I have been asked to identify genes that are specific to the suprachiasmatic nucleus (SCN) in mice. The RNA-seq datasets I have access to are from many different tissues. One of the data sets is from SCN tissue itself. Another of the data sets is from the brain. Which part of the brain you may ask? Recent papers on identifying tissue specific genes identify brain as a single tissue (here, here, here, and here). It is important to include brain as it has been identified as a tissue that has a large proportion of tissue specific genes.
The ideal experiment would be to compare genes found in SCN tissue to genes found in many other tissues including brain tissue that has had the SCN excised. But in the time frame I have it isnt possible to get data from the brains of mice that have had the SCN removed.
Because the SCN is part of the brain..... any genes found in SCN will be found in brain tissue. So how do I identify SCN specific genes?
The only idea Ive had to do this properly is to compare SCN tissue read counts with brain tissue read counts. If gene 1 produces X amount of reads in SCN tissue, and the same amount in brain tissue, then the SCN tissue accounts for all of the reads in brain tissue. Therefore it is SCN specific. The big catch though is that tissue specific genes tend produce a low number of reads. So I will be comparing very small numbers...that may not be statistically reliable (Im not a stat head but Im aware statistics tend to be important!)
Thanks in advance for the help.