shRNA construct. (A) Normalized read counts of the Smn gene using size factor normalization (see Materials and Methods). Testing for differential expression shows that Smn is not significantly down-regulated in the C24 strain (adjp-value > 0.05). (B) Number of raw sequencing reads aligned along the Smn gene in WT and C24 libraries. Gray box marks the Smn region targeted by the shRNA transcript. No significant difference between the two strains is observed, suggesting that endogenous gene quantification is not biased by the detection of shRNA derived transcripts.