Going back to portal and portal 2 I can see many similarities between the Aperture lab and the Combine citadel that are even mentioned in the wiki.
The hard light bridge in portal and the Combine field bridge
The Combine force fields and the early Aperture emancipation grill (even the way that materials disintegrate is similar)
The Combine energy ball and the Aperture energy pellet
The railways through both facilities
There are too many similar technologies for it to be just a coincidence, any ideas on what might be or might have been going on? I think its very likely that the combine might have been in some sort of partnership with aperture long before the resonance cascade and the combine might have even been expecting something from aperture with regard to the Borealis. What do you think?