Remove the prepositional phrase of very high cell densities in the embryoid body outgrowths from the sentence and what is the subject? That word is still the subject with the prepositional phrase in the sentence.
In addition, which word (presence or densities) shows subject-verb agreement? Makes is used for third person singular nouns.
Ditto AlanCarmack. In general, when searching for a subject or verb, it is ofteen helpful to drop out qualifying words and phrases. Drop any adjectives or adverbs, and then any phrase that starts with a preposition, like "of ...", "to ...", "for ..." etc. What's left should be the "heart" of the sentence.