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The underlying mechanisms of macrophage polarization have been detected by genome-wide transcriptome analysis in a variety of mammals. However, the transcriptome profile of rat genes in bone marrow-derived macrophages (BMM) at different activation statuses has not been reported. Therefore, we performed RNA-Sequencing to identify gene expression signatures of rat BMM polarized in vitro with different stimuli. The differentially expressed genes (DEGs) among unactivated (M0), classically activated pro-inflammatory (M1), and alternatively activated anti-inflammatory macrophages (M2) were analyzed by using Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analysis. In this study, not only we have identified the changes of global gene expression in rat M0, M1 and M2, but we have also made clear systematically the key genes and signaling pathways in the differentiation process of M0 to M1 and M2. These will provide a foundation for future researches of macrophage polarization. • The transcriptome profile of rat genes in bone marrow-derived macrophages at different activation statuses is investigated. • The global gene expression in rat M0, M1 and M2 has been described. • The key genes and signaling pathways in the differentiation process of M0 to M1 and M2 have been systematically determined. • Our results will provide a basis for future researches of macrophage polarization. [ABSTRACT FROM AUTHOR]