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The display was located near a recently-dismantled pro-Palestinian encampment on campus.
Several Israeli and American flags were placed on Deering Meadow were defaced just hours after putting it up on Sunday.
Jewish student Samuel Feldman helped with the flag display. Over the weekend, he and about 14 other Northwestern students decided to put up 1,200 flags for roughly each person who died in the Hamas attack on October 7, and marking Israel's Memorial Day.
Feldman said when he returned to see the flags hours later, he saw someone ripping them out.
"I saw somebody wearing a mask, going and uprooting the flags one by one. As I came closer, she ran away," Feldman said.
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RELATED | American, Israeli flags set up near former Northwestern pro-Palestinian encampment vandalized
President Michael Schill released the following statement on Monday night:
"I became aware that several Israeli and American flags placed on Deering Meadow were defaced overnight.
Earlier on Sunday, a woman tore down several signs and banners hanging at the Meadow.
Northwestern's commitment to freedom of expression does not include vandalism. A
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And let me be clear - spraying red paint over Israeli or American flags is vandalism and is unacceptable.
The University will investigate these incidents thoroughly, and if individuals from Northwestern can be identified, we will pursue disciplinary action."
Anyone with information is asked to call university police.
READ ALSO | House committee investigating Northwestern University's response to antisemitism on campus
The House committee hearing in Washington DC at which Schill is expected to speak is scheduled for May 23.