RNAseq question: tissue-specific gene transcripts showing up in unexpected tissues??
Hello! I hope it's okay to post this here. I'm a PhD student working on some DEseq time-course comparisons with milkfat and blubber/adipose samples (I work with seals). A few of my blubber samples are showing really high counts of a small handful of milk-specific genes like caseins and beta-lactoglobulin-2. I don't think it's a sample mix-up or cross-contamination because wouldn't a lot more super highly expressed milk-specific transcripts 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 caseins 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?