Recently, graph embedding emerges as an effective approach for graph analysis tasks such as node classification and link prediction. The goal of network embedding is to find low dimensional representation of graph nodes that preserves the graph structure. Since there might be signals on nodes as features, recent methods like Graph Convolutional Networks (GCNs) try to consider node signals besides the node relations. On the other hand, multi-layered graph analysis has been received much attention. However, the recent methods for node embedding have not been explored in these networks. In this paper, we study the problem of node embedding in multi-layered graphs and propose a deep method that embeds nodes using both relations (connections within and between layers of the graph) and nodes signals. We evaluate our method on node classification tasks. Experimental results demonstrate the superiority of the proposed method to other multi-layered and single-layered competitors and also proves the effect of using cross-layer edges.