The agencies on Tuesday told passengers they should turn them off before entering a station or boarding a vehicle because of concerns the device's battery can burst into flames.
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Samsung has told owners to power them down and return them.
Both the MTA and NJ Transit have not had any reported cases of the Note 7 catching fire.
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Back in February, New Jersey Transit restricted customers and employees from using, charging, storing or transporting hoverboards following similar fire safety concerns.
(Some information from the Associated Press)