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Let's say that I have a population of Mus musculus in the lab. I divide it in a control group and a test group. The test group is constantly subjected to a stress (example: elevated UV radiation). Both groups are allowed to reproduce for 20 generations. I want to fully characterize and compare what changed in each offspring (control vs test group) by using omics. The objective is then to integrate all these information in a new database with the pathways that change and by what magnitude.

  1. Should I use genomics or/and exomics or/and epigenomics?
  2. If I do one of the above and proteomics, why could I need the transcriptomics for?
  3. Would the metabolomics, which are mainly punctual measures, add any valuable information?

This is a purely didatic exercise.

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Should I use genomics or/and exomics or/and epigenomics?

Depends on what you want to look at. Whole genome sequencing will give you all the mutations. If you are interested only in the coding part of the genome then you can go for exome sequencing. Though, exome sequencing will save your time and resources considerably, you may lose out a lot of relevant information from the non-coding and regulatory part of the genome.

Epigenomics is a very broad term. There are several aspects to it. You can go for the DNA methylome, Nucleosome positioning, or ChIP-Seq for Histone modification/variants.

I would suggest that if you can afford it then go for whole genome sequencing. Next choice would be exome sequencing. Once you have these data it might be relevant to add the third layer of DNA methylome.

If I do one of the above and proteomics, why could I need the transcriptomics for?

  1. Transcriptomics is easier and better standardized than proteomics. There are also many good analysis tools.
  2. There are several ncRNA, which has been shown to play important role in cellular homeostasis and gene regulation. You will miss out those.
  3. You will save money. The reagents used for the transcriptomics experiments are the same as the ones used for the genomics experiments. Proteomics is a different domain altogether. You might need to look for collaborators.

Would the metabolomics, which are mainly punctual measures, add any valuable information?

Sure, they do add information. Whether of great value or not depends on the study that you are carrying out. For e.g if you are studying the role of stress in diabetes then doing a metabolomics study may be of great value.

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  • $\begingroup$ Small note.. Do exome if you don't have money/resources for WGS.. else do WGS. $\endgroup$ – WYSIWYG Mar 15 '14 at 13:35

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