NEW YORK (CBSNewYork) – Subway service resumed Friday for parts of the New York City Subway system knocked out by superstorm Sandy.

R trains are now running again between the Jay Street-Metrotech station in Brooklyn and Whitehall Street in Manhattan.

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The R line Montague Tube under the East River was badly damaged by the storm.

Until now, R service had been restored in Manhattan only.

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With the tunnel out of service for the past several weeks, the 65,000 commuters who use this line had to find alternative ways to get to their destination, the MTA said.

Flooding extended for a span of more than 4,000 feet, requiring the pumping of 27 million gallons of water and the removal of tons of debris that had washed into the tunnels.

Significant damage was sustained to the power feeds and controls to one pump room, and two fan plants were lost when components and controls for these pumps and fans were extensively damaged.

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The electrical and signal system had to be rebuilt virtually from scratch, including wiring, relays, track circuits, lighting stop motors and other equipment associated with the safe movement of subway trains.