I am having exactly the same situation as you did 2 years ago. We have a knockout mouse, and I am seeing differences in the expression of a protein that is located in a different cromossome than the knockout gene. And this difference is also present in cells that do not express the gene that was knockout...
It would be great to know how your story turned out. Maybe it would help to give me some direction to what to do next...
Thanks a lot!
Gene not expressed in wild-type and knockout yet differences in microarray
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