Jacob Beacher, a 24-year-old man from New Brunswick, N.J., has been charged with vandalizing the building on April 10.
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Beacher has no affiliation with Rutgers University, police said.
The investigation is still ongoing and additional charges are pending.
Crews spent days cleaning up the damage.
The Center for Islamic Life is described as a home away from home for some 6,000 Muslim students on the campus of Rutgers University.
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"It's so disheartening and scary because it just solidifies the fact that we aren't safe here," said student Nehad Ali.
Center for Islamic Life chaplain Kaiser Aslam took video of the damage, which was extensive, and it happened on Eid al-Fitr, which wraps up the month of Ramadan.
There was artwork that contained Muslim prayers that was destroyed. Also, a Palestinian flag that was in the center was ripped down.