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In conventional multi-user multiple-input multiple-output (MU-MIMO) systems with frequency division duplexing (FDD), channel acquisition and precoder optimization processes have been designed separately although they are highly coupled. This paper studies an end-to-end design of downlink MU-MIMO systems which include pilot sequences, limited feedback, and precoding. To address this problem, we propose a novel deep learning (DL) framework which jointly optimizes the feedback information generation at users and the precoder design at a base station (BS). Each procedure in the MU-MIMO systems is replaced by intelligently designed multiple deep neural networks (DNN) units. At the BS, a neural network generates pilot sequences and helps the users obtain accurate channel state information. At each user, the channel feedback operation is carried out in a distributed manner by an individual user DNN. Then, another BS DNN collects feedback information from the users and determines the MIMO precoding matrices. A joint training algorithm is proposed to optimize all DNN units in an end-to-end manner. In addition, a training strategy which can avoid retraining for different network sizes for a scalable design is proposed. Numerical results demonstrate the effectiveness of the proposed DL framework compared to classical optimization techniques and other conventional DNN schemes.