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United manager Louis van Gaal is reported to be facing the sack after a run of six games without victory in all competitions and has described the trip to the Britannia Stadium as "must-win".
Rooney, who has scored only two league goals this season, was the only change Van Gaal made to the team beaten 2-1 at home by Norwich City last weekend, with Spanish midfielder Ander Herrera replacing him.
Asked if the decision to leave out the 30-year-old was tactical, Van Gaal told Sky Sports: "Yes, of course."
He added: "That is always what you want, with your game plan. I think that with this game plan it was better to play with Ander Herrera instead of Wayne Rooney."
In Rooney's absence, French striker Anthony Martial looked likely to lead the line.
United went into the match in fifth place in the English top flight, nine points below leaders Leicester City.