A prayer room used by Muslim students at New York University was struck by vandals who etched and drew graffiti on the walls and soaked Islamic prayer mats with urine, according to N.Y.U. officials and members of the university’s Muslim community.

The soiled mats and other vandalism were discovered Thursday afternoon in a worship space inside Bobst Library, the university’s towering red building across from Washington Square Park in Greenwich Village.

An image of male genitalia was drawn onto the wall of the room, along with the letters “AEPI,” the nickname of Alpha Epsilon Pi, a nationwide Jewish fraternity that was suspended from N.Y.U. in 2015 for hazing, according to a university directory of suspended fraternities and sororities.

N.Y.U. said it had reported the vandalism to the police and would conduct its own investigation to find and punish the vandals. The university said those found to be responsible would be “subject to the most serious sanctions available through our disciplinary process.”

“This desecration of a religious space is vile, reprehensible and utterly unacceptable,” the university said in a statement on Thursday. “It contravenes every principle of our community, and we condemn it.”

Jonathan Pierce, a spokesman for Alpha Epsilon Pi’s national organization, said it “strongly condemns” the vandalism and would “fully cooperate with the administration’s investigation.”

“We are not aware that any of our members were involved in this disrespectful action,” he said. “Hopefully, the investigation will find the perpetrator and, when they are found, we hope they are punished appropriately by the university.”

The vandalism came amid rising concerns about Islamophobia and antisemitism on college campuses, including N.Y.U.’s, since the start of the war in Gaza in October 2023. The campus conflicts have led to the departures of several university presidents and have driven policy changes since President Trump took office again in January.

The Trump administration has detained international students — many of them Muslim — whom it has vowed to deport because of their involvement in campus protests against the war or their criticism of the Israeli government.

The administration has also revoked federal funding from universities, including Columbia and the University of Pennsylvania, that it accuses of doing too little to crack down on antisemitism or the participation of transgender women in college sports.

Faiyaz Jaffer, a Muslim chaplain at N.Y.U., said a student discovered the vandalism on Thursday afternoon and rushed to his office to tell him what she had seen. He then notified campus security and university administrators, he said.

“She was in a state of shock, naturally, and I think I was as well,” Dr. Jaffer said, referring to the student. “And then I realized we are kind of used to this. We hear about things like this all the time, but they often go unreported because of a gap between law enforcement and Muslims since 9/11 or because of a distrust people feel toward the authorities.”

Dr. Jaffer called campus security. Word of the vandalism quickly spread among students on social media and WhatsApp.

Safiatu Diagana, 25, a nursing and public health student from Queens, said the incident had left many students feeling hurt and confused. She said she was happy to hear the university say it planned to investigate the vandalism but wanted to see results.

“A lot of us were wondering why — why did this have to happen?” Ms. Diagana said. “We deserve to feel safe on campus, and it is very hurtful and scary that an incident like this can happen here.”

A police spokesman said the vandalism appeared to involve graffiti etched into a wall and written on it in chalk. The spokesman said the department’s Hate Crimes Task Force had been notified and an investigation was underway.

Afaf Nasher, the chairwoman of the New York chapter of the Council on American-Islamic Relations, said the group wanted state and federal law enforcement authorities to open a hate crime investigation into the matter.

“This vile act of desecration is a direct assault on the Muslim community at N.Y.U. and beyond,” she said. “For any student to walk into their prayer space — a sacred space — only to find it defiled, is deeply disturbing.”

The university’s Islamic Center, which provides services and support for Muslim students, said the vandalism was especially disturbing coming so close to Ramadan, which ended last weekend. Center officials said in a statement that the episode was part of a larger tide of anti-Muslim sentiment in the United States.

“This incident is not isolated,” the statement said. “Many in our Muslim community have endured increasing Islamophobia and anti-Muslim rhetoric in recent years. What happened in our prayer space reflects the broader discrimination and challenges Muslims face nationwide.”

The Trump administration intends to block $510 million in federal contracts and grants for Brown University, expanding its campaign to hold universities accountable for what it says is relentless antisemitism on campus, according to two White House officials familiar with the plans.

Brown became the fifth university known to face a potentially dire loss of federal funding, leaving other universities that the administration has targeted wondering when their turn might come.

If the administration pauses $510 million, even over a period of years, the consequences for Brown could be significant. In its 2024 fiscal year, Brown received about $184 million through federal grants and contracts.

In an email to campus leaders on Thursday, Brown’s provost, Frank Doyle, said the university was aware of “troubling rumors emerging about federal action on Brown research grants.” But he said that the university had “no information to substantiate any of these rumors.”

The Daily Caller was the first to report the pause.

The newly appointed secretary of education, Linda McMahon, has been explicit about the administration’s focus on elite universities, which Mr. Trump has criticized as bastions of left-wing thought. She has said that taxpayer support is a “privilege” that can be withdrawn if universities do not adhere to civil rights law.

Like many of its Ivy League peers, Brown was the site of clashes over the war in Gaza. But it was also one of a small number of universities that made deals with students to end their protest encampments in the spring, agreements that came under criticism for being too soft on students.

Brown became one of only a handful of universities to agree to a board vote on divesting from Israel. The Brown Corporation, the school’s governing board, ultimately voted against divestment, saying it held no direct investments in companies protesters had named as having ties to Israel.

After the Trump administration threatened to pull hundreds of millions of dollars in research grants and contracts from Columbia University and the University of Pennsylvania last month, Brown was one of the few universities that released a statement in response, saying that it would not compromise on academic freedom.

In the statement, Christina H. Paxson, the president of Brown, said that some of Mr. Trump’s demands “raise new and previously unthinkable questions about the future of academic freedom and self-governance.” She said that if Brown’s essential academic and operational functions were threatened, the university “would be compelled to vigorously exercise our legal rights to defend these freedoms.”

Recently, Brown has also been considering whether to adopt a new policy that would limit statements issued by the university on political and social issues that are “unrelated to its mission.” It would join a number of other schools that have moved to adopt “neutrality” policies as they face pressure over their response to pro-Palestinian demonstrations.

Before the Trump administration targeted Princeton University for cuts on Tuesday, its president, Christopher L. Eisgruber, had also been vocal about the federal attack on colleges. He called the targeting of Columbia “the greatest threat to American universities since the Red Scare of the 1950s.”

The government’s campaign against specific universities began in February, when a new federal task force against antisemitism issued a list of 10 universities that it planned to investigate. The administration cited claims that the schools may have failed to protect Jewish students and faculty members from discrimination during pro-Palestinian protests on campuses in 2023 and 2024.

The Education Department’s Office for Civil Rights then expanded the list to 60 colleges, including both private and public universities.

Columbia became the first university affected when the government canceled $400 million in federal funding on March 7. Officials at the school, which had some of the most disruptive protests, were left scrambling to find a way to restore it. In the following weeks, the Trump administration announced actions against three more universities. That included a pause of $175 million in funding to the University of Pennsylvania; a review of roughly $9 billion in federal grants and contracts to Harvard and its affiliates, including its teaching hospitals; and the suspension of dozens of grants to Princeton.

Universities have said the loss of funding would compromise the United States’ leadership in scientific, medical and technological research.

Almost all the employees of the Wilson Center, a prominent nonpartisan foreign policy think tank in Washington, were placed on leave on Thursday and blocked from their work email accounts as Elon Musk’s task force quickly shut down most of the center.

About 130 employees received orders telling them not to return to the office after the end of the day, according to an email reviewed by The New York Times and people with direct knowledge of the actions.

The Wilson Center employees are to be paid while on leave but will be fired soon, in line with what has happened at other institutions that Mr. Musk’s workers have dismantled in recent weeks.

Only five employees will remain — a president, two federal employees and two researchers on fellowships. Those positions are mandated in the center’s congressional charter. The cuts align with an executive order President Trump signed in March.

Private donations to the center will be returned to the donors, according to a person familiar with the center who spoke on the condition of anonymity to avoid retribution. It was not clear what would be done with the center’s endowment.

On Thursday afternoon, dozens of employees carried boxes and bags filled with papers, plants and posters out of the center’s offices in the Ronald Reagan Building, which houses several government agency offices.

Tears glistened on the face of one woman as she departed. Workers wheeled out carts full of documents.

It was not clear on Thursday how the offices will be used, but the center’s charter requires the space to be part of the Woodrow Wilson Memorial.

On Monday, four members of the Musk team entered the center’s offices and began taking over its systems. The next day, the center’s president, Mark Green, resigned.

The Trump White House fired the center’s board members in recent weeks, one person briefed on the events said. Mr. Green, a former Republican congressman and ambassador, was told this week he would be fired if he did not resign, another person said. The White House declined to comment.

Mr. Musk’s government-overhauling workers have gutted several other institutions in Washington, including the United States Agency for International Development.

They have shut down centers that receive federal funding but that have done independent research for decades with the goal of giving nonideological expert assessments to policymakers, lawmakers and people outside government.

The Wilson Center, created in 1968 as a working memorial to honor the 28th president, Woodrow Wilson, receives about 30 percent of its funding from Congress; the rest comes from private donations.

The center has been run by former Democratic and Republican officials appointed by the board. Before Mr. Green, who led U.S.A.I.D. in the first Trump administration, became president and chief executive of the center in 2021, Jane Harman, a former Democratic congresswoman from California, ran the think tank.

The center has been a gathering place for scholars in all areas of foreign policy over the decades. It houses the personal library of George F. Kennan, the diplomat and policymaker who studied the Soviet Union. On Thursday, the director of the Wilson Center’s Kennan Institute, Michael Kimmage, posted photos of the library online and compared it to the library of ancient Alexandria, which “fell victim to political vicissitudes and war,” he wrote.

One question is what will happen to those materials and extensive digital archives that the Wilson Center has compiled. Researchers from around the world have used the archives for projects, and scholars especially value the center’s records of documents from the Cold War era.

A person familiar with the center said that it also housed historical records from Wilson’s campaign and presidency.

The center’s more than 50 fellows were expected to be paid until the end of their program, but those who are foreign citizens expect to have their visas canceled. Two of the fellows are at the center through a program for scholars whose work endangers them in their home countries, according to a person familiar with the center.

Each class of fellows is usually made up of academic researchers and one or more journalists working on book projects. Reporters from The New York Times have received fellowships.

A Trump administration official said that Natasha Jacome, a senior adviser to Mr. Green, was the center’s new president.