Single-cell RNA-seq has inspired new discoveries and innovation in the field of developmental and cell biology for the past few years and is useful for studying cellular responses at individual cell resolution. But, due to the paucity of starting RNA, the data acquired have dropouts. To address this, we propose a deep matrix factorization-based method, deepMc, to impute missing values in gene expression data. For the deep architecture of our approach, we draw our motivation from great success of deep learning in solving various machine learning problems. In this study, we support our method with positive results on several evaluation metrics such as clustering of cell populations, differential expression analysis, and cell type separability.