1-Look at the gut microbiome...

Perturbations in immune genes usually result in changes in the intestinal microbiome consortium...Several companies do microbiome profiling and all you need to do is to collect feces from mice and freeze at -800C,...Or you can try to run the sequencing yourself if you have a reliable core facility.

It can be a very rewarding analysis!!!

2- Collect serum or plasma for metabolomic analysis....You can define a metabolic profile associated with the perturbation of your gene of interest

3-Read about the gene or its homologs or paralogs...Every gene leads its own life(s)...Its stories have contexts...There is no one-analysis-fits-all strategy...Therefore, if a gene has an impact on immune-cell survival, then you delve into death pathways...If a gene has an impact in epigenetic reprogramming, you can do epigenetic profiling (e.g. ChiPSeq, ATAC-seq)...So on...

One way to find out the best assays is where this gene is most expressed...Is it restricted to lymphocytes? Or Myeloid cells? Is it broadly expressed?

For example, one lncRNA called Morbidd regulates survival of eosinophils, and other myeloid cells [but not lymphocytes]...In this case, it made sense to look at survival in response to cytokines and interactions with apoptotic effectors.

Kotzin, J. J., Spencer, S. P., McCright, S. J., Kumar, D. B. U., Collet, M. A., Mowel, W. K., … Henao-Mejia, J. (2016). The long non-coding RNA Morrbid regulates Bim and short-lived myeloid cell lifespan. Nature, 537(7619), 239–243.doi:10.1038/nature19346 

This can narrow down your analysis and prioritize your experiments...

Best of luck!!!

Dear It depends on the issues you are looking at. That will guide you.

Check out my articles, as well as my links to articles by immunologists and immunotoxicologists.

https://www.researchgate.net/profile/PF_Zabrodskii/research