I was recently doing a Co-IP work. And I got some weird result as show in the picture, the target protein was not seen in the whole cell lysate but it was seen in the supernatant after IP. The samples were run on the same gel and with the same amount of total protein. The samples were IP with protein X antibody, and I want to see the pull-down efficiency. By see this result, I don't know how to explain it.
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