Setting the experimental design in a germline translatome analysis

Question

[Assa Yeroslaviz]

I have a general question about an experiment we're planning. We would like to analyze how well various germline mRNA are being translated. For that we're planning to extract germline ribosome via Immunoprecipitation specifically for germline ribosomes.

For that i have two question. The first one is about the Input samples I should use. As I'm only interested in germline translational activity, I was wondering if it make sense to dissect the germlines for the input samples. The reason for that is that by dissecting them, I would make the input and the IPed samples more comparable (I think).

The second question is whether or not a depletion of the extract is needed in the purified ribosomal samples?

thanks