It happened Sunday night at the Steinway Street station in Astoria.
Two trains, a Manhattan-bound R train and a Forest Hills-bound R train, hit the CitiBike or parts of bicycle.
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The operators of both trains triggered their emergency brake.
"This was an attack on all of New York City that took place in the transit system," MTA spokesperson Tim Minton said. "The miscreants who threw that bike in the path of an oncoming train should be prosecuted for their reckless disregard for safety of subway riders and workers."
The NYPD said the incident is under investigation.
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