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Will Dana, managing editor of Rolling Stone, wrote a note on its campus rape story. Credit Richard Perry/The New York Times

Started nearly a half-century ago as a chronicle of 1960s counterculture, Rolling Stone established its journalistic credibility with provocative coverage of politics and current affairs.

While its cover remains coveted real estate for those looking to assert their pop-culture bona fides, writers like Matt Taibbi and Michael Hastings have influenced public perceptions in recent years on issues like the financial crisis and the war in Afghanistan — in the same way that celebrated predecessors like Richard Ben Cramer and Tom Wolfe had done in previous years. 

The magazine seemed to have struck again last month with a vivid account of a young woman who said she was gang-raped at a University of Virginia fraternity party, a story that helped drive the national debate over the problem of sexual assault on college campuses. 

But late last week Rolling Stone found itself facing a crisis that threatened its reputation as a place for serious, significant journalism. Faced with reporting in The Washington Post that appeared to undermine crucial details of the accuser’s account, and a rebuttal of some aspects from the fraternity, the magazine published a note to readers on Friday saying that it had reservations about the article. It also acknowledged that it had erred in relying solely on the word of the accuser, named only as Jackie, and in agreeing not to try to contact the men she accused. 

“I have serious questions about what happened, and I am at this point not ready to say what happened that night,” the magazine’s managing editor, Will Dana, said in an interview Friday. “There should never be a story in Rolling Stone where I feel that way.”

With that, Rolling Stone found itself listed among a series of media crises in recent weeks, including The New Republic, where there were mass resignations, and First Look Media, the start-up that lost staff members and canceled a planned website after a dispute between journalists and managers.

Rolling Stone was harshly criticized by media critics for its journalistic lapses, and by women’s groups who said it set back the cause of encouraging sexual assault victims to come forward.

Even the magazine’s apology seemed to backfire. The note to readers initially said that Rolling Stone’s trust in Jackie was “misplaced” — which some read as criticizing Jackie and undermining her story. This weekend, as it faced further criticism for that characterization, it quietly changed the note to say that it was “mistaken in honoring Jackie’s request to not contact the alleged assaulters to get their account.” It also said, “These mistakes are on Rolling Stone, not on Jackie.”

In a post on Twitter, Mr. Taibbi said he, like others at the magazine, was “both mortified and sorry — for the public, for anyone affected, and for the source herself.”

Jann Wenner, a founder of Rolling Stone and its publisher, declined repeatedly to be interviewed, or to offer any comment. But in the interview Friday, Mr. Dana said the article stemmed from a feeling he and other senior editors had over summer that the issue of unpunished campus rapes would make a compelling and important story. 

They decided to assign Sabrina Rubin Erdely, a contributing editor who has also written for GQ and The New Yorker, and who has been nominated for two National Magazine awards, according to her website. Ms. Erdely did not return calls and messages seeking comment. But she has said publicly that she sought out the right story, on the right campus, and that she found what she was looking for in Jackie. 

The accuser appeared to be distressed, perhaps as a result of her trauma, according to a person familiar with the newsroom’s process, who spoke on the condition of anonymity in order to describe sensitive events. She had repeatedly asked Ms. Erdely that those she accused of raping her not be contacted. When the magazine brought up the issue again later, she threatened to withdraw from the story. 

That concern, combined with a feeling that it should err on the side of sensitivity, persuaded the magazine to accept her wishes. “Sabrina had talked to quite a few other women who had said, ‘If you talk to me, you can’t go talk to my attacker,’ ” Mr. Dana said, and so it seemed like a reasonable request. 

“These are hard stories to do,” said Bruce Shapiro, executive director of Columbia University’s Dart Center for Journalism and Trauma, which focuses on the issues of reporting on violence and conflict. An engaged and empathetic reporter, he said, will naturally be concerned about potentially inflicting new trauma on the victim of a harrowing incident. “I do think that when the emotional valence of a story is this high, you really have to verify it.”

Experienced reporters on the topic, he said, often only work with women who feel strong enough to deal with the due diligence required to bring the article to publication. 

The details of a heartbreaking conversation recounted in the story, in which Jackie tells her friends of her rape and is told that she should stay quiet, also came only from Jackie, Mr. Dana said. One of the friends declined to comment, and Ms. Erdely could not reach the others. 

The magazine faces some potential legal liability, said Eugene Volokh, a University of California, Los Angeles, law professor who also writes for The Washington Post. “Based on the facts as I have read about them in the media,” he said, “I would not have approved the publication of a story that names a fraternity, when there hadn’t been a call to the alleged rapists.”

Ms. Erdely delivered a manuscript in September. When he first read it, Mr. Dana said, “I thought, ‘Are you sure?’ ” But he, other editors and fact-checkers felt that Jackie was credible, and the magazine’s lawyers had no problems with it, so the magazine ran it. After publication, Jackie seemed pleased, too, Mr. Dana said.  

But others wrote that they had problems with the article, and with the magazine’s decision not to seek out the men accused. Mr. Dana said that, despite the barrage of criticism, Rolling Stone had not suspected that anything might be significantly wrong until late last week. The magazine said on Sunday that it had not identified specific problems in the article beyond the questions that had already been made public, but said it is investigating further. 

It is not clear what consequences Ms. Erdely and the article’s editor will face, if any, Mr. Dana said, and he has not made any specific decisions.

Mr. Shapiro, of the Dart Center, said the issue of corroboration in accounts of rape and other trauma is a common one. He says that more reporters should be trained in interviewing traumatized people, to protect both themselves and their sources. 

“It would be really unfortunate if the controversy around the sourcing of this story were to distract from the core and critical issue of sexual assault on college campuses,” he said, an issue with which Mr. Dana said he agreed. 

Mr. Dana said the magazine planned to do further reporting on the story, as it tries to determine the truth of what happened at the University of Virginia and rebuild its own journalistic reputation.

“Right now,” he said, “we’re picking up the pieces.”