Hi!
Im studying adipose and skeletal muscle tissue atm. As a quick sanity check of Cuffdiff results on isoforms detection and quantification, I want to look at well described isoforms.
What I mean is to look at i.e. two isoforms that occur in a fixed ratio within the tissue. And then to see if the RNAseq results also quantifies the same ratio.
Does anyone know of such examples for skeletal muscle/adipose tissue, or have other sanity check methods (both dry- and wet-lab based).
Thank you!
I also asked a similar question here:
http://seqanswers.com/forums/showthread.php?p=150370#post150370
Hello Sindre,
I'm not sure if I can answer your question directly, but these papers may provide some useful information (or point you in the right direction). There are several “references genes” (i.e. housekeeping genes) in skeletal muscle that are (supposedly) universally expressed. Perhaps you could take the ratio between two of them?
http://www.ncbi.nlm.nih.gov/pubmed/20045408
http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0001854
http://www.biomedcentral.com/1471-2199/9/79
http://ajpregu.physiology.org/content/294/1/R192
I hope this helps,
James
Hi!
Thank you. The last link is very interesting, they refer to a previously study on three COX1 variants in skeletal muscle.
Sindre,
I hope the articles help! For questions regarding the COX isoforms in skeletal muscle, the lead author of that article (Dr. Todd Trappe) would be the person to talk to:
http://cms.bsu.edu/academics/centersandinstitutes/hpl/people/facultydirectory/faculty/trappetodd
Take care,
James
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