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: