RNAseq question: tissue-specific gene transcripts showing up in unexpected tissues??
Hello! I'm a PhD student working on some DEseq time-course comparisons with milkfat and blubber/adipose samples (I work with seals). A couple of my blubber samples are showing really high counts of a small handful of milk-specific genes like CSN-related transcripts and beta-lactoglobulin-2. I don't think it's a simple explanation like sample mix-up or cross-contamination, because wouldn't a lot more milk-linked transcripts (like LALBA for example) show up? Also, besides the couple of milk genes, the rest of the expression patterns otherwise align with my expectations pretty well. I can't find anything in the literature to suggest that these genes could be expressed like this in adipose tissue. I'm super puzzled and don't know whether to filter out these transcripts or not. Has anyone dealt with this problem before? Maybe the homology filter we used on the gtf file for the DEseqs gave me spurious annotations...?