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Jackson first appeared on the Apollo stage with his brothers in 1967. The Jackson 5 won the Amateur Night contest, an event that helped launch their career.
Jackson last appeared at the Apollo in 2002, at the invitation of former President Bill Clinton for a Democratic National Committee fundraiser.
The theater has become an impromptu memorial site in recent days; fans began gathering there within minutes of the reports of Jackson's death last Thursday.
Tuesday's public tribute will begin with a eulogy by the Rev. Al Sharpton, a Jackson family confidant. There will be a moment of silence at 5:26 p.m., the time at which Jackson's death was confirmed.
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The Associated Press contributed to this story.