I am currently analyzing the protein-coding transcriptome of a tissue from my organism of interest (non-model organism). I want to see whether I can also study the transcriptomes of this tissue in other species (mouse, fruitfly, zebrafish, etc) using publicly deposited RNA-seq data in NCBI SRA. So far, what I have done is finding the "control" libraries of published experiments and analyzing them to get an idea of what genes are expressed in this particular tissue in this particular species. I wonder if this can give me insights into functional specializations of this tissue in different tissues.
However, there are some caveats to this that I can currently think of about doing this that could significantly confound the "differences" I am seeing, like 1) different sequencing depth, 2) differences in library preparation, 3) disparate quality (one library I see is ~40% rRNA).
I do see some posts about similar problems, but I think that what I am comparing is on a more general scale? However, I can totally see that these data sets just not comparable at all. Anyways, I would very much like to hear everyone's thoughts about it. No one else in my lab does this sort of thing, so I have a hard time getting my questions answered.
Thank you all so much for your help and insights!