I am working with an organism that has been engineered with a transgene to perform RNA-interference. I have whole-transcriptome RNASeq data for this organism. Now:

• I expect RNA reads coming from the transgene in my sample
• I also expect RNA reads from the downregulated transcript, but less than the wild type

The sequencing is illumina sequencing, 125 nt read length, 2 replicates. In both replicates I find both conditions verified.

I am asking:

• Do you agree with these two statements?
• Do you have good literature to cite in support / aganist this?

I am writing a manuscript and need to pile up as much evidence as possible. So far I wasn't able to find a good reference to say that the sequencing can uptake transgenic molecules, and that targeted molecules are still present even if targeted and can occasionally be sequenced.

EDIT: found it! for future readers, this paper is a good literature reference:

http://www.annualreviews.org/doi/full/10.1146/annurev-biophys-083012-130404